Save2traj - Revision history

Cchem: 1 revision

2019-03-04T03:58:23Z

1 revision

Speleo3: see save_traj

2019-02-25T11:20:59Z

see save_traj

Bell: 6 revisions

2014-03-28T03:09:11Z

6 revisions

Slaw at 20:45, 23 October 2009

2009-10-23T20:45:41Z

Slaw at 20:25, 23 October 2009

2009-10-23T20:25:21Z

Slaw at 20:23, 23 October 2009

2009-10-23T20:23:06Z

Slaw at 17:31, 23 October 2009

2009-10-23T17:31:16Z

Slaw at 15:35, 23 October 2009

2009-10-23T15:35:06Z

Slaw: Created page with '==Description== WARNING: This script is still under development so please use at your own risk! This script can be used to generate a DCD trajectory file after you have loaded …'

2009-10-23T15:34:43Z

Created page with '==Description== WARNING: This script is still under development so please use at your own risk! This script can be used to generate a DCD trajectory file after you have loaded …'

New page

==Description==

WARNING: This script is still under development so please use at your own risk!

This script can be used to generate a DCD trajectory file after you have loaded multiple states into a single object.

Currently, the only supported trajectory format is DCD but there will be support for other formats in the future.

===USAGE===

load the script using the [[run]] command

<source lang="python">
save2traj (selection, name)
</source>

"name" corresponds to the output name and ".dcd" will be appended to the end of the name automatically.

===EXAMPLES===

save2traj 1bna & c. A+B, output

This will select chains A and B from the object 1bna and save the selection from each state into the trajectory file called "output.dcd".

===Script===

#WARNING: This script is still under development so please use at your own risk!

<source lang="python">

from pymol import cmd
from pymol import stored
import struct

def save2traj (selection,name,format="dcd"):

#Author: Sean Law
#Michigan State University

#Get NATOMS, NSTATES
NATOMS=cmd.count_atoms(selection)
NSTATES=cmd.count_states()

#Determine Trajectory Format
format=format.lower()
if (format == "charmm"):
name=name+".dcd"
elif (format == "amber"):
print "The amber format has not been implemented yet"
return
name=name+".trj"
elif (format == "trj"):
print "The amber format has not been implemented yet"
return
name=name+".trj"
format="amber"
else:
name=name+".dcd"
format="charmm"

f=open(name,'wb')

#Write Trajectory Header Information
if (format == "charmm"):
writeCHARMMheader(f,NSTATES,NATOMS)
elif (format == "amber"):
print "The amber format has not been implemented yet"
return
else:
print "Unknown format"
return

#Write Trajectory Coordinates
if (format == "charmm"):
fmt=str(NATOMS)+'f'
for state in range(cmd.count_states()):
stored.xyz=[]
cmd.iterate_state(state,selection,"stored.xyz.append([x,y,z])")
for xyz in range (3):
coor=[]
for atom in range (NATOMS):
coor.append(stored.xyz[atom][xyz])
writeFortran(f,coor,fmt,length=NATOMS*4)
elif (format == "amber"):
print "The amber format has not been implemented yet"
return
else:
print "Unknown format"
return

f.close()
return
cmd.extend("save2traj",save2traj)

def writeCHARMMheader (f,NSTATES,NATOMS):
header=['CORD']
fmt='4s9i1f10i'
icontrol=[]
for i in range(20):
#Initialize icontrol
icontrol.insert(i,0)
icontrol[0]=NSTATES
icontrol[1]=1
icontrol[2]=1
icontrol[3]=NSTATES
icontrol[7]=NATOMS*3-6
icontrol[9]=2.045473
icontrol[19]=27

for i in range(20):
header.append(icontrol[i])

writeFortran(f,header,fmt)

#Title
fmt='i80s80s'
title=[2]
title.append('* TITLE')
while (len(title[1])<80):
title[1]=title[1]+' '
title.append('* Generated by savetraj.py (Author: Sean Law)')
while (len(title[2])< 80):
title[2]=title[2]+' '

writeFortran(f,title,fmt,length=160+4)

#NATOM
fmt='i'
writeFortran(f,[NATOMS],fmt)

return
cmd.extend("writeCHARMMheader",writeCHARMMheader)

def readtraj (name):
f=open(name,'rb')
#Read Header
fmt='4s9i1f10i'
header=readFortran(f,fmt)

#Read Title
readCHARMMtitle(f)

#Read NATOMS
fmt='i'
[NATOMