PyMOL Wiki - User contributions [en]

CreateSecondaryStructure

2007-08-22T14:01:27Z

Jurgenfd:

===DESCRIPTION===
To build a peptide sequence.

===SETUP===
run CreateSecondaryStructure.py

===NOTES / STATUS===
*Tested on Pymolv1.0, Windows platform
*Many bugs to be found

===USAGE===
*seqInfo = getTableFromCsvFile("seqInfo.csv")
with in the file something like:
MET,-54,-47
PRO,-54,-47

*seqInfo = [['MET',-57,-47],['PRO',-57,-47]]
*createPeptide(seqInfo)

===EXAMPLES===
seqInfo = [['MET',-57,-47],['PRO',-57,-47]]
createPeptide(seqInfo)

===SCRIPTS (CreateSecondaryStructures.py)===
CreateSecondaryStructures.py
<source lang="python">
##############################################
# Original Author: Dan Kulp
# Date : 9/8/2005
# MOdified by Jurgen F. Doreleijers
# For Hamid Eghbalnia
#
#############################################
# Call in window like :
# @C:\Documents and Settings\jurgen.WHELK.000\workspace\Wattos\python\Wattos\Utils\CreateSecondaryStructures.py
# Next line is a pymol directive
python
import string
import urllib

# Well I guess one can build a protein with it but the vdw contacts would be horrible.
# Peptide needs to be at least 2 residues.
def createPeptide(seqInfo):
cmd.delete("all")
# Creates residue TWO
editor.attach_amino_acid('pk1',seqInfo[1][0])
# Creates residue ONE
createSS('resi 2', sequence=seqInfo[0][0],terminal='N')
print "found sequence info for number of residues: ", len(seqInfo)
for i in range(2,len(seqInfo) ):
# resn is the residue number of the new residue
resn = i + 1
print "Adding residue: ", resn, seqInfo[i][0]
# Note that the previous residue is numbered i.
resi = 'resi '+`i`
createSS(resi, sequence=seqInfo[i][0])
for i in range( len(seqInfo) ):
resi = 'resi '+`i+1`
# print "Setting backbone angles for residue: ", (i+1), seqInfo[i][0],seqInfo[i][1],seqInfo[i][2]
set_phipsi(resi,seqInfo[i][1],seqInfo[i][2])

# Create generic secondary structure, based off a selection
def createSS(sel, sequence='ALA',repeat=1,terminal='C'):

# Set selection
selection = "%s and name %s" % (sel,terminal)

# Pick atom for editing - interestingly only need to do this for the first addition
cmd.edit(selection,None,None,None,pkresi=0,pkbond=0)

# Array of residues
seq = string.split(sequence,",")

# Get residue numbering .. potential bug here if number is inconsistent.. (Only works at c-terminal)
resi = int(cmd.get_model(sel).atom[0].resi) + 1
# Loop and build new residues
for i in range(1,repeat+1):
for s in seq:
# print "residue[%i]: %s %s" % (i,s,terminal)
editor.attach_amino_acid('pk1',s)

# Remove extra OXT carboxylate atom (OXT1, OXT2 ?) .. fix as needed
if terminal == 'C':
cmd.remove("%s and name OXT" % sel)

def set_phipsi(sel,phi,psi):
# Get atoms from selection
atoms = cmd.get_model("byres ("+sel+")")

# Loop through atoms in selection
for at in atoms.atom:
if at.name == "N":
# Check for a null chain id (some PDBs contain this)
unit_select = ""
if not at.chain == "":
unit_select = "chain "+str(at.chain)+" and "

try:
# Define residue selections
residue_def_prev = unit_select+'resi '+str(int(at.resi)-1)
residue_def = unit_select+'resi '+str(at.resi)
# print "residue_def_prev: [%s]" % residue_def_prev
# print "residue_def : [%s]" % residue_def
if at.resn == "PRO":
print "Skipping setting phi for PRO"
else:
old_phi = cmd.get_dihedral(residue_def_prev+' and name C',residue_def+' and name N', residue_def+' and name CA',residue_def+' and name C')
cmd.set_dihedral( residue_def_prev+' and name C',residue_def+' and name N', residue_def+' and name CA',residue_def+' and name C' ,phi)
print "Changed residue %4s %4s phi: from %6.1f to %6.1f" % (at.resn, at.resi, old_phi, float(phi))
except:

print "Note skipping set of phi because of error; this is normal for a N-terminal residue"
try:
residue_def = unit_select+'resi '+str(at.resi)
residue_def_next = unit_select+'resi '+str(int(at.resi)+1)
# print "residue_def : [%s]" % residue_def
# print "residue_def_next: [%s]" % residue_def_next
old_psi = cmd.get_dihedral(residue_def +' and name N',residue_def+' and name CA',residue_def+' and name C', residue_def_next+' and name N')
cmd.set_dihedral( residue_def +' and name N',residue_def+' and name CA',residue_def+' and name C', residue_def_next+' and name N',psi)
print "Changed residue %4s %4s psi: from %6.1f to %6.1f" % (at.resn, at.resi, old_psi, float(psi))
except:
print "Note skipping set of psi; this is normal for a C terminal residue"

def getTableFromCsvFile(urlLocation):
result = []
r1 = urllib.urlopen(urlLocation)
data = r1.read()
r1.close()
dataLines = data.split("\n")
for dataLine in dataLines:
if dataLine:
result.append( dataLine.split(',') )
return result

