PyMOL Wiki - User contributions [en]

Intra rms

2005-05-23T14:52:13Z

Tree: /* USER EXAMPLES/COMMENTS */

===DESCRIPTION===
"intra_rms" calculates rms fit values for all states of an object over an atom selection relative to the indicated state. Coordinates are left unchanged. The rms values are returned as a python array.

===PYMOL API===
<source lang="python">
cmd.intra_rms( string selection, int state)
</source>

===PYTHON EXAMPLE===
<source lang="python">
from pymol import cmd
rms = cmd.intra_rms("(name ca)",1)
</source>

===USER EXAMPLES/COMMENTS===
[[Fit]], [[Rms]], [[Rms_Cur]] are finicky and only work when all atom identifiers match: segi, chain, resn, name, alt. If they don't then you'll need to use the alter command to change the identifiers to that they do -- typically that means clearing out the SEGI field, renaming chains, and sometimes renumbering.

I tried made two selections A, and D as

PyMOL>sel A, 1gh2 and n. CA and i. 65-99
Selector: selection "A" defined with 35 atoms.

PyMOL>sel D, 1kao and n. CA and i. 64-98
Selector: selection "D" defined with 35 atoms

which as you can see both yield 35 atoms. Now,
rms_cur A, D
won't work, due to the aforementioned reason. To fix this, one needs to do,
alter all,segi=''
alter all,chain=''
alter D, resi=str(int(resi)+1) # I don't actually use this line
and now
rms_cur A, D
should work.

===SEE ALSO===
[[Fit]], [[Rms]], [[Rms_Cur]], [[Intra_Fit]], [[Intra_Rms_Cur]], [[Pair_Fit]]

[[Category:Commands|intra_rms]]

Cartoon

2005-05-16T21:22:38Z

Tree:

==Cartoon Command==
===DESCRIPTION===
"cartoon" changes the default cartoon for a set of atoms.

===USAGE===
cartoon type, (selection)

type = skip | automatic | loop | rectangle | oval | tube | arrow | dumbbell

===PYMOL API===
<source lang="python">
cmd.cartoon(string type, string selection )
</source>

===EXAMPLES===
cartoon rectangle,(chain A)
cartoon skip,(resi 145:156)

===NOTES===
the "automatic" mode utilizes ribbons according to the
information in the PDB HELIX and SHEET records.

[[Category:Commands|cartoon]]

==Adjusting width of cartoon==

Try varying the following.

For strands:
<source lang="python">
cartoon_rect_length
cartoon_rect_width
</source>

For helices:
<source lang="python">
cartoon_oval_length
cartoon_oval_width
</source>

or for "fancy" helices:
<code>
cartoon_dumbell_length
cartoon_dumbell_width
cartoon_dumbell_radius (radius of cylinder at edge of helix ribbon)
</code>
In each case "length" refers to what some might call the width and "width" refers to what some might call the thickness.

[[Image:Cartoon_ex.png|thumb|center|Cartoon Representation Example|300px]]

===Forcing Exact Boundaries in Coloring Secondary Structures===
To force PyMol to respect secondary structural elements color-wise (PyMol smooths out colors near color chagnes for a prettier image) use the following
PyMol command:
<code>
set cartoon_discrete_colors, on
</code>

[[Image:Cartoon_discrete_color0.png|Discrete Coloring Off|center|thumb]] [[Image:Cartoon_discrete_color1.png|Discrete Coloring On|center|thumb]]

== Sausage Representation ==
The familiar sausage representation in PyMol is called, "putty". To enable the putty/sausage view simply do,
show cartoon
cartoon putty
unset cartoon_smooth_loops
unset cartoon_flat_sheets

==Black and White Representation==
For those who want a nifty black and white representation of their protein try the following:
# Ray trace your protein of choice in a cartoon representation use a BLACK background
# Save the image
# Load the image in GIMP. [[Image:Bw1.jpeg|thumb|Black BG Ribbon|center|350px]]
# Desaturate or Grayscale the image. [[Image:Bw2.jpeg|thumb|Grayscale|center|350px]]
# Run the filter: Filter->Edge-Detect->Edge. [[Image:Bw3.jpeg|thumb|Edge Detect|center|350px]]
# Select: Layers->Color->Invert. [[Image:Bw4.jpeg|thumb|Invert Color|center|350px]]
# Different methods of edge detection will give you different results. In the last example, I used Laplace Edge-Detect, then painted an all white layer beneath the current layer to achieve the results. [[Image:Bw5.jpeg|thumb|Other Styles|center|350px|Comments]]

I'm sure there are other ways to do this. If you want to include it in a publication make sure you ray traced it large enough. For that, see [[:Category:Advanced_Issues_Image_Manipulation_Publication_Quatlity_Images|Creating Publication Quality Images]].

== See Also ==
[[Cmd cartoon]]

[[Category:Representations|Cartoon]]

Cartoon

2005-05-16T21:14:13Z

Tree: /* Forcing Exact Boundaries in Coloring Secondary Structures */

==Cartoon Command==
===DESCRIPTION===
"cartoon" changes the default cartoon for a set of atoms.

===USAGE===
cartoon type, (selection)

type = skip | automatic | loop | rectangle | oval | tube | arrow | dumbbell

===PYMOL API===
<source lang="python">
cmd.cartoon(string type, string selection )
</source>

===EXAMPLES===
cartoon rectangle,(chain A)
cartoon skip,(resi 145:156)

===NOTES===
the "automatic" mode utilizes ribbons according to the
information in the PDB HELIX and SHEET records.

[[Category:Commands|cartoon]]

==Adjusting width of cartoon==

Try varying the following.

For strands:
<source lang="python">
cartoon_rect_length
cartoon_rect_width
</source>

For helices:
<source lang="python">
cartoon_oval_length
cartoon_oval_width
</source>

or for "fancy" helices:
<code>
cartoon_dumbell_length
cartoon_dumbell_width
cartoon_dumbell_radius (radius of cylinder at edge of helix ribbon)
</code>
In each case "length" refers to what some might call the width and "width" refers to what some might call the thickness.

[[Image:Cartoon_ex.png|thumb|Cartoon Representation Example]]

===Forcing Exact Boundaries in Coloring Secondary Structures===
To force PyMol to respect secondary structural elements color-wise (PyMol smooths out colors near color chagnes for a prettier image) use the following
PyMol command:
<code>
set cartoon_discrete_colors, on
</code>

[[Image:Cartoon_discrete_color0.png|Discrete Coloring Off|left|thumb]] [[Image:Cartoon_discrete_color1.png|Discrete Coloring On|left|thumb]]

== Sausage Representation ==
The familiar sausage representation in PyMol is called, "putty". To enable the putty/sausage view simply do,
show cartoon
cartoon putty
unset cartoon_smooth_loops
unset cartoon_flat_sheets

==Black and White Representation==
For those who want a nifty black and white representation of their protein try the following:
* Ray trace your protein of choice in a cartoon representation use a BLACK background
* Save the image
* Load the image in GIMP [[Image:Bw1.jpeg|thumb|Black BG Ribbon]]
* Desaturate or Grayscale the image [[Image:Bw2.jpeg|thumb|Grayscale]]
* Run the filter: Filter->Edge-Detect->Edge [[Image:Bw3.jpeg|thumb|Edge Detect]]
* Select: Layers->Color->Invert [[Image:Bw4.jpeg|thumb|Invert Color]]

Comments: Different methods of edge detection will give you different results. In the last example, I used Laplace Edge-Detect, then painted an all white layer beneath the current layer to achieve the results. [[Image:Bw5.jpeg|thumb|Other Styles]]

I'm sure there are other ways to do this. If you want to include it in a publication make sure you ray traced it large enough. For that, see [[:Category:Advanced_Issues_Image_Manipulation_Publication_Quatlity_Images|Creating Publication Quality Images]].

== See Also ==
[[Cmd cartoon]]

[[Category:Representations|Cartoon]]

User talk:Tmwsiy

2005-05-16T21:11:16Z

Tree: Media Uploads

Sorry about that its: http://dwkulp.homelinux.net/tiki/tiki-index.php

http://dwkulp.homelinux.net/tiki-index.php

Is a 404. You may want to double check it.

-- Jason

== Talk Pages ==

Dan,

Yeah, I think these talk pages are similar to public messages to folks. Also, every page has a discussion page -- so you can talk about the page under question. WikiPedia does this quite a bit in case there are disputes to content: is someone being spiteful and posting bunk, or is the content controversial or whatnot. Here, I imagine it'll be, "how do I..." type questions.

[[User:Tree|Tree]] 16:11, 12 May 2005 (CDT)

== Media Uploads ==

Dan,

Try now. I enabled zip, tar, bz2, and some more. So, to avoid scripts and IE-unsafe stuff, let's try to keep things images or compressed.

[[User:Tree|Tree]] 16:11, 16 May 2005 (CDT)

User talk:Tmwsiy

2005-05-12T21:11:16Z

Tree: Talk Pages

Hide

2005-03-09T04:41:58Z

Tree:

===DESCRIPTION===

"hide" turns of atom and bond representations.

The available representations are:

lines spheres mesh ribbon cartoon
sticks dots surface labels
nonbonded nb_spheres

===USAGE===

hide reprentation [,object]
hide reprentation [,(selection)]
hide (selection)

===PYMOL API===
<source lang="python">
cmd.hide( string representation="", string selection="")
</source>

===EXAMPLES===

hide lines,all
hide ribbon

===SEE ALSO===

[[Cmd show]], [[Cmd enable]], [[Cmd disable]]

[[Category:hide|hide]]

Alter State

2005-03-09T04:38:30Z

Tree:

===DESCRIPTION===

"alter_state" changes the atomic coordinates of a particular state
using the python evaluator with a separate name space for each
atom. The symbols defined in the name space are:

x,y,z

===USAGE===

alter_state state,(selection),expression

===EXAMPLES===

alter_state 1,(all),x=x+5

===SEE ALSO===

[[Cmd iterate_state]], [[Cmd alter]], [[Cmd iterate]]

[[Category:Commands|alter_state]]

Unbond

2005-03-09T04:36:53Z

Tree:

===DESCRIPTION===

"unbond" removes all bonds between two selections.

===USAGE===

unbond atom1,atom2

===PYMOL API===
<source lang="python">
cmd.unbond(selection atom1="(pk1)",selection atom2="(pk2)")
</source>

===SEE ALSO===

[[Cmd bond]], [[Cmd fuse]], [[Cmd remove_picked]], [[Cmd attach]], [[Cmd detach]], [[Cmd replace]]

[[Category:Commands|unbond]]

Attach

2005-03-09T04:35:04Z

Tree:

DESCRIPTION

"attach" adds a single atom onto the picked atom.

USAGE

attach element, geometry, valence

PYMOL API

cmd.attach( element, geometry, valence )

NOTES

Immature functionality. See code for details.

[[Category:Commands|attach]]

Bounding Box

2005-03-08T22:15:44Z

Tree:

<source lang="python">
import math
from pymol import querying
from pymol.cgo import *
from pymol import cmd

#NOTE!! : These packages (numarray, Scientific) must be present in pymol's
#'$PYMOLDIR/py23/lib/python2.3/site-packages/' directory!!
from numarray import *
from numarray.ma import average
from numarray import linear_algebra as la

from Scientific.Geometry import Vector, Tensor, Transformation

def boundingBox(selectionName, colourRGB=[1,1,1]):
"""
The main function to call :

run "box.py"
boundingBox("peptide")

Should make a box around "peptide" (assuming it exists!). For a different colour use:

boundingBox("peptide", colourRGB=[1, 0, 1])

Or whatever. The box should be a cgo called 'peptide-box' (for this example).
"""
model = querying.get_model(selectionName)
coords = model.get_coord_list()

#find the least square plane through the coordinates
eigenvalues, eigenvectors, centroid = findPlaneWithEigenVectors(coords)
normal = eigenvectors[eigenvalues.argmin()]
eigenvectors.remove(normal)

#orient the axes correctly
x, y, normal = orientAxes(eigenvectors[0], eigenvectors[1], normal)

#determine the dimensions and the structure's orientation wrt the origin
minDimensions, rotation = findMinDimensionsAndRotation(coords, centroid, x, y, normal)

#'create' the box(IE: make the corners) and 'draw' it (IE: make a cgo)
box = makeBox(minDimensions, rotation, centroid)
drawBox(box, selectionName, colourRGB)

def findPlaneWithEigenVectors(coords):
centroid = average(coords)
coords -= centroid
B = matrixmultiply(transpose(coords), coords)
eigenvalues, eigenvectors = la.eigenvectors(B)
return eigenvalues, [Vector(e) for e in eigenvectors], Vector(centroid)

def orientAxes(x, y, z):
XcrossY = x.cross(y)
ZXY = around(math.degrees(z.angle(XcrossY)))
if (ZXY == 180): x, y = y, x
return x, y, z

def makeBox(dimensions, rotation, centroid):
x, y, z = dimensions
v = [[]] * 8

#make a cuboid with the lower corner on the origin
v[0] = [0, 0, 0] # [0, 0, 0]
v[1] = [x, 0, 0] # [1, 0, 0]
v[2] = [x, y, 0] # [1, 1, 0]
v[3] = [x, 0, z] # [1, 0, 1]
v[4] = [0, y, 0] # [0, 1, 0]
v[5] = [0, 0, z] # [0, 0, 1]
v[6] = [0, y, z] # [0, 1, 1]
v[7] = [x, y, z] # [1, 1, 1]

#move to the origin, THEN move to the centroid of the points, then rotate
translationToOrigin = Transformation.Translation(-Vector(x/2, y/2, z/2))
translationToCentroid = Transformation.Translation(centroid)
transform = translationToCentroid * rotation * translationToOrigin

#use the Transformation to transform the corners of the box
v = [transform(Vector(i)) for i in v]

bot = [v[0], v[1], v[2], v[4]] # O, x, xy, y
top = [v[7], v[3], v[5], v[6]] # xyz, xz, z, yz
minL = [v[0], v[4], v[6], v[5]] # O, y, yz, z
minR = [v[0], v[5], v[3], v[1]] # O, z, xz, x
maxL = [v[4], v[2], v[7], v[6]] # y, xy, xyz, yz
maxR = [v[3], v[1], v[2], v[7]] # xz, x, xy, xyz
box = [bot, minR, minL, maxR, maxL, top]

return box

def drawBox(box, name, colourRGB):
boxObj = []
for side in box:
boxObj.append(BEGIN)
boxObj.append(LINE_STRIP)
boxObj.append(COLOR)
boxObj.extend(colourRGB)
for point in side:
boxObj.append(VERTEX)
boxObj.extend(point)
boxObj.append(END)

cmd.set('auto_zoom', 0)
cmd.load_cgo(boxObj, "%s-box" % name)
cmd.set('auto_zoom', 1)

def findMinDimensionsAndRotation(coords, centroid, x, y, z):
O = Vector(0, 0, 0)
X = Vector(1, 0, 0)
Y = Vector(0, 1, 0)
Z = Vector(0, 0, 1)

#Create a Transformation t = |x, y, z| . |X, Y, Z| ^ -1
mfinal = array([array(X), array(Y), array(Z)])
morig = array([array(x), array(y), array(z)])
rotmatrix = matrixmultiply(morig, transpose(mfinal))
tTotal = Transformation.Rotation(Tensor(rotmatrix))

#Transform the coordinates and find the min, max dimensions
coordArray = array([array(tTotal(Vector(c))) for c in coords])
minDimensions = [max(coordArray[:,i]) - min(coordArray[:,i]) for i in range(3)]

#Now, compose the inverse rotation used to move the bounding box to the right place
tForward = Transformation.Rotation(Tensor(matrixmultiply(mfinal, transpose(morig))))

return minDimensions, tForward
</source>

[[Category:Scripting_Script_Library|Bounding Box]]

Bounding Box

2005-03-08T22:14:57Z

Tree:

Show hydrophilic

2005-03-08T03:50:17Z

Tree:

<source lang="python">
#
# Show side chain sticks for hydrophilic residues
#
# (script for PyMol)
# Tom Stout, 08/05/2004
#

mstop
dss
hide all
#zoom all
#orient
show cartoon,all
color gray,all

select hydrophilics,(resn arg+lys+his+glu+asp+asn+gln+thr+ser+cys)
show sticks, (hydrophilics and !name c+n+o)
color green,hydrophilics
disable hydrophilics
set cartoon_smooth_loops,0</source>

[[Category:Scripting_Script_Library|Show Hydrophilic]]

Show charged

2005-03-08T03:50:05Z

Tree:

<source lang="python">
#
# Show side chain sticks for charged residues
#
# (script for PyMol)
# Tom Stout, 08/05/2004
#

mstop
dss
hide all
#zoom all
#orient
show cartoon,all
color gray,all

select pos,(resn arg+lys+his)
show sticks, (pos and !name c+n+o)
color marine,pos
disable pos
select neg,(resn glu+asp)
show sticks, (neg and !name c+n+o)
color red,neg
disable neg
set cartoon_smooth_loops,0</source>

[[Category:Scripting_Script_Library|Show Charged]]

Show hydrophobics

2005-03-08T03:49:54Z

Tree:

<source lang="python">
#
#
#
# Show side chain sticks for hydrophobic residues
#
# (script for PyMol)
# Tom Stout, 08/05/2004
#

mstop
dss
hide all
#zoom all
#orient
show cartoon,all
color gray,all

select hydrophobes,(resn ala+gly+val+ile+leu+phe+met)
show sticks, (hydrophobes and (!name c+n+o))
color orange,hydrophobes
disable hydrophobes
set cartoon_smooth_loops,0</source>

[[Category:Scripting_Script_Library|Show Hydrophobics]]

Show aromatics

2005-03-08T03:49:40Z

Tree:

<source lang="python">
#
#
# Show side chain sticks for aromatic residues
#
# (script for PyMol)
# Tom Stout, 08/05/2004
#

mstop
dss
hide all
#zoom all
#orient
show cartoon,all
color gray,all

select aromatics,(resn phe+tyr+trp+his)
show sticks, (aromatics and (!name c+n+o))
color green,aromatics
disable aromatics
set cartoon_smooth_loops,0</source>

[[Category:Scripting_Script_Library|Show Aromatics]]

User talk:Philaltist

2005-03-06T04:33:32Z

Tree:

Hi everyone !

I have created a script because I was tired of browsing the pdb for endless searches of structures relevant to my field. This scripts takes as input a text file in which you copied your favourite keywords, and the number of days you want to search back (by default, it will look at the structures added the last 50 days). It generates a report text file that contains the pdb id and name of the relevant structures that have been recently added. All you need to do is add 'run pdbsurvey.py' to your startup file, and create a text file called 'keywords.txt' with your keywords separated by an end-of-line character. Then you're ready to go. Just hit 'pdbsurvey' from within your PyMol instance, and the program returns the report file. The pdb ftp server is updated every tuesday.

I am still new to wiki, so I don't know yet how to upload this script. Could someone help ?

P.S. Here's the script in raw text format :

<source lang="python">
from pymol import cmd

def pdbsurvey(days=50):

"""USAGE : pdbsurvey (<days>)
Surveys the updates added to the PDB (ftp.rcsb.org) in the last
50 days (or otherwise specified when calling this function) for
entries that contain the words specified in the file
keywords.txt.
"""
print days

import ftplib
import time
import os
import string

def todaymerge():
"""Puts today's date in a pdb format string.
"""
date=time.localtime()
fyear="%i" %(date[0])
fmonth="%i" %(date[1])
if date[1]<10:
fmonth="0"+"%i" %(date[1])
fday="%i" %(date[2])
if date[2]<10:
fday="0"+"%i" %(date[2])
dateS=fyear+fmonth+fday
return dateS

def file2list(filename):
"""Low-level routine to brainlessly implement
file.read().
"""
fq=open(filename,'rb')
linesS=fq.read()
fq.close()
LIST=linesS.splitlines()
return LIST

def connect2pdb():
"""Opens an anonymous socket to ftp://ftp.rcsb.org
"""
f=ftplib.FTP()
f.connect ('ftp.rcsb.org')
f.login ()
print "Remote connection established","\n"
return f

def decrementdate(dateS):
"""given a string date (pdb format yyyymmdd)
this routine returns a string of the day before
(sadly assuming that every month has 31 days, but
no big deal here...).
"""
#decompose dateS into components
yearS=dateS[0]+dateS[1]+dateS[2]+dateS[3]
monthS=dateS[4]+dateS[5]
dayS=dateS[6]+dateS[7]

#convert each into integers
yearI=int(yearS)
monthI=int(monthS)
dayI=int(dayS)

#actual stuff
dayI=dayI-1
if dayI==0:
dayI=31
monthI=monthI-1
if monthI==0:
monthI=12
yearI=yearI-1
dayS="%i" %(dayI)
monthS="%i" %(monthI)
yearS="%i" %(yearI)
if dayI<10:
dayS="0"+dayS
if monthI<10:
monthS="0"+monthS
#and finally...
dateS=yearS+monthS+dayS
return dateS

def findlastdir(dateS,f,days):
"""Puts the names of the "recent" directories in the
list named "directoriesL".
"""
directoriesL=['']
j=p=0
while p<days:
dateS=decrementdate(dateS)
attempt="/pub/pdb/data/status/"+dateS
try :
f.cwd(attempt)
directoriesL[j:j]=[attempt]
j=j+1
except :
pass
p=p+1
directoriesL.pop()
return directoriesL

def compilinfile(directoriesL,f):
"""lists all structures in the added.pdb files
contained in the directories specified in directoriesL
"""
command="RETR added.pdb"
handle=open("donotedit.dat","wrb")
for k in directoriesL:
f.cwd(k)
print "Currently in directory ",f.pwd()
f.retrbinary(command,handle.write)
handle.close()
return len(directoriesL)

def listparser():
"""Extracts the pdbids from donotedit.dat file,
and stacks them into the list pdbidsL
"""
linesL=file2list("donotedit.dat")
pdbidsL=[]
for iter in linesL:
pdbidsL.append(iter[57:61])
for iter in pdbidsL:
iter=string.lower(iter)
pdbidsL.sort()
return pdbidsL

def currentrelease(f):
"""Stores the content of cmpd_res.idx file
This file contains the equivalencies pdbid<->title
for all current entries of the PDB.
"""
command="RETR cmpd_res.idx"
f.cwd("/pub/pdb/derived_data/index/")
print "Currently in directory ",f.pwd()
fq=open("dictionnary.dat",'wrb')
f.retrbinary(command,fq.write)
fq.close()
dictL=file2list("dictionnary.dat")
return dictL

def extract(pdbidsL,dictL):
"""Populates dictionnaryD with pdb entries found in the
latest releases.
"""
dictionnaryD={}
problemL=[]
extractL=[dictionnaryD,problemL]
for i in dictL:
tempS=string.lower(i[0:4])
for ii in pdbidsL:
if ii == tempS:
title=i[14:216]
extractL[0][ii]=title
if len(extractL[0].keys()) != len(pdbidsL):
print "Dimension mismatch, seeking troublemaker..."
for i in pdbidsL:
equiv=0
for ii in extractL[0].keys():
if i==ii:
equiv=equiv+1
if equiv==0:
extractL[1].append(i)
return extractL

def disconnectpdb(f):
"""Diconnects the current ftp session
"""
f.quit()
print "Remote connection terminated","\n"
return f

def releventries(dictionnaryD):
"""Generates a cleaned dictionnary with only entries
that have one or more keywords specified in the local
user-defined keywords.txt file
"""
keywL=file2list("keywords.txt")
relevdicD={}
for i in keywL:
for elem in dictionnaryD.keys():
temp=dictionnaryD[elem]
if temp.find(i) != -1:
relevdicD[elem]=temp
return relevdicD

def diskcleanup(filelist=["donotedit.dat","dictionnary.dat"]):
"""Lo-level disk cleanup to free up memory without the user
"""
for filename in filelist:
command='DEL '+filename
os.system(command)
return "clean"

print "Welcome in the auto-PDB updater !"

print "Survey of updates made since",days,"days ago."

print "Acquisition of local time..."
dateS=todaymerge() #Initializes dateS
print "today is ",dateS
print "Connecting to remote ftp server..."
f=connect2pdb() #Connect anonymously to ftp.rcsb.org

print "Acquisition of latest added remote directories..."
directoriesL=findlastdir(dateS,f,days) #Lists recent directories in directoriesL
if len(directoriesL)==0:
print "No updates have been found since",days,"ago. Starting over with 50 days ago."
directoriesL=findlastdir(dateS,f,50)

print "Acquisition of latest addedremote files..."
updatesnumberI=compilinfile(directoriesL,f) #Concatenates the corresponding added.pdb into donotedit.dat

print "Parsing of latest entries..."
pdbidsL=listparser() #Recent names now present in the pdbidsL list (one name per element)

print "Acquisition of the current pdb distribution..."
dictL=currentrelease(f) #Populates dictL with the current entries of the PDB

print "Parsing of the current pdb distribution into [code,title] tuples..."
extractL=extract(pdbidsL,dictL) #generates the dictionnary of latest releases key:PDBid ; definition:pdbtitle

print "Disconnection from the remote ftp server..."
f=disconnectpdb(f) #Closes the ftp instance

print "Extraction of the relevant entries..."
relevdicD=releventries(extractL[0]) #Generates a subset of dictionnary D with criterion being "has keywords contained in keywords.txt in its title"

print "Cleaning program-generated temporary files..."
clean=diskcleanup() #Cleans the mess generated by the program

reportL=[]
reportL.append("\n")
reportL.append("###############REPORT########################################\n")
reportL.append("\n")
lendictS="%i" %(len(dictL))
chmilblik = 'The current pdb version (as of '+dateS+") has "+lendictS+" entries.\n"
reportL.append(chmilblik)
line="The most recent directory is : "+directoriesL[0]+".\n"
reportL.append(line)
updatesnumberS="%i" %(updatesnumberI)
entriesnumber="%i" %(len(extractL[0].keys()))
line="The "+updatesnumberS+" last updates ("+entriesnumber+" entries) have been examined.\n"
reportL.append(line)
diclengthS="%i" %(len(relevdicD.keys()))
line=diclengthS+" are relevant to you :\n"
reportL.append(line)
for i in relevdicD.keys():
entry=i+" : "+relevdicD[i]+"\n"
reportL.append(entry)
problemS=""
for i in extractL[1]:
problemS=i+";"+problemS
problemS="["+problemS
problemS=problemS.strip(";")
problemS=problemS+"]"
lineS="The entries "+problemS+" raised problems,"
reportL.append(lineS)
reportL.append("they should be examined manually.")
reportL.append("\n")
reportL.append("###############END OF REPORT#################################\n")
report=open("report.aut","w")
for elem in reportL:
print elem
elem=elem+'\n'
report.writelines(elem)
report.close()
command2='start keywords.txt'
command3='start report.aut'
os.system(command2)
os.system(command3)

cmd.extend("pdbsurvey",pdbsurvey)
</source>

Philaltist,

To make scripts available to folks, the simplest method is to upload the script as you did and then just wrap the script in <python> and </python> code. Look at what I did to your code for an example. If you want line numbers in your code, use "npython" instead of "python".

-- tree

User talk:Philaltist

2005-03-06T04:30:15Z

Tree:

Category:FAQ

2005-03-06T03:25:36Z

Tree:

==FAQ==

===Overview===
Please post your FAQs here. I suggest you write a Q&A style list with a short answer. More involved answers should link to its own page. Just my suggestion. Should we have topics?

==FAQs==

Main Page

2005-03-06T03:20:02Z

Tree: /* Links of Interest */

Main Page

2005-03-06T03:19:31Z

Tree: /* Links of Interest */

TOPTOC

2005-03-06T03:18:27Z

Tree: /* PyMolWiki Top-Level Table Of Contents */

== Section Layout ==
Please see [[:Talk:Main Page|Discussion]] for more thoughts on the site organizaiton.

== PyMolWiki Top-Level Table Of Contents ==
# [[:Category:News|News]]
# [[:Category:FAQ|Frequently Asked Questions]]
# [[:Category:Brag|Brag]] -- show off your best images or movies.
## [[:Category:News Discussion|Discussion]]
## [[:Category:News PyMol Beta|PyMol Beta]]
# [[:Category:Technical Issues|Technical Issues]]
## [[:Category:Technical Issues Installation|Installation]]
### [[:Category:Technical Issues Installation OS Dependent|OS Dependent]]
#### [[:Category:Technical Issues Installation OS Dependent Linux|Linux]]
#### [[:Category:Technical Issues Installation OS Dependent MAC|MAC]]
#### [[:Category:Technical Issues Installation OS Dependent Windows|Windows]]
# [[:Category:Launching PyMOL|Launching PyMOL]]
## [[:Category:Launching PyMOL Command Line Options| Command Line Options]]
## [[:Category:Launching PyMOL Launching From a Script|Launching From a Script]]
# [[:Category:Using Pymol|Using PyMol]]
## [[:Category:Using Pymol Mouse Controls|Mouse Controls]]
## [[:Category:Using Pymol Objects and Selections|Objects and Selections]]
### [[:Category:Using Pymol Objects and Selections Working with Objects|Working with Objects]]
### [[:Category:Using Pymol Objects and Selections Working with Selections|Working with Selections]]
### [[:Category:Using Pymol Objects and Selections Selector Quick Reference|Selector Quick Reference]]
#### [[:Category:Using Pymol Objects and Selections Selector Quick Reference Single-word Selectors|Single-word Selectors]]
#### [[:Category:Using Pymol Objects and Selections Selector Quick Reference Property Selectors|Property Selectors]]
#### [[:Category:Using Pymol Objects and Selections Selector Quick Reference Selection Algebra|Selection Algebra]]
#### [[:Category:Using Pymol Objects and Selections Selector Quick Reference Selection Macros|Selection Macros]]
### [[:Category:Using Pymol Objects and Selections Representations|Representations]]
#### [[:Category:Using Pymol Objects and Selections Representations Lines|Lines]]
#### [[:Category:Using Pymol Objects and Selections Representations Sticks|Sticks]]
#### [[:Category:Using Pymol Objects and Selections Representations Cartoon|Cartoon]]
#### [[:Category:Using Pymol Objects and Selections Representations Surface|Surface]]
#### [[:Category:Using Pymol Objects and Selections Representations Mesh|Mesh]]
#### [[:Category:Using Pymol Objects and Selections Representations Spheres|Spheres]]
#### [[:Category:Using Pymol Objects and Selections Representations Dots|Dots]]
### [[:Category:Using Pymol Objects and Selections Color|Color]]
### [[:Category:Using Pymol Objects and Selections Displaying Biochemical Properties|Displaying biochemical properties]]
## [[:Category:Using Pymol Display Settings|Display Settings]]
## [[:Category:Using Pymol Stereo 3D Display|Stereo 3D Display]] -- wrong place
### [[:Category:Using Pymol Hardware Options|Hardware Options]] -- wrong place?
### [[Linux XFree86 Configuration]] -- wrong place
## [[:Category:Using Pymol Scenes|Scenes]]
## [[:Category:Using Pymol Mouse Settings|Mouse Settings]]
## [[:Category:Using Pymol Wizards|Wizards]]
## [[:Category:Using Pymol Ray-tracing|Ray-tracing]]
## [[:Category:Using Pymol Settings Reference|Settings Reference]]
## [[:Category:Using Pymol Movies and Animations|Movies and Animations]]
## [[:Category:Using Pymol Structure Alignment|Structure Alignment]]
## [[:Category:Using Pymol Structure Alignment Editor|Structure Alignment Editor]]
# [[:Category:Commands|Command Language]]
## [[:Category:Commands PyMOL Command Script|PyMOL Command Script]]
## [[:Category:Commands PyMOL Python API|PyMOL Python API]]
# [[:Category:Advanced Issues|Advanced Issues]]
## [[:Category:Advanced Issues Modeling and Editing Structures|Modeling and editing structures]]
### [[:Category:Advanced Issues Modeling and Editing Structures Editing atoms|Editing Atoms]]
### [[:Category:Advanced Issues Modeling and Editing Structures Molecular Sculpting|Molecular sculpting]]
### [[:Category:Advanced Issues Modeling and Editing Structures Homology Modeling|Homology modeling]]
## [[:Category:Advanced Issues Image Manipulation|Image Manipulation]]
### [[:Category:Advanced Issues Image Manipulation labels|labels]]
### [[:Category:Advanced Issues Image Manipulation Photoshop and GIMP|Photoshop/GIMP]]
### [[:Category:Advanced Issues Image Manipulation Stereo Figures|Stereo Figures]]
### [[:Category:Advanced Issues Image Manipulation Publication Quatlity Images|Publication-quality images]]
# [[:Category:Scripting|Scripting]]
## [[:Category:Scripting Example Scripts|Example Scripts]]
## [[:Category:Scripting Script Library|Script Library]]
# [[:Category:Plugins|Plugins]]
## [[:Category:Plugins Electrostatics and Energy Minimization| How to do electrostatics and energy minimization.]]
### [[:Category:Plugins Electrostatics and Energy Minimization APBS| APBS Plugin]]
## [[:Category:Plugins rtools | rtools]]
## [[:Category:Plugins Tutorial|Tutorial on writing plugins]]
## [[:Category:Plugins Others| Others]]
# [[:Category:High-Level Applications|High-Level Applications]]
## [[:Category:High-Level Applications Crystallography Applications|Crystallography Applications]]
### [[:Category:High-Level Applications Symmetry|Symmetry]]
### [[:Category:High-Level Applications Electron Density|Electron Density]]
## [[:Category:High-Level Applications NMR Applications|NMR Applications]]
### [[:Category:High-Level Applications NMR Applications Working with a Family of Structures|Working with Structure Families]]
### [[:Category:High-Level Applications NMR Applications Superimposition and RMSD|Superimposition and RMSD]]
### [[:Category:High-Level Applications NMR Applications NMR Restraints Analysis|NMR Restraints and Analysis]]
# [[:Category:Third Party Software|Third Party Software]]
## [[:Category:Third Party Software PovRay|PovRay]]
## [[:Category:Third Party Software Movies|Movies]]
## [[:Category:Third Party Software Codecs|Codecs]]
# [[:Category:Python Integration|Python Integration]]
# [[:Category:Using PyMol For Unintended Uses|Unintended Uses]] (OpenGL Object Renderer)
## [[:Category:Using PyMol For Unintended Uses Arbitrary Graphics Objects| Arbitrary Graphics Objects]]
# [[:Category:Uncategorized|Uncategorized]] For new pages, misplaced pages, etc.
----
[[User:Tree|Tree]] 02:09, 16 Feb 2005 (CST)
----

File:Cartoon discrete color1.png

2005-03-06T02:01:27Z

Tree: Discrete Coloring On

Discrete Coloring On

File:Cartoon discrete color0.png

2005-03-06T02:00:40Z

Tree: Discrete Coloring Off

Discrete Coloring Off

Category:Third Party Software

2005-03-04T05:59:45Z

Tree:

Third Party Software Information here.

Category:Plugins rtools

2005-03-04T05:57:59Z

Tree:

[[Category:Plugins|rTools]]

Category:Using Pymol

2005-03-04T05:42:33Z

Tree:

Here you will find basic information about using PyMol.

TOPTOC

2005-03-02T07:26:44Z

Tree: /* PyMolWiki Top-Level Table Of Contents */

== Section Layout ==
Please see [[:Talk:Main Page|Discussion]] for more thoughts on the site organizaiton.

== PyMolWiki Top-Level Table Of Contents ==
# [[:Category:News|News]]
# [[:Category:Brag|Brag]] -- show off your best images or movies.
## [[:Category:News Discussion|Discussion]]
## [[:Category:News PyMol Beta|PyMol Beta]]
# [[:Category:Technical Issues|Technical Issues]]
## [[:Category:Technical Issues Installation|Installation]]
### [[:Category:Technical Issues Installation OS Dependent|OS Dependent]]
#### [[:Category:Technical Issues Installation OS Dependent Linux|Linux]]
#### [[:Category:Technical Issues Installation OS Dependent MAC|MAC]]
#### [[:Category:Technical Issues Installation OS Dependent Windows|Windows]]
# [[:Category:Launching PyMOL|Launching PyMOL]]
## [[:Category:Launching PyMOL Command Line Options| Command Line Options]]
## [[:Category:Launching PyMOL Launching From a Script|Launching From a Script]]
# [[:Category:Using Pymol|Using PyMol]]
## [[:Category:Using Pymol Mouse Controls|Mouse Controls]]
## [[:Category:Using Pymol Objects and Selections|Objects and Selections]]
### [[:Category:Using Pymol Objects and Selections Working with Objects|Working with Objects]]
### [[:Category:Using Pymol Objects and Selections Working with Selections|Working with Selections]]
### [[:Category:Using Pymol Objects and Selections Selector Quick Reference|Selector Quick Reference]]
#### [[:Category:Using Pymol Objects and Selections Selector Quick Reference Single-word Selectors|Single-word Selectors]]
#### [[:Category:Using Pymol Objects and Selections Selector Quick Reference Property Selectors|Property Selectors]]
#### [[:Category:Using Pymol Objects and Selections Selector Quick Reference Selection Algebra|Selection Algebra]]
#### [[:Category:Using Pymol Objects and Selections Selector Quick Reference Selection Macros|Selection Macros]]
### [[:Category:Using Pymol Objects and Selections Representations|Representations]]
#### [[:Category:Using Pymol Objects and Selections Representations Lines|Lines]]
#### [[:Category:Using Pymol Objects and Selections Representations Sticks|Sticks]]
#### [[:Category:Using Pymol Objects and Selections Representations Cartoon|Cartoon]]
#### [[:Category:Using Pymol Objects and Selections Representations Surface|Surface]]
#### [[:Category:Using Pymol Objects and Selections Representations Mesh|Mesh]]
#### [[:Category:Using Pymol Objects and Selections Representations Spheres|Spheres]]
#### [[:Category:Using Pymol Objects and Selections Representations Dots|Dots]]
### [[:Category:Using Pymol Objects and Selections Color|Color]]
### [[:Category:Using Pymol Objects and Selections Displaying Biochemical Properties|Displaying biochemical properties]]
## [[:Category:Using Pymol Display Settings|Display Settings]]
## [[:Category:Using Pymol Stereo 3D Display|Stereo 3D Display]] -- wrong place
### [[:Category:Using Pymol Hardware Options|Hardware Options]] -- wrong place?
### [[Linux XFree86 Configuration]] -- wrong place
## [[:Category:Using Pymol Scenes|Scenes]]
## [[:Category:Using Pymol Mouse Settings|Mouse Settings]]
## [[:Category:Using Pymol Wizards|Wizards]]
## [[:Category:Using Pymol Ray-tracing|Ray-tracing]]
## [[:Category:Using Pymol Settings Reference|Settings Reference]]
## [[:Category:Using Pymol Movies and Animations|Movies and Animations]]
## [[:Category:Using Pymol Structure Alignment|Structure Alignment]]
## [[:Category:Using Pymol Structure Alignment Editor|Structure Alignment Editor]]
# [[:Category:Commands|Command Language]]
## [[:Category:Commands PyMOL Command Script|PyMOL Command Script]]
## [[:Category:Commands PyMOL Python API|PyMOL Python API]]
# [[:Category:Advanced Issues|Advanced Issues]]
## [[:Category:Advanced Issues Modeling and Editing Structures|Modeling and editing structures]]
### [[:Category:Advanced Issues Modeling and Editing Structures Editing atoms|Editing Atoms]]
### [[:Category:Advanced Issues Modeling and Editing Structures Molecular Sculpting|Molecular sculpting]]
### [[:Category:Advanced Issues Modeling and Editing Structures Homology Modeling|Homology modeling]]
## [[:Category:Advanced Issues Image Manipulation|Image Manipulation]]
### [[:Category:Advanced Issues Image Manipulation labels|labels]]
### [[:Category:Advanced Issues Image Manipulation Photoshop and GIMP|Photoshop/GIMP]]
### [[:Category:Advanced Issues Image Manipulation Stereo Figures|Stereo Figures]]
### [[:Category:Advanced Issues Image Manipulation Publication Quatlity Images|Publication-quality images]]
# [[:Category:Scripting|Scripting]]
## [[:Category:Scripting Example Scripts|Example Scripts]]
## [[:Category:Scripting Script Library|Script Library]]
# [[:Category:Plugins|Plugins]]
## [[:Category:Plugins Electrostatics and Energy Minimization| How to do electrostatics and energy minimization.]]
### [[:Category:Plugins Electrostatics and Energy Minimization APBS| APBS Plugin]]
## [[:Category:Plugins rtools | rtools]]
## [[:Category:Plugins Tutorial|Tutorial on writing plugins]]
## [[:Category:Plugins Others| Others]]
# [[:Category:High-Level Applications|High-Level Applications]]
## [[:Category:High-Level Applications Crystallography Applications|Crystallography Applications]]
### [[:Category:High-Level Applications Symmetry|Symmetry]]
### [[:Category:High-Level Applications Electron Density|Electron Density]]
## [[:Category:High-Level Applications NMR Applications|NMR Applications]]
### [[:Category:High-Level Applications NMR Applications Working with a Family of Structures|Working with Structure Families]]
### [[:Category:High-Level Applications NMR Applications Superimposition and RMSD|Superimposition and RMSD]]
### [[:Category:High-Level Applications NMR Applications NMR Restraints Analysis|NMR Restraints and Analysis]]
# [[:Category:Third Party Software|Third Party Software]]
## [[:Category:Third Party Software PovRay|PovRay]]
## [[:Category:Third Party Software Movies|Movies]]
## [[:Category:Third Party Software Codecs|Codecs]]
# [[:Category:Python Integration|Python Integration]]
# [[:Category:Using PyMol For Unintended Uses|Unintended Uses]] (OpenGL Object Renderer)
## [[:Category:Using PyMol For Unintended Uses Arbitrary Graphics Objects| Arbitrary Graphics Objects]]
# [[:Category:Uncategorized|Uncategorized]] For new pages, misplaced pages, etc.
----
[[User:Tree|Tree]] 02:09, 16 Feb 2005 (CST)
----

PyMOLWiki:Community Portal

2005-03-02T07:19:35Z

Tree:

== CP ==
Look here for ways to get involved in the PyMolWiki!

Editors, you can upload images for your examples and supporting text! Check out [[Special:Upload]].

== Helping ==
* Importing the email list content: We have (lots) of email to sift through, extract data from and import into the Wiki
* If you feel you have the time to help import data into the PyMol wiki, please email [[User:Tree|Tree]].

=== New! GeShi: Syntax Highlighting for Python & More ===
'''Update''': I have added the option for numbered syntax highlighting and non-numbered.
<pre>
<source lang="python">Non line-numbered code here</source>
</pre>

<pre>
<npython>line-numbered code here</npython>
</pre>

Now with line numbers (or not)!

<npython>
# axes.py
from pymol.cgo import *
from pymol import cmd
from pymol.vfont import plain

# create the axes object, draw axes with cylinders coloured red, green,
#blue for X, Y and Z

obj = [
CYLINDER, 0., 0., 0., 50., 0., 0., 0.2, 1.0, 1.0, 1.0, 1.0, 0.0, 0.,
CYLINDER, 0., 0., 0., 0., 50., 0., 0.2, 1.0, 1.0, 1.0, 0., 1.0, 0.,
CYLINDER, 0., 0., 0., 0., 0., 50., 0.2, 1.0, 1.0, 1.0, 0., 0.0, 1.0,
]

# add labels to axes object (requires pymol version 0.8 or greater, I
# believe

cyl_text(obj,plain,[-5.,-5.,-1],'Origin',0.20,axes=[[3,0,0],[0,3,0],[0,0,3]])
cyl_text(obj,plain,[50.,0.,0.],'X',0.20,axes=[[3,0,0],[0,3,0],[0,0,3]])
cyl_text(obj,plain,[0.,50.,0.],'Y',0.20,axes=[[3,0,0],[0,3,0],[0,0,3]])
cyl_text(obj,plain,[0.,0.,50.],'Z',0.20,axes=[[3,0,0],[0,3,0],[0,0,3]])

# then we load it into PyMOL
cmd.load_cgo(obj,'axes')
</npython>

See [http://qbnz.com/highlighter/index.php The Geshi Home Page]

[[User:Tree|Tree]]

PyMOLWiki:Community Portal

2005-03-02T07:17:50Z

Tree: /* New! GeShi: Syntax Highlighting for Python & More */

== CP ==
Look here for ways to get involved in the PyMolWiki!

== Helping ==
* Importing the email list content: We have (lots) of email to sift through, extract data from and import into the Wiki
* If you feel you have the time to help import data into the PyMol wiki, please email [[User:Tree|Tree]].

=== New! GeShi: Syntax Highlighting for Python & More ===
'''Update''': I have added the option for numbered syntax highlighting and non-numbered.
<pre>
<source lang="python">Non line-numbered code here</source>
</pre>

<pre>
<npython>line-numbered code here</npython>
</pre>

Now with line numbers (or not)!

<npython>
# axes.py
from pymol.cgo import *
from pymol import cmd
from pymol.vfont import plain

# create the axes object, draw axes with cylinders coloured red, green,
#blue for X, Y and Z

obj = [
CYLINDER, 0., 0., 0., 50., 0., 0., 0.2, 1.0, 1.0, 1.0, 1.0, 0.0, 0.,
CYLINDER, 0., 0., 0., 0., 50., 0., 0.2, 1.0, 1.0, 1.0, 0., 1.0, 0.,
CYLINDER, 0., 0., 0., 0., 0., 50., 0.2, 1.0, 1.0, 1.0, 0., 0.0, 1.0,
]

# add labels to axes object (requires pymol version 0.8 or greater, I
# believe

cyl_text(obj,plain,[-5.,-5.,-1],'Origin',0.20,axes=[[3,0,0],[0,3,0],[0,0,3]])
cyl_text(obj,plain,[50.,0.,0.],'X',0.20,axes=[[3,0,0],[0,3,0],[0,0,3]])
cyl_text(obj,plain,[0.,50.,0.],'Y',0.20,axes=[[3,0,0],[0,3,0],[0,0,3]])
cyl_text(obj,plain,[0.,0.,50.],'Z',0.20,axes=[[3,0,0],[0,3,0],[0,0,3]])

# then we load it into PyMOL
cmd.load_cgo(obj,'axes')
</npython>

See [http://qbnz.com/highlighter/index.php The Geshi Home Page]

[[User:Tree|Tree]]

PyMOLWiki:Community Portal

2005-03-02T07:17:31Z

Tree: /* Helping */

== CP ==
Look here for ways to get involved in the PyMolWiki!

== Helping ==
* Importing the email list content: We have (lots) of email to sift through, extract data from and import into the Wiki
* If you feel you have the time to help import data into the PyMol wiki, please email [[User:Tree|Tree]].

=== New! GeShi: Syntax Highlighting for Python & More ===
'''Update''': I have added the option for numbered syntax highlighting and non-numbered.
<pre>
<source lang="python">Non line-numbered code here</source>
</pre>

<pre>
<npython>line-numbered code here</npython>
</pre>

Now with line numbers!

<npython>
# axes.py
from pymol.cgo import *
from pymol import cmd
from pymol.vfont import plain

# create the axes object, draw axes with cylinders coloured red, green,
#blue for X, Y and Z

obj = [
CYLINDER, 0., 0., 0., 50., 0., 0., 0.2, 1.0, 1.0, 1.0, 1.0, 0.0, 0.,
CYLINDER, 0., 0., 0., 0., 50., 0., 0.2, 1.0, 1.0, 1.0, 0., 1.0, 0.,
CYLINDER, 0., 0., 0., 0., 0., 50., 0.2, 1.0, 1.0, 1.0, 0., 0.0, 1.0,
]

# add labels to axes object (requires pymol version 0.8 or greater, I
# believe

cyl_text(obj,plain,[-5.,-5.,-1],'Origin',0.20,axes=[[3,0,0],[0,3,0],[0,0,3]])
cyl_text(obj,plain,[50.,0.,0.],'X',0.20,axes=[[3,0,0],[0,3,0],[0,0,3]])
cyl_text(obj,plain,[0.,50.,0.],'Y',0.20,axes=[[3,0,0],[0,3,0],[0,0,3]])
cyl_text(obj,plain,[0.,0.,50.],'Z',0.20,axes=[[3,0,0],[0,3,0],[0,0,3]])

# then we load it into PyMOL
cmd.load_cgo(obj,'axes')
</npython>

See [http://qbnz.com/highlighter/index.php The Geshi Home Page]

[[User:Tree|Tree]]

Main Page

2005-03-02T06:53:34Z

Tree:

Main Page

2005-03-02T06:28:30Z

Tree:

TOPTOC

2005-03-02T06:27:49Z

Tree: /* Layout Schema */

== Section Layout ==
Please see [[:Talk:Main Page|Discussion]] for more thoughts on the site organizaiton.

== PyMolWiki Top-Level Table Of Contents ==
# [[:Category:News|News]]
## [[:Category:News Discussion|Discussion]]
## [[:Category:News PyMol Beta|PyMol Beta]]
# [[:Category:Technical Issues|Technical Issues]]
## [[:Category:Technical Issues Installation|Installation]]
### [[:Category:Technical Issues Installation OS Dependent|OS Dependent]]
#### [[:Category:Technical Issues Installation OS Dependent Linux|Linux]]
#### [[:Category:Technical Issues Installation OS Dependent MAC|MAC]]
#### [[:Category:Technical Issues Installation OS Dependent Windows|Windows]]
# [[:Category:Launching PyMOL|Launching PyMOL]]
## [[:Category:Launching PyMOL Command Line Options| Command Line Options]]
## [[:Category:Launching PyMOL Launching From a Script|Launching From a Script]]
# [[:Category:Using Pymol|Using PyMol]]
## [[:Category:Using Pymol Mouse Controls|Mouse Controls]]
## [[:Category:Using Pymol Objects and Selections|Objects and Selections]]
### [[:Category:Using Pymol Objects and Selections Working with Objects|Working with Objects]]
### [[:Category:Using Pymol Objects and Selections Working with Selections|Working with Selections]]
### [[:Category:Using Pymol Objects and Selections Selector Quick Reference|Selector Quick Reference]]
#### [[:Category:Using Pymol Objects and Selections Selector Quick Reference Single-word Selectors|Single-word Selectors]]
#### [[:Category:Using Pymol Objects and Selections Selector Quick Reference Property Selectors|Property Selectors]]
#### [[:Category:Using Pymol Objects and Selections Selector Quick Reference Selection Algebra|Selection Algebra]]
#### [[:Category:Using Pymol Objects and Selections Selector Quick Reference Selection Macros|Selection Macros]]
### [[:Category:Using Pymol Objects and Selections Representations|Representations]]
#### [[:Category:Using Pymol Objects and Selections Representations Lines|Lines]]
#### [[:Category:Using Pymol Objects and Selections Representations Sticks|Sticks]]
#### [[:Category:Using Pymol Objects and Selections Representations Cartoon|Cartoon]]
#### [[:Category:Using Pymol Objects and Selections Representations Surface|Surface]]
#### [[:Category:Using Pymol Objects and Selections Representations Mesh|Mesh]]
#### [[:Category:Using Pymol Objects and Selections Representations Spheres|Spheres]]
#### [[:Category:Using Pymol Objects and Selections Representations Dots|Dots]]
### [[:Category:Using Pymol Objects and Selections Color|Color]]
### [[:Category:Using Pymol Objects and Selections Displaying Biochemical Properties|Displaying biochemical properties]]
## [[:Category:Using Pymol Display Settings|Display Settings]]
## [[:Category:Using Pymol Stereo 3D Display|Stereo 3D Display]] -- wrong place
### [[:Category:Using Pymol Hardware Options|Hardware Options]] -- wrong place?
### [[Linux XFree86 Configuration]] -- wrong place
## [[:Category:Using Pymol Scenes|Scenes]]
## [[:Category:Using Pymol Mouse Settings|Mouse Settings]]
## [[:Category:Using Pymol Wizards|Wizards]]
## [[:Category:Using Pymol Ray-tracing|Ray-tracing]]
## [[:Category:Using Pymol Settings Reference|Settings Reference]]
## [[:Category:Using Pymol Movies and Animations|Movies and Animations]]
## [[:Category:Using Pymol Structure Alignment|Structure Alignment]]
## [[:Category:Using Pymol Structure Alignment Editor|Structure Alignment Editor]]
# [[:Category:Commands|Command Language]]
## [[:Category:Commands PyMOL Command Script|PyMOL Command Script]]
## [[:Category:Commands PyMOL Python API|PyMOL Python API]]
# [[:Category:Advanced Issues|Advanced Issues]]
## [[:Category:Advanced Issues Modeling and Editing Structures|Modeling and editing structures]]
### [[:Category:Advanced Issues Modeling and Editing Structures Editing atoms|Editing Atoms]]
### [[:Category:Advanced Issues Modeling and Editing Structures Molecular Sculpting|Molecular sculpting]]
### [[:Category:Advanced Issues Modeling and Editing Structures Homology Modeling|Homology modeling]]
## [[:Category:Advanced Issues Image Manipulation|Image Manipulation]]
### [[:Category:Advanced Issues Image Manipulation labels|labels]]
### [[:Category:Advanced Issues Image Manipulation Photoshop and GIMP|Photoshop/GIMP]]
### [[:Category:Advanced Issues Image Manipulation Stereo Figures|Stereo Figures]]
### [[:Category:Advanced Issues Image Manipulation Publication Quatlity Images|Publication-quality images]]
# [[:Category:Scripting|Scripting]]
## [[:Category:Scripting Example Scripts|Example Scripts]]
## [[:Category:Scripting Script Library|Script Library]]
# [[:Category:Plugins|Plugins]]
## [[:Category:Plugins Electrostatics and Energy Minimization| How to do electrostatics and energy minimization.]]
### [[:Category:Plugins Electrostatics and Energy Minimization APBS| APBS Plugin]]
## [[:Category:Plugins rtools | rtools]]
## [[:Category:Plugins Tutorial|Tutorial on writing plugins]]
## [[:Category:Plugins Others| Others]]
# [[:Category:High-Level Applications|High-Level Applications]]
## [[:Category:High-Level Applications Crystallography Applications|Crystallography Applications]]
### [[:Category:High-Level Applications Symmetry|Symmetry]]
### [[:Category:High-Level Applications Electron Density|Electron Density]]
## [[:Category:High-Level Applications NMR Applications|NMR Applications]]
### [[:Category:High-Level Applications NMR Applications Working with a Family of Structures|Working with Structure Families]]
### [[:Category:High-Level Applications NMR Applications Superimposition and RMSD|Superimposition and RMSD]]
### [[:Category:High-Level Applications NMR Applications NMR Restraints Analysis|NMR Restraints and Analysis]]
# [[:Category:Third Party Software|Third Party Software]]
## [[:Category:Third Party Software PovRay|PovRay]]
## [[:Category:Third Party Software Movies|Movies]]
## [[:Category:Third Party Software Codecs|Codecs]]
# [[:Category:Python Integration|Python Integration]]
# [[:Category:Using PyMol For Unintended Uses|Unintended Uses]] (OpenGL Object Renderer)
## [[:Category:Using PyMol For Unintended Uses Arbitrary Graphics Objects| Arbitrary Graphics Objects]]
# [[:Category:Uncategorized|Uncategorized]] For new pages, misplaced pages, etc.
----
[[User:Tree|Tree]] 02:09, 16 Feb 2005 (CST)
----

TOPTOC

2005-03-02T06:27:21Z

Tree:

== Section Layout ==
Please see [[:Talk:Main Page|Discussion]] for more thoughts on the site organizaiton.

=== Layout Schema ===
# [[:Category:News|News]]
## [[:Category:News Discussion|Discussion]]
## [[:Category:News PyMol Beta|PyMol Beta]]
# [[:Category:Technical Issues|Technical Issues]]
## [[:Category:Technical Issues Installation|Installation]]
### [[:Category:Technical Issues Installation OS Dependent|OS Dependent]]
#### [[:Category:Technical Issues Installation OS Dependent Linux|Linux]]
#### [[:Category:Technical Issues Installation OS Dependent MAC|MAC]]
#### [[:Category:Technical Issues Installation OS Dependent Windows|Windows]]
# [[:Category:Launching PyMOL|Launching PyMOL]]
## [[:Category:Launching PyMOL Command Line Options| Command Line Options]]
## [[:Category:Launching PyMOL Launching From a Script|Launching From a Script]]
# [[:Category:Using Pymol|Using PyMol]]
## [[:Category:Using Pymol Mouse Controls|Mouse Controls]]
## [[:Category:Using Pymol Objects and Selections|Objects and Selections]]
### [[:Category:Using Pymol Objects and Selections Working with Objects|Working with Objects]]
### [[:Category:Using Pymol Objects and Selections Working with Selections|Working with Selections]]
### [[:Category:Using Pymol Objects and Selections Selector Quick Reference|Selector Quick Reference]]
#### [[:Category:Using Pymol Objects and Selections Selector Quick Reference Single-word Selectors|Single-word Selectors]]
#### [[:Category:Using Pymol Objects and Selections Selector Quick Reference Property Selectors|Property Selectors]]
#### [[:Category:Using Pymol Objects and Selections Selector Quick Reference Selection Algebra|Selection Algebra]]
#### [[:Category:Using Pymol Objects and Selections Selector Quick Reference Selection Macros|Selection Macros]]
### [[:Category:Using Pymol Objects and Selections Representations|Representations]]
#### [[:Category:Using Pymol Objects and Selections Representations Lines|Lines]]
#### [[:Category:Using Pymol Objects and Selections Representations Sticks|Sticks]]
#### [[:Category:Using Pymol Objects and Selections Representations Cartoon|Cartoon]]
#### [[:Category:Using Pymol Objects and Selections Representations Surface|Surface]]
#### [[:Category:Using Pymol Objects and Selections Representations Mesh|Mesh]]
#### [[:Category:Using Pymol Objects and Selections Representations Spheres|Spheres]]
#### [[:Category:Using Pymol Objects and Selections Representations Dots|Dots]]
### [[:Category:Using Pymol Objects and Selections Color|Color]]
### [[:Category:Using Pymol Objects and Selections Displaying Biochemical Properties|Displaying biochemical properties]]
## [[:Category:Using Pymol Display Settings|Display Settings]]
## [[:Category:Using Pymol Stereo 3D Display|Stereo 3D Display]] -- wrong place
### [[:Category:Using Pymol Hardware Options|Hardware Options]] -- wrong place?
### [[Linux XFree86 Configuration]] -- wrong place
## [[:Category:Using Pymol Scenes|Scenes]]
## [[:Category:Using Pymol Mouse Settings|Mouse Settings]]
## [[:Category:Using Pymol Wizards|Wizards]]
## [[:Category:Using Pymol Ray-tracing|Ray-tracing]]
## [[:Category:Using Pymol Settings Reference|Settings Reference]]
## [[:Category:Using Pymol Movies and Animations|Movies and Animations]]
## [[:Category:Using Pymol Structure Alignment|Structure Alignment]]
## [[:Category:Using Pymol Structure Alignment Editor|Structure Alignment Editor]]
# [[:Category:Commands|Command Language]]
## [[:Category:Commands PyMOL Command Script|PyMOL Command Script]]
## [[:Category:Commands PyMOL Python API|PyMOL Python API]]
# [[:Category:Advanced Issues|Advanced Issues]]
## [[:Category:Advanced Issues Modeling and Editing Structures|Modeling and editing structures]]
### [[:Category:Advanced Issues Modeling and Editing Structures Editing atoms|Editing Atoms]]
### [[:Category:Advanced Issues Modeling and Editing Structures Molecular Sculpting|Molecular sculpting]]
### [[:Category:Advanced Issues Modeling and Editing Structures Homology Modeling|Homology modeling]]
## [[:Category:Advanced Issues Image Manipulation|Image Manipulation]]
### [[:Category:Advanced Issues Image Manipulation labels|labels]]
### [[:Category:Advanced Issues Image Manipulation Photoshop and GIMP|Photoshop/GIMP]]
### [[:Category:Advanced Issues Image Manipulation Stereo Figures|Stereo Figures]]
### [[:Category:Advanced Issues Image Manipulation Publication Quatlity Images|Publication-quality images]]
# [[:Category:Scripting|Scripting]]
## [[:Category:Scripting Example Scripts|Example Scripts]]
## [[:Category:Scripting Script Library|Script Library]]
# [[:Category:Plugins|Plugins]]
## [[:Category:Plugins Electrostatics and Energy Minimization| How to do electrostatics and energy minimization.]]
### [[:Category:Plugins Electrostatics and Energy Minimization APBS| APBS Plugin]]
## [[:Category:Plugins rtools | rtools]]
## [[:Category:Plugins Tutorial|Tutorial on writing plugins]]
## [[:Category:Plugins Others| Others]]
# [[:Category:High-Level Applications|High-Level Applications]]
## [[:Category:High-Level Applications Crystallography Applications|Crystallography Applications]]
### [[:Category:High-Level Applications Symmetry|Symmetry]]
### [[:Category:High-Level Applications Electron Density|Electron Density]]
## [[:Category:High-Level Applications NMR Applications|NMR Applications]]
### [[:Category:High-Level Applications NMR Applications Working with a Family of Structures|Working with Structure Families]]
### [[:Category:High-Level Applications NMR Applications Superimposition and RMSD|Superimposition and RMSD]]
### [[:Category:High-Level Applications NMR Applications NMR Restraints Analysis|NMR Restraints and Analysis]]
# [[:Category:Third Party Software|Third Party Software]]
## [[:Category:Third Party Software PovRay|PovRay]]
## [[:Category:Third Party Software Movies|Movies]]
## [[:Category:Third Party Software Codecs|Codecs]]
# [[:Category:Python Integration|Python Integration]]
# [[:Category:Using PyMol For Unintended Uses|Unintended Uses]] (OpenGL Object Renderer)
## [[:Category:Using PyMol For Unintended Uses Arbitrary Graphics Objects| Arbitrary Graphics Objects]]
# [[:Category:Uncategorized|Uncategorized]] For new pages, misplaced pages, etc.
----
[[User:Tree|Tree]] 02:09, 16 Feb 2005 (CST)
----

Main Page

2005-03-02T06:27:15Z

Tree:

PyMOLWiki:Community Portal

2005-03-02T06:26:42Z

Tree: /* Section Layout */

PyMOLWiki:Community Portal

2005-02-28T17:55:27Z

Tree: /* New! GeShi: Syntax Highlighting for Python & More */

== CP ==
Look here for ways to get involved in the PyMolWiki!

== Helping ==
* A wiki edit/user policy is needed.
* Graphic design and CSS layout: We need logos, BG images and CSS layout
* Importing the email list content: We have (lots) of email to sift through, extract data from and import into the Wiki
* If you feel you have the time to help import data into the PyMol wiki, please email [[User:Tree|Tree]].

=== Categories/Content ===
You may now add content to the wiki. This is a semi-structured wiki in that the categories are pseudo-hierarchically linked.
If you feel we're missing a category, please find where it would most logically fit, add it to the main page via the [[Top Level Schema Policy]].

== Section Layout ==
Please see [[:Talk:Main Page|Discussion]] for more thoughts on the site organizaiton.

=== Layout Schema ===
# [[:Category:News|News]]
## [[:Category:News Discussion|Discussion]]
## [[:Category:News PyMol Beta|PyMol Beta]]
# [[:Category:Technical Issues|Technical Issues]]
## [[:Category:Technical Issues Installation|Installation]]
### [[:Category:Technical Issues Installation OS Dependent|OS Dependent]]
#### [[:Category:Technical Issues Installation OS Dependent Linux|Linux]]
#### [[:Category:Technical Issues Installation OS Dependent MAC|MAC]]
#### [[:Category:Technical Issues Installation OS Dependent Windows|Windows]]
# [[:Category:Launching PyMOL|Launching PyMOL]]
## [[:Category:Launching PyMOL Command Line Options| Command Line Options]]
## [[:Category:Launching PyMOL Launching From a Script|Launching From a Script]]
# [[:Category:Using Pymol|Using PyMol]]
## [[:Category:Using Pymol Mouse Controls|Mouse Controls]]
## [[:Category:Using Pymol Objects and Selections|Objects and Selections]]
### [[:Category:Using Pymol Objects and Selections Working with Objects|Working with Objects]]
### [[:Category:Using Pymol Objects and Selections Working with Selections|Working with Selections]]
### [[:Category:Using Pymol Objects and Selections Selector Quick Reference|Selector Quick Reference]]
#### [[:Category:Using Pymol Objects and Selections Selector Quick Reference Single-word Selectors|Single-word Selectors]]
#### [[:Category:Using Pymol Objects and Selections Selector Quick Reference Property Selectors|Property Selectors]]
#### [[:Category:Using Pymol Objects and Selections Selector Quick Reference Selection Algebra|Selection Algebra]]
#### [[:Category:Using Pymol Objects and Selections Selector Quick Reference Selection Macros|Selection Macros]]
### [[:Category:Using Pymol Objects and Selections Representations|Representations]]
#### [[:Category:Using Pymol Objects and Selections Representations Lines|Lines]]
#### [[:Category:Using Pymol Objects and Selections Representations Sticks|Sticks]]
#### [[:Category:Using Pymol Objects and Selections Representations Cartoon|Cartoon]]
#### [[:Category:Using Pymol Objects and Selections Representations Surface|Surface]]
#### [[:Category:Using Pymol Objects and Selections Representations Mesh|Mesh]]
#### [[:Category:Using Pymol Objects and Selections Representations Spheres|Spheres]]
#### [[:Category:Using Pymol Objects and Selections Representations Dots|Dots]]
### [[:Category:Using Pymol Objects and Selections Color|Color]]
### [[:Category:Using Pymol Objects and Selections Displaying Biochemical Properties|Displaying biochemical properties]]
## [[:Category:Using Pymol Display Settings|Display Settings]]
## [[:Category:Using Pymol Stereo 3D Display|Stereo 3D Display]] -- wrong place
### [[:Category:Using Pymol Hardware Options|Hardware Options]] -- wrong place?
### [[Linux XFree86 Configuration]] -- wrong place
## [[:Category:Using Pymol Scenes|Scenes]]
## [[:Category:Using Pymol Mouse Settings|Mouse Settings]]
## [[:Category:Using Pymol Wizards|Wizards]]
## [[:Category:Using Pymol Ray-tracing|Ray-tracing]]
## [[:Category:Using Pymol Settings Reference|Settings Reference]]
## [[:Category:Using Pymol Movies and Animations|Movies and Animations]]
## [[:Category:Using Pymol Structure Alignment|Structure Alignment]]
## [[:Category:Using Pymol Structure Alignment Editor|Structure Alignment Editor]]
# [[:Category:Commands|Command Language]]
## [[:Category:Commands PyMOL Command Script|PyMOL Command Script]]
## [[:Category:Commands PyMOL Python API|PyMOL Python API]]
# [[:Category:Advanced Issues|Advanced Issues]]
## [[:Category:Advanced Issues Modeling and Editing Structures|Modeling and editing structures]]
### [[:Category:Advanced Issues Modeling and Editing Structures Editing atoms|Editing Atoms]]
### [[:Category:Advanced Issues Modeling and Editing Structures Molecular Sculpting|Molecular sculpting]]
### [[:Category:Advanced Issues Modeling and Editing Structures Homology Modeling|Homology modeling]]
## [[:Category:Advanced Issues Image Manipulation|Image Manipulation]]
### [[:Category:Advanced Issues Image Manipulation labels|labels]]
### [[:Category:Advanced Issues Image Manipulation Photoshop and GIMP|Photoshop/GIMP]]
### [[:Category:Advanced Issues Image Manipulation Stereo Figures|Stereo Figures]]
### [[:Category:Advanced Issues Image Manipulation Publication Quatlity Images|Publication-quality images]]
# [[:Category:Scripting|Scripting]]
## [[:Category:Scripting Example Scripts|Example Scripts]]
## [[:Category:Scripting Script Library|Script Library]]
# [[:Category:Plugins|Plugins]]
## [[:Category:Plugins Electrostatics and Energy Minimization| How to do electrostatics and energy minimization.]]
### [[:Category:Plugins Electrostatics and Energy Minimization APBS| APBS Plugin]]
## [[:Category:Plugins rtools | rtools]]
## [[:Category:Plugins Tutorial|Tutorial on writing plugins]]
## [[:Category:Plugins Others| Others]]
# [[:Category:High-Level Applications|High-Level Applications]]
## [[:Category:High-Level Applications Crystallography Applications|Crystallography Applications]]
### [[:Category:High-Level Applications Symmetry|Symmetry]]
### [[:Category:High-Level Applications Electron Density|Electron Density]]
## [[:Category:High-Level Applications NMR Applications|NMR Applications]]
### [[:Category:High-Level Applications NMR Applications Working with a Family of Structures|Working with Structure Families]]
### [[:Category:High-Level Applications NMR Applications Superimposition and RMSD|Superimposition and RMSD]]
### [[:Category:High-Level Applications NMR Applications NMR Restraints Analysis|NMR Restraints and Analysis]]
# [[:Category:Third Party Software|Third Party Software]]
## [[:Category:Third Party Software PovRay|PovRay]]
## [[:Category:Third Party Software Movies|Movies]]
## [[:Category:Third Party Software Codecs|Codecs]]
# [[:Category:Python Integration|Python Integration]]
# [[:Category:Using PyMol For Unintended Uses|Unintended Uses]] (OpenGL Object Renderer)
## [[:Category:Using PyMol For Unintended Uses Arbitrary Graphics Objects| Arbitrary Graphics Objects]]
# [[:Category:Uncategorized|Uncategorized]] For new pages, misplaced pages, etc.
----
[[User:Tree|Tree]] 02:09, 16 Feb 2005 (CST)
----

=== New! GeShi: Syntax Highlighting for Python & More ===
'''Update''': I have added the option for numbered syntax highlighting and non-numbered.
<pre>
<source lang="python">Non line-numbered code here</source>
</pre>

<pre>
<npython>line-numbered code here</npython>
</pre>

We now have a syntax highlighter installed. It now supports something like 28 programming languages! When you paste your code simply wrap it in
<language_name> ... code here ... </language_name>.