# next line is a pymol directive.
python end

os.chdir("C:\Documents and Settings\jurgen.WHELK.000\workspace\Wattos\python\Wattos\Utils")
seqInfo = getTableFromCsvFile("seqInfo.csv")
createPeptide(seqInfo)

</source>

[[Category:Script_Library|CreateSecondaryStructure]]

[[Category:Structural_Biology_Scripts|CreateSecondaryStructure]]

CreateSecondaryStructure

2007-08-21T01:16:41Z

Jurgenfd: Added example

===DESCRIPTION===
To build a peptide sequence.

===SETUP===
run CreateSecondaryStructure.py

===NOTES / STATUS===
*Tested on Pymolv1.0, Windows platform
*Many bugs to be found

===USAGE===
*seqInfo = getTableFromCsvFile("seqInfo.csv")
with in the file something like:
MET,-54,-47
PRO,-54,-47

*seqInfo = [['MET',-57,-47],['PRO',-57,-47]]
*createPeptide(seqInfo)

===EXAMPLES===
seqInfo = [['MET',-57,-47],['PRO',-57,-47]]
createPeptide(seqInfo)

===SCRIPTS (CreateSecondaryStructures.py)===
CreateSecondaryStructures.py
<source lang="python">
##############################################
# Original Author: Dan Kulp
# Date : 9/8/2005
# MOdified by Jurgen F. Doreleijers
# For Hamid Eghbalnia
#
#############################################
# Call in pymol window like :
# @C:\Documents and Settings\jurgen.WHELK.000\workspace\Wattos\python\Wattos\Utils\CreateSecondaryStructures.py
# Next line is a pymol directive
python
import string
import urllib

# Well I guess one can build a protein with it but the vdw contacts would be horrible.
# Peptide needs to be at least 2 residues.
def createPeptide(seqInfo):
cmd.delete("all")
# Creates residue TWO
editor.attach_amino_acid('pk1',seqInfo[1][0])
# Creates residue ONE
createSS('resi 2', sequence=seqInfo[0][0],terminal='N')
print "found sequence info for number of residues: ", len(seqInfo)
for i in range(2,len(seqInfo) ):
# resn is the residue number of the new residue
resn = i + 1
print "Adding residue: ", resn, seqInfo[i][0]
# Note that the previous residue is numbered i.
resi = 'resi '+`i`
createSS(resi, sequence=seqInfo[i][0])
for i in range( len(seqInfo) ):
resi = 'resi '+`i+1`
print "Setting backbone angles for residue: ", i, seqInfo[i][0],seqInfo[i][1],seqInfo[i][2]
set_phipsi(resi,seqInfo[i][1],seqInfo[i][2])

# Create generic secondary structure, based off a selection
def createSS(sel, sequence='ALA',repeat=1,terminal='C'):

# Set selection
selection = "%s and name %s" % (sel,terminal)

# Pick atom for editing - interestingly only need to do this for the first addition
cmd.edit(selection,None,None,None,pkresi=0,pkbond=0)

# Array of residues
seq = string.split(sequence,",")

# Get residue numbering .. potential bug here if number is inconsistent.. (Only works at c-terminal)
resi = int(cmd.get_model(sel).atom[0].resi) + 1
# Loop and build new residues
for i in range(1,repeat+1):
for s in seq:
# print "residue[%i]: %s %s" % (i,s,terminal)
editor.attach_amino_acid('pk1',s)

# Remove extra OXT carboxylate atom (OXT1, OXT2 ?) .. fix as needed
if terminal == 'C':
cmd.remove("%s and name OXT" % sel)

def set_phipsi(sel,phi,psi):
# Get atoms from selection
atoms = cmd.get_model("byres ("+sel+")")

# Loop through atoms in selection
for at in atoms.atom:
if at.name == "N":
# Check for a null chain id (some PDBs contain this)
unit_select = ""
if not at.chain == "":
unit_select = "chain "+str(at.chain)+" and "

try:
# Define residue selections
residue_def_prev = unit_select+'resi '+str(int(at.resi)-1)
residue_def = unit_select+'resi '+str(at.resi)
# print "residue_def_prev: [%s]" % residue_def_prev
# print "residue_def : [%s]" % residue_def
if at.resn == "PRO":
print "Skipping setting phi for PRO"
else:
old_phi = cmd.get_dihedral(residue_def_prev+' and name C',residue_def+' and name N', residue_def+' and name CA',residue_def+' and name C')
print "Changing phi: "+at.resn+str(at.resi)+" from "+str(old_phi)+" to "+str(phi)
cmd.set_dihedral( residue_def_prev+' and name C',residue_def+' and name N', residue_def+' and name CA',residue_def+' and name C' ,phi)
except:
print "Note skipping set of phi; this is normal for a N-terminal residue"
try:
residue_def = unit_select+'resi '+str(at.resi)
residue_def_next = unit_select+'resi '+str(int(at.resi)+1)
# print "residue_def : [%s]" % residue_def
# print "residue_def_next: [%s]" % residue_def_next
old_psi = cmd.get_dihedral(residue_def +' and name N',residue_def+' and name CA',residue_def+' and name C', residue_def_next+' and name N')
print "Changing psi: "+at.resn+str(at.resi)+" from "+str(old_psi)+" to "+str(psi)
cmd.set_dihedral( residue_def +' and name N',residue_def+' and name CA',residue_def+' and name C', residue_def_next+' and name N',psi)
except:
print "Note skipping set of psi; this is normal for a C terminal residue"

def getTableFromCsvFile(urlLocation):
result = []
r1 = urllib.urlopen(urlLocation)
data = r1.read()
r1.close()
dataLines = data.split("\n")
for dataLine in dataLines:
if dataLine:
result.append( dataLine.split(',') )
return result

# next line is a pymol directive.
python end

os.chdir("C:\Documents and Settings\jurgen.WHELK.000\workspace\Wattos\python\Wattos\Utils")
seqInfo = getTableFromCsvFile("seqInfo.csv")
createPeptide(seqInfo)

</source>

[[Category:Script_Library|CreateSecondaryStructure]]

[[Category:Structural_Biology_Scripts|CreateSecondaryStructure]]

CreateSecondaryStructure

2007-08-20T21:55:23Z

Jurgenfd: Pretty big rewrite

===DESCRIPTION===
To build a peptide sequence.

===SETUP===
run CreateSecondaryStructure.py

===NOTES / STATUS===
*Tested on Pymolv1.0, Windows platform
*Many bugs to be found

===USAGE===
*seqInfo = getTableFromCsvFile("seqInfo.csv")
or
*seqInfo = [['MET',-57,-47],['PRO',-57,-47]]
*createPeptide(seqInfo)

===EXAMPLES===
seqInfo = [['MET',-57,-47],['PRO',-57,-47]]
createPeptide(seqInfo)

===SCRIPTS (CreateSecondaryStructures.py)===
CreateSecondaryStructures.py
<source lang="python">
##############################################
# Original Author: Dan Kulp
# Date : 9/8/2005
# MOdified by Jurgen F. Doreleijers
# For Hamid Eghbalnia
#
#############################################
# Call in pymol window like :
# @C:\Documents and Settings\jurgen.WHELK.000\workspace\Wattos\python\Wattos\Utils\CreateSecondaryStructures.py
# Next line is a pymol directive
python
import string
import urllib

# Well I guess one can build a protein with it but the vdw contacts would be horrible.
# Peptide needs to be at least 2 residues.
def createPeptide(seqInfo):
cmd.delete("all")
# Creates residue TWO
editor.attach_amino_acid('pk1',seqInfo[1][0])
# Creates residue ONE
createSS('resi 2', sequence=seqInfo[0][0],terminal='N')
print "found sequence info for number of residues: ", len(seqInfo)
for i in range(2,len(seqInfo) ):
# resn is the residue number of the new residue
resn = i + 1
print "Adding residue: ", resn, seqInfo[i][0]
# Note that the previous residue is numbered i.
resi = 'resi '+`i`
createSS(resi, sequence=seqInfo[i][0])
for i in range( len(seqInfo) ):
resi = 'resi '+`i+1`
print "Setting backbone angles for residue: ", i, seqInfo[i][0],seqInfo[i][1],seqInfo[i][2]
set_phipsi(resi,seqInfo[i][1],seqInfo[i][2])

# Create generic secondary structure, based off a selection
def createSS(sel, sequence='ALA',repeat=1,terminal='C'):

# Set selection
selection = "%s and name %s" % (sel,terminal)

# Pick atom for editing - interestingly only need to do this for the first addition
cmd.edit(selection,None,None,None,pkresi=0,pkbond=0)

# Array of residues
seq = string.split(sequence,",")

# Get residue numbering .. potential bug here if number is inconsistent.. (Only works at c-terminal)
resi = int(cmd.get_model(sel).atom[0].resi) + 1
# Loop and build new residues
for i in range(1,repeat+1):
for s in seq:
# print "residue[%i]: %s %s" % (i,s,terminal)
editor.attach_amino_acid('pk1',s)