Here's an example:
<pre>
<python>
# axes.py
from pymol.cgo import *
from pymol import cmd
from pymol.vfont import plain

# create the axes object, draw axes with cylinders coloured red, green,
#blue for X, Y and Z

obj = [
CYLINDER, 0., 0., 0., 50., 0., 0., 0.2, 1.0, 1.0, 1.0, 1.0, 0.0, 0.,
CYLINDER, 0., 0., 0., 0., 50., 0., 0.2, 1.0, 1.0, 1.0, 0., 1.0, 0.,
CYLINDER, 0., 0., 0., 0., 0., 50., 0.2, 1.0, 1.0, 1.0, 0., 0.0, 1.0,
]

# add labels to axes object (requires pymol version 0.8 or greater, I
# believe

cyl_text(obj,plain,[-5.,-5.,-1],'Origin',0.20,axes=[[3,0,0],[0,3,0],[0,0,3]])
cyl_text(obj,plain,[50.,0.,0.],'X',0.20,axes=[[3,0,0],[0,3,0],[0,0,3]])
cyl_text(obj,plain,[0.,50.,0.],'Y',0.20,axes=[[3,0,0],[0,3,0],[0,0,3]])
cyl_text(obj,plain,[0.,0.,50.],'Z',0.20,axes=[[3,0,0],[0,3,0],[0,0,3]])

# then we load it into PyMOL
cmd.load_cgo(obj,'axes')

<python>
</pre>

gives us the code
<source lang="python">
# axes.py
from pymol.cgo import *
from pymol import cmd
from pymol.vfont import plain

# create the axes object, draw axes with cylinders coloured red, green,
#blue for X, Y and Z

obj = [
CYLINDER, 0., 0., 0., 50., 0., 0., 0.2, 1.0, 1.0, 1.0, 1.0, 0.0, 0.,
CYLINDER, 0., 0., 0., 0., 50., 0., 0.2, 1.0, 1.0, 1.0, 0., 1.0, 0.,
CYLINDER, 0., 0., 0., 0., 0., 50., 0.2, 1.0, 1.0, 1.0, 0., 0.0, 1.0,
]

# add labels to axes object (requires pymol version 0.8 or greater, I
# believe

cyl_text(obj,plain,[-5.,-5.,-1],'Origin',0.20,axes=[[3,0,0],[0,3,0],[0,0,3]])
cyl_text(obj,plain,[50.,0.,0.],'X',0.20,axes=[[3,0,0],[0,3,0],[0,0,3]])
cyl_text(obj,plain,[0.,50.,0.],'Y',0.20,axes=[[3,0,0],[0,3,0],[0,0,3]])
cyl_text(obj,plain,[0.,0.,50.],'Z',0.20,axes=[[3,0,0],[0,3,0],[0,0,3]])

# then we load it into PyMOL
cmd.load_cgo(obj,'axes')
</source>

Now with line numbers!

<npython>
# axes.py
from pymol.cgo import *
from pymol import cmd
from pymol.vfont import plain

# create the axes object, draw axes with cylinders coloured red, green,
#blue for X, Y and Z

obj = [
CYLINDER, 0., 0., 0., 50., 0., 0., 0.2, 1.0, 1.0, 1.0, 1.0, 0.0, 0.,
CYLINDER, 0., 0., 0., 0., 50., 0., 0.2, 1.0, 1.0, 1.0, 0., 1.0, 0.,
CYLINDER, 0., 0., 0., 0., 0., 50., 0.2, 1.0, 1.0, 1.0, 0., 0.0, 1.0,
]

# add labels to axes object (requires pymol version 0.8 or greater, I
# believe

cyl_text(obj,plain,[-5.,-5.,-1],'Origin',0.20,axes=[[3,0,0],[0,3,0],[0,0,3]])
cyl_text(obj,plain,[50.,0.,0.],'X',0.20,axes=[[3,0,0],[0,3,0],[0,0,3]])
cyl_text(obj,plain,[0.,50.,0.],'Y',0.20,axes=[[3,0,0],[0,3,0],[0,0,3]])
cyl_text(obj,plain,[0.,0.,50.],'Z',0.20,axes=[[3,0,0],[0,3,0],[0,0,3]])

# then we load it into PyMOL
cmd.load_cgo(obj,'axes')
</npython>

See [http://qbnz.com/highlighter/index.php The Geshi Home Page]

[[User:Tree|Tree]]

Main Page

2005-02-28T17:53:04Z

Tree:

Main Page

2005-02-28T17:51:54Z

Tree:

== PyMol Wiki Home ==
You have reached the (new) home of the PyMolWiki, a user-driven web-oriented CMS.

We (will) strive to provide
* updates on PyMol
* a stable user-oriented documentation base
* a thorough treatment of the PyMol program
* feature rich scripts for general PyMol use

== Links of Interest ==
* Updated! [[PyMolWiki:Community_Portal| How to get involved!]] -- read me if you want to add something
* [[:Category:Scripting Script Library| Script Library]] -- add one!
* [[:Category:Commands|PyMol Commands]] (>130 documented!)
* [[:Special:Allpages| All Pages]]
* [[:Category:Plugins|Plugins]]
* [[:Special:Categories| See All Categories]]

<source lang="python">
#############################################################################
# $Id$
#############################################################################

import sys;
import os;
import math;
import re;
import getopt;

from Bio.PDB.PDBParser import PDBParser

import imgWriter
#my imageWriter using GD
#import dali.imageWriter

class point:
"""
point is a simple representation of a 3D point in space

"""

def __init__(self, ray = [] ):
"""
Constructor

"""

if ( len(ray) != 3 ):
print "ERROR: What, so macromolecules are 2-dimensional now? I don't th
ink so."
sys.exit(2)

# assign instance variables
self.x = ray[0]
self.y = ray[1]
self.z = ray[2]

# calculate the length from origin
self.length = math.sqrt( self.x**2 + self.y**2 + self.z**2 )

</source>

<npython>
#############################################################################
# $Id$
#############################################################################

import sys;
import os;
import math;
import re;
import getopt;

from Bio.PDB.PDBParser import PDBParser

import imgWriter
#my imageWriter using GD
#import dali.imageWriter

class point:
"""
point is a simple representation of a 3D point in space

"""

def __init__(self, ray = [] ):
"""
Constructor

"""

if ( len(ray) != 3 ):
print "ERROR: What, so macromolecules are 2-dimensional now? I don't th
ink so."
sys.exit(2)

# assign instance variables
self.x = ray[0]
self.y = ray[1]
self.z = ray[2]

# calculate the length from origin
self.length = math.sqrt( self.x**2 + self.y**2 + self.z**2 )

</npython>

File:Dots ex.png

2005-02-27T08:19:19Z

Tree: Dots Representation Example

Dots Representation Example

File:Spheres ex.png

2005-02-27T08:18:09Z

Tree: Spheres Example

Spheres Example

File:Mesh ex.png

2005-02-27T08:16:59Z

Tree: Mesh Example.

Mesh Example.

File:Surface ex.png

2005-02-27T08:12:45Z

Tree: Surface Representation Example.

Surface Representation Example.

File:Cartoon ex.png

2005-02-27T08:11:18Z

Tree: Cartoon Example.

Cartoon Example.

File:Lines ex.png

2005-02-27T08:09:57Z

Tree: Lines Example.

Lines Example.

File:Sticks ex.png

2005-02-27T08:08:29Z

Tree: Sticks Example.

Sticks Example.

Main Page

2005-02-24T15:27:03Z

Tree:

Save

2005-02-24T15:25:52Z

Tree:

===DESCRIPTION===

"save" writes selected atoms to a file. The file format is
autodetected if the extesion is ".pdb", ".pse", ".mol", ".mmod", or
".pkl"

Note that if the file extension ends in ".pse" (PyMOL Session), the
complete PyMOL state is always saved to the file (the selection and
state parameters are thus ignored).

===USAGE===
<pre>
save file [,(selection) [,state [,format]] ]
</pre>
===PYMOL API===
<source lang="python">
cmd.save(file, selection, state, format)
</source>

===NOTES===

When saving a session file, then "state" has no effect.
When state = 0 (default), only the current state is written.
When state = -1, then a multi-state output file is written (PDB only).

===SEE ALSO===

[[Cmd load]], [[Cmd get_model]]

[[Category:Commands|save]]

Center

2005-02-24T15:24:51Z

Tree:

== DEPRECATED ==
See [[CmdScript.center|center]]

===DESCRIPTION===

"center" translates the window, the clipping slab, and the
origin to a point centered within the atom selection.

===PYMOL API===
<source lang="python">
cmd.center( string selection, int state = 0, int origin = 1 )
</source>

===NOTES===

state = 0 (default) use all coordinate states
state = -1 use only coordinates for the current state
state > 0 use coordinates for a specific state

origin = 1 (default) move the origin
origin = 0 leave the origin unchanged

===SEE ALSO===

[[Cmd origin]], [[Cmd orient]], [[Cmd zoom]]

[[Category:Commands|center]]

Ray

2005-02-24T15:01:46Z

Tree:

===DESCRIPTION===

"ray" creates a ray-traced image of the current frame. This
can take some time (up to several minutes, depending on image
complexity).

===USAGE===

ray [width,height [,renderer [,angle [,shift ]]]

angle and shift can be used to generate matched stereo pairs

===EXAMPLES===

ray
ray 1024,768
ray renderer=0

===PYMOL API===
<source lang="python">
cmd.ray(int width,int height,int renderer=-1,float shift=0)
</source>

===NOTES

renderer = -1 is default (use value in ray_default_renderer)
renderer = 0 uses PyMOL's internal renderer
renderer = 1 uses PovRay's renderer. This is Unix-only
and you must have "x-povray" in your path. It utilizes two
two temporary files: "tmp_pymol.pov" and "tmp_pymol.png".

===SEE ALSO===

"help faster" for optimization tips with the builtin renderer.
"help povray" for how to use PovRay instead of PyMOL's built-in
ray-tracing engine.

==USER Comments==
====How do I ray trace a publication-ready (~300dpi) image using PyMol?====
This answer is in the [[:Category:Advanced_Issues|Advanced Issues]] (Image Manipulation Section).

[[Category:Commands|ray]]