# Remove extra OXT carboxylate atom (OXT1, OXT2 ?) .. fix as needed
if terminal == 'C':
cmd.remove("%s and name OXT" % sel)

def set_phipsi(sel,phi,psi):
# Get atoms from selection
atoms = cmd.get_model("byres ("+sel+")")

# Loop through atoms in selection
for at in atoms.atom:
if at.name == "N":
# Check for a null chain id (some PDBs contain this)
unit_select = ""
if not at.chain == "":
unit_select = "chain "+str(at.chain)+" and "

try:
# Define residue selections
residue_def_prev = unit_select+'resi '+str(int(at.resi)-1)
residue_def = unit_select+'resi '+str(at.resi)
# print "residue_def_prev: [%s]" % residue_def_prev
# print "residue_def : [%s]" % residue_def
if at.resn == "PRO":
print "Skipping setting phi for PRO"
else:
old_phi = cmd.get_dihedral(residue_def_prev+' and name C',residue_def+' and name N', residue_def+' and name CA',residue_def+' and name C')
print "Changing phi: "+at.resn+str(at.resi)+" from "+str(old_phi)+" to "+str(phi)
cmd.set_dihedral( residue_def_prev+' and name C',residue_def+' and name N', residue_def+' and name CA',residue_def+' and name C' ,phi)
except:
print "Note skipping set of phi; this is normal for a N-terminal residue"
try:
residue_def = unit_select+'resi '+str(at.resi)
residue_def_next = unit_select+'resi '+str(int(at.resi)+1)
# print "residue_def : [%s]" % residue_def
# print "residue_def_next: [%s]" % residue_def_next
old_psi = cmd.get_dihedral(residue_def +' and name N',residue_def+' and name CA',residue_def+' and name C', residue_def_next+' and name N')
print "Changing psi: "+at.resn+str(at.resi)+" from "+str(old_psi)+" to "+str(psi)
cmd.set_dihedral( residue_def +' and name N',residue_def+' and name CA',residue_def+' and name C', residue_def_next+' and name N',psi)
except:
print "Note skipping set of psi; this is normal for a C terminal residue"

def getTableFromCsvFile(urlLocation):
result = []
r1 = urllib.urlopen(urlLocation)
data = r1.read()
r1.close()
dataLines = data.split("\n")
for dataLine in dataLines:
if dataLine:
result.append( dataLine.split(',') )
return result

# next line is a pymol directive.
python end

os.chdir("C:\Documents and Settings\jurgen.WHELK.000\workspace\Wattos\python\Wattos\Utils")
seqInfo = getTableFromCsvFile("seqInfo.csv")
createPeptide(seqInfo)

</source>

[[Category:Script_Library|CreateSecondaryStructure]]

[[Category:Structural_Biology_Scripts|CreateSecondaryStructure]]

CreateSecondaryStructure

2007-08-16T17:12:51Z

Jurgenfd: /* SCRIPTS (CreateSecondaryStructures.py) */

*Many bugs found, need to be worked out before further use... stay tuned.

===DESCRIPTION===
To enable growing of a peptide sequence of one of the terminals. The growing can be set to any secondary structure (phi,psi pairing). Only extendHelix is currently implemented, but it should be rather simple to add more functions in or tweak the existing ones.

Functions:
*extendHelix
*createSS
*set_phipsi

===SETUP===
run CreateSecondaryStructure.py

===NOTES / STATUS===
*Tested on Pymolv0.97, Windows platform
*N-terminal growing doesn't work: adds residues, but doesn't set angles correctly
*Many bugs found, need to be worked out before further use... stay tuned.

===USAGE===
extendHelix selection,sequence,repeat [, phi] [, psi] [, terminal ]
set_phipsi selection, phi, psi

===EXAMPLES===
extendHelix('resi 1371', 'ALA,GLN,HIS,ALA', 5)
set_phipsi('resi 1371', -60, -60)

===SCRIPTS (CreateSecondaryStructures.py)===
CreateSecondaryStructures.py
<source lang="python">

##############################################
# Author: Dan Kulp
# Date : 9/8/2005
#
#
# Notes:
# - Simple builds a string of residues
# and sets the phi,psi angles.
# - No energies are computed.
# - This will generate a starting point.
# - Defaultly grows from C-term,
# - N-term growing currently broken
#############################################

import string

# Wrapper Functions...
print "extendHelix(selection,sequence,repeat)"
print "Example:\n\t extendHelix('resi 1371', 'ALA,GLN,HIS,ALA', 5)"
print "Note: simple build of residue type and phi,psi angle; no energy computed"

def extendHelix(sel,seq,repeat=1,phi=-60,psi=-60,terminal='C'):
createSS(sel,seq,repeat,phi,psi,string.upper(terminal))
cmd.select("extendedHelix","all")
cmd.deselect()
cmd.save("./extendedHelix.pdb","extendedHelix")

# Create generic secondary structure, based off a selection
def createSS(sel, sequence='ALA',repeat=1,phi=-60,psi=-60,terminal='C'):

# Set selection
selection = "%s and name %s" % (sel,terminal)

# Pick atom for editing - interestingly only need to do this for the first addition
cmd.edit(selection,None,None,None,pkresi=0,pkbond=0)

# Array of residues
seq = string.split(sequence,",")

# Get residue numbering .. potential bug here if number is inconsistent.. (Only works at c-terminal)
resi = int(cmd.get_model(sel).atom[0].resi) + 1

# Loop and build new residues
for i in range(1,repeat+1):
for s in seq:
print "residue[%i]: %s" % (i,s)
editor.attach_amino_acid('pk1',s)

# Loop and set phi,psi angles for new residues
if terminal == 'N':
resi -= repeat

for i in range(0,repeat+1):
for s in seq:
set_phipsi("resi %i" % (resi), phi,psi)
resi += 1

# Remove extra OXT carboxylate atom (OXT1, OXT2 ?) .. fix as needed
if terminal == 'C':
cmd.remove("%s and name OXT" % sel)

def set_phipsi(sel,phi,psi):

# Set up some variables..
residues = ['dummy'] # Keep track of residues already done
probs = [] # probability of each residue conformation

# Get atoms from selection
atoms = cmd.get_model("byres ("+sel+")")

# Loop through atoms in selection
for at in atoms.atom:
try:
# Don't process Glycines or Alanines
if at.resn == 'GLY' or at.chain+":"+at.resn+":"+at.resi in residues:
continue

residues.append(at.chain+":"+at.resn+":"+at.resi)

# Check for a null chain id (some PDBs contain this)
unit_select = ""
if not at.chain == "":
unit_select = "chain "+str(at.chain)+" and "

# Define selections for residue i-1, i and i+1
residue_def = unit_select+'resi '+str(at.resi)
residue_def_prev = unit_select+'resi '+str(int(at.resi)-1)
# residue_def_next = unit_select+'resi '+str(int(at.resi)+1)

# Compute phi/psi angle
old_phi = cmd.get_dihedral(residue_def+' and name CB',residue_def+' and name CA',residue_def+' and name N',residue_def_prev+' and name C')
old_psi = cmd.get_dihedral(residue_def+' and name O',residue_def+' and name C',residue_def+' and name CA',residue_def+' and name CB')

print "Changing "+at.resn+str(at.resi)+" from "+str(old_phi)+","+str(old_psi)+" to "+str(phi)+","+str(psi)

cmd.set_dihedral(residue_def+' and name CB',residue_def+' and name CA',residue_def+' and name N',residue_def_prev+' and name C',phi)
cmd.set_dihedral(residue_def+' and name O',residue_def+' and name C',residue_def+' and name CA',residue_def+' and name CB', psi)

except:
print "Exception Thrown"
continue

</source>

[[Category:Script_Library|CreateSecondaryStructure]]

[[Category:Structural_Biology_Scripts|CreateSecondaryStructure]]

Category:FAQ

2007-08-01T17:01:55Z

Jurgenfd: /* Overview */

==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? Please note, not all AQ are FAQ. Also, many answers to frequently recurring problems are probably best sought by searching for your terms in the Wiki.

----------

Q: Is there any way to export PyMol models onto CAD standards (autocad, archicad) or 3D modeling software (blender, 3DStudio, Maya)? Thanks a lot.

----------

Q: I am wondering how to change the default settings for a color "spectrum". I would like to color by b-factor but not with the default spectrum but from white-to-red.

Alex

---------

Q: I was wondering what the percentage given under the mutengensis wizard means? Thanks...

----
Q: I've installed PyMol_0_98 correctly but I can't open my files in .mol2 or .pdb format from the menubar. Instead I can open them with the program. I can't even save the images I create in PyMol and obviously the mivie too.

Could you help me to solve these problems.
Thanks
Vittorio

A1: Vittorio, if I understand you correctly, then you need to (a) make sure you have the PDB file on your machine, say Desktop (or home directory, for *nix), then in the GUI click on, "File"->"Open" then use the dialog to find the file you want to load. You can save time if you know where the file is by just using PyMol's "load" command
load fileName, objectName
loads the fileName into a new object called objectName, for example,
load /tmp/1ggz.pdb, 1ggz

See [[Cmd load|load]],

A2: To save images you have a couple options. First, to save a quick raw screen dump type, "png fileName" to save a PNG image (IE and other programs can view these files). Or, secondly, if you prefer a higher quality image with ray-traced shadows and textures you can do, "ray" then, the above "png" command.

See [[Cmd ray|ray]], [[Cmd png|png]], [[:Category:Using_Pymol|Using PyMol]]

Hope this helps. If it didn't please restate your question to make it more clear.
----

Q: I've installed PyMol_0_98, and recently my structures have stopped displaying. I've tried uninstalling PyMol_0_98 and installing PyMol_0_97, and yet i've ran into the same problem...my .pdb files no longer display, although it is evident that they are being loaded and I can edit them.

Does anybody have any clue as to what might be the problem?
Thanks, shebsmehr

----
Q: Hi I have a problem. For some reason PyMOl do not display certain areas (several loops) of my .pdb file (1DAN) when in cartoon. When I display the structure in "lines" or "sticks" everything is ok. Furthermore, other .pdb viewers dont have this problem. I have tried several things:
1. Upgraded to the newest version og PyMol.
2. Redefined secondary structure using the "alter command".
3. Imported the .pdb file into SwissViewer, saved as the imported structure as a .pdb file, and then imported into PyMOl.

None of these things have solved the problem. Help please! (I would hate to have to start using another pdb-viewer!!)
Cheers
Kasper

----
Q: I want to move one object while keeping another fixed. How do I do this?

A: Load the proteins as separate objects, put the mouse into 3-button editing mode, then shift-middle click-and-drag on the molecule to translate and shift-left-click-and-drag to rotate. (Warren DeLano answer)

----
Q: I'd like to select residues that are in contact with a surface, or else be able to select buried/non-buried residues, is there any way to do this ? [[User:Xevi|Xevi]] 03:52, 16 Jun 2006 (CDT)

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Q: I am doing some MD simulations using CHARMM (not AMBER) and would like to visualize the .dcd files output by CHARMM. I understand that PyMol can open .trj files from AMBER but is there a way to open up these .dcd files and if not, are there any plans to implement this? Thank you for your time!

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Q: I would like the distance labels generated with the 'distance' command to be single-digit only, e.g. 2.8 instead of 2.77. How can I do this? Thanks, MindFrog

A: Setting startup settings and python commands can be done in a file: ~/.pymolrc
E.g. command in there: cmd.set('label_distance_digits',1)
On my windows machine this is in C:\Documents and Settings\jurgen.WHELK.000\.pymolrc

All states

2006-09-14T21:26:00Z

Jurgenfd: /* Example */

==Overview==

When set "on", this setting causes PyMOL to display all states or in NMR jargon: all the models in the ensemble.
The 'default' behavior (OFF) can be overridden by placing the "set all_states, on" statement into your '.pymolrc' file, located in your login directory (under all flavors of unix).

==Syntax==
<source lang="python">
set all_states, on
set all_states, off
</source>
==Example==
<source lang="python">
import urllib2
pdbCode = '1BRV'
pdbUrl = 'http://www.rcsb.org/pdb/downloadFile.do?fileFormat=pdb&compression=NO&structureId='+pdbCode
pdbFile = urllib2.urlopen(pdbUrl)
pdbContent = pdbFile.read()
cmd.read_pdbstr(pdbContent, pdbCode)

set all_states, on
</source>

All states

2006-09-14T20:28:09Z

Jurgenfd:

==Overview==

When set "on", this setting causes PyMOL to display all states or in NMR jargon: all the models in the ensemble.
The 'default' behavior (OFF) can be overridden by placing the "set all_states, on" statement into your '.pymolrc' file, located in your login directory (under all flavors of unix).

==Syntax==
<source lang="python">
set all_states, on
set all_states, off
</source>
==Example==
<source lang="python">
load 1brv.pdb # Get it locally first by e.g. using the Plugin: "PDB Loader Service"
set all_states, on
</source>

All states

2006-09-14T20:26:33Z

Jurgenfd: /* Example */

All states

2006-09-14T20:05:12Z

Jurgenfd:

Settings

2006-09-14T19:59:26Z

Jurgenfd:

These are all the PyMol settings. If you feel like documenting them, and what they do, feel free. 42 done, 476 to go !

active_selections ray_default_renderer
[[all_states]] ray_direct_shade
ambient ray_hint_camera
angle_label_position ray_hint_shadow
angle_size ray_improve_shadows
animation ray_interior_color
animation_duration ray_interior_mode
[[antialias]] ray_interior_reflect
async_builds ray_interior_shadows
atom_name_wildcard ray_interior_texture
auto_classify_atoms ray_legacy_lighting
auto_color ray_max_passes
auto_dss [[ray_opaque_background]]
auto_hide_selections [[ray_orthoscopic]]
auto_indicate_flags ray_oversample_cutoff
auto_number_selections ray_pixel_scale
auto_remove_hydrogens [[ray_shadow]]
auto_sculpt ray_shadow_decay_factor
auto_show_lines ray_shadow_decay_range
auto_show_nonbonded ray_shadow_fudge
auto_show_selections [[ray_shadows]]
auto_show_spheres ray_texture
[[auto_zoom]] ray_texture_settings
[[backface_cull]] ray_trace_depth_factor
batch_prefix ray_trace_disco_factor
[[bg_rgb]] [[ray_trace_fog]]
bonding_vdw_cutoff ray_trace_fog_start
button_mode [[ray_trace_frames]]
button_mode_name ray_trace_gain
cache_display ray_trace_mode
cache_frames ray_trace_slope_factor
cache_memory ray_transparency_contrast
[[cartoon_color]] ray_transparency_shadows
[[Cartoon Helix Settings|cartoon_cylindrical_helices]] ray_transparency_spec_cut
cartoon_debug ray_transparency_specular
[[cartoon_discrete_colors]] ray_triangle_fudge
cartoon_dumbbell_length reflect
cartoon_dumbbell_radius reflect_power
cartoon_dumbbell_width retain_order
[[Cartoon Helix Settings|cartoon_fancy_helices]] ribbon_color
[[cartoon_fancy_sheets]] ribbon_nucleic_acid_mode
cartoon_flat_cycles ribbon_power
cartoon_flat_sheets ribbon_power_b
cartoon_helix_radius ribbon_radius
[[cartoon_highlight_color]] [[ribbon_sampling]]
cartoon_ladder_color ribbon_side_chain_helper
cartoon_ladder_mode ribbon_smooth
cartoon_ladder_radius ribbon_throw
cartoon_loop_cap ribbon_trace_atoms
cartoon_loop_quality [[ribbon_width]]
cartoon_loop_radius robust_logs
[[cartoon_nucleic_acid_color]] rock_delay
[[cartoon_nucleic_acid_mode]] roving_byres
cartoon_oval_length roving_cartoon
cartoon_oval_quality roving_delay
cartoon_oval_width roving_detail
cartoon_power roving_isomesh
cartoon_power_b roving_isosurface
cartoon_putty_quality roving_labels
cartoon_putty_radius roving_lines
cartoon_putty_range roving_map1_level
cartoon_putty_scale_max roving_map1_name
cartoon_putty_scale_min roving_map2_level
cartoon_putty_scale_power roving_map2_name
cartoon_rect_length roving_map3_level
cartoon_rect_width roving_map3_name
cartoon_refine roving_nb_spheres
cartoon_refine_normals roving_nonbonded
cartoon_refine_tips roving_origin
cartoon_ring_color roving_origin_z
cartoon_ring_finder roving_origin_z_cushion
[[cartoon_ring_mode]] roving_polar_contacts
cartoon_ring_radius roving_polar_cutoff
[[cartoon_ring_transparency]] roving_ribbon
cartoon_ring_width roving_selection
[[cartoon_round_helices]] roving_spheres
[[cartoon_sampling]] roving_sticks
cartoon_side_chain_helper scene_animation
cartoon_smooth_cycles scene_animation_duration
cartoon_smooth_first scene_current_name
cartoon_smooth_last scene_loop
[[cartoon_smooth_loops]] scene_restart_movie_delay
cartoon_throw scenes_changed
cartoon_trace_atoms sculpt_angl_weight
[[cartoon_transparency]] sculpt_auto_center
cartoon_tube_cap sculpt_avd_excl
cartoon_tube_quality sculpt_avd_gap
cartoon_tube_radius sculpt_avd_range
cavity_cull sculpt_avd_weight
cgo_dot_radius sculpt_bond_weight
cgo_dot_width sculpt_field_mask
cgo_line_radius sculpt_hb_overlap
cgo_line_width sculpt_hb_overlap_base
cgo_ray_width_scale sculpt_line_weight
cgo_sphere_quality sculpt_max_max
cgo_transparency sculpt_max_min
clamp_colors sculpt_max_scale
connect_bonded sculpt_max_weight
connect_cutoff sculpt_memory
connect_mode sculpt_min_max
coulomb_cutoff sculpt_min_min
coulomb_dielectric sculpt_min_scale
coulomb_units_factor sculpt_min_weight
cull_spheres sculpt_nb_interval
[[Dash_Gap]] sculpt_plan_weight
[[Dash_Length]] sculpt_pyra_weight
[[Dash_Radius]] sculpt_tors_tolerance
[[Dash_Round_Ends]] sculpt_tors_weight
dash_width sculpt_tri_max
debug_pick sculpt_tri_min
defer_builds_mode sculpt_tri_mode
defer_updates sculpt_tri_scale
depth_cue sculpt_tri_weight
dihedral_label_position sculpt_vdw_scale
dihedral_size sculpt_vdw_scale14
direct sculpt_vdw_vis_max
dist_counter sculpt_vdw_vis_mid
distance_exclusion sculpt_vdw_vis_min
dot_color sculpt_vdw_vis_mode
dot_density sculpt_vdw_weight
dot_hydrogens sculpt_vdw_weight14
dot_lighting sculpting
dot_mode sculpting_cycles
dot_normals secondary_structure
dot_radius security
dot_solvent sel_counter
[[dot_width]] selection_overlay
draw_frames selection_round_points
editor_auto_dihedral selection_visible_only
editor_auto_origin [[selection_width]]
editor_label_fragments selection_width_max
fast_idle selection_width_scale
fetch_path [[seq_view]]
[[Field_Of_View]] seq_view_alignment
fit_iterations seq_view_color
fit_tolerance seq_view_discrete_by_state
float_labels seq_view_fill_char
fog seq_view_fill_color
fog_start seq_view_format
frame seq_view_label_color
full_screen seq_view_label_mode
gamma seq_view_label_spacing
gaussian_b_adjust seq_view_label_start
gaussian_b_floor [[seq_view_location]]
gaussian_resolution seq_view_overlay
gl_ambient seq_view_unaligned_color
h_bond_cone seq_view_unaligned_mode
h_bond_cutoff_center session_file
h_bond_cutoff_edge session_migration
h_bond_exclusion session_version_check
h_bond_max_angle shininess
h_bond_power_a show_alpha_checker
h_bond_power_b show_progress
[[half_bonds]] simplify_display_lists
hash_max single_image
hide_underscore_names slice_dynamic_grid
idle_delay slice_dynamic_grid_resolution
ignore_case slice_grid
ignore_pdb_segi slice_height_map
image_dots_per_inch slice_height_scale
internal_feedback slice_track_camera
[[Internal Gui|internal_gui]] slow_idle
internal_gui_control_size smooth_color_triangle
internal_gui_mode solvent_radius
internal_gui_width spec_count
[[internal_prompt]] spec_direct
isomesh_auto_state spec_direct_power
[[label_color]] spec_power
[[Label_font_id]] [[spec_reflect]]
[[Label_outline_color]] specular
label_position specular_intensity
[[label_shadow_mode]] [[sphere_color]]
[[label_size]] sphere_mode
legacy_mouse_zoom sphere_point_max_size
legacy_vdw_radii sphere_point_size
light sphere_quality
light2 [[sphere_scale]]
light3 sphere_solvent
light4 sphere_transparency
light5 spheroid_fill
light6 spheroid_scale
light7 spheroid_smooth
light8 ss_helix_phi_exclude
light9 ss_helix_phi_include
light_count ss_helix_phi_target
line_radius ss_helix_psi_exclude
[[line_smooth]] ss_helix_psi_include
line_stick_helper ss_helix_psi_target
line_width ss_strand_phi_exclude
log_box_selections ss_strand_phi_include
log_conformations ss_strand_phi_target
logging ss_strand_psi_exclude
matrix_mode ss_strand_psi_include
max_threads ss_strand_psi_target
max_triangles state
mesh_color static_singletons
mesh_lighting stereo
mesh_mode stereo_angle
mesh_normals stereo_double_pump_mono
mesh_quality stereo_mode
mesh_radius stereo_shift
mesh_solvent stick_ball
mesh_type stick_ball_ratio
mesh_width stick_color
min_mesh_spacing stick_fixed_radius
mouse_limit [[stick_nub]]
mouse_restart_movie_delay stick_overlap
mouse_scale stick_quality
mouse_selection_mode stick_radius
movie_delay stick_transparency
movie_loop stick_valence_scale
multiplex stop_on_exceptions
no_idle surface_best
nonbonded_size surface_carve_cutoff
normal_workaround surface_carve_selection
normalize_ccp4_maps surface_carve_state
normalize_grd_maps surface_circumscribe
normalize_o_maps surface_clear_cutoff
nvidia_bugs surface_clear_selection
opaque_background surface_clear_state
[[orthoscopic]] surface_color
overlay surface_debug
overlay_lines surface_miserable
pdb_conect_all surface_mode
pdb_discrete_chains surface_normal
pdb_echo_tags surface_optimize_subsets
pdb_hetatm_sort surface_poor
pdb_honor_model_number surface_proximity
pdb_insertions_go_first surface_quality
pdb_insure_orthogonal surface_ramp_above_mode
pdb_literal_names surface_solvent
pdb_no_end_record surface_trim_cutoff
pdb_reformat_names_mode surface_trim_factor
pdb_retain_ids surface_type
pdb_standard_order suspend_updates
pdb_truncate_residue_name swap_dsn6_bytes
pdb_unbond_cations sweep_angle
pdb_use_ter_records sweep_mode
[[pickable]] sweep_phase
png_file_gamma sweep_speed
png_screen_gamma test1
power test2
pqr_no_chain_id text
presentation texture_fonts
presentation_auto_quit [[transparency]]
presentation_auto_start transparency_mode
presentation_mode transparency_picking_mode
preserve_chempy_ids triangle_max_passes
pymol_space_max_blue trim_dots
pymol_space_max_green [[two_sided_lighting]]
pymol_space_max_red use_display_lists
pymol_space_min_factor [[valence]]
raise_exceptions valence_default
rank_assisted_sorts valence_size
ray_blend_blue validate_object_names
ray_blend_colors virtual_trackball
ray_blend_green wildcard
ray_blend_red wizard_prompt_mode
ray_color_ramps wrap_output

[[Category:Settings|All Settings]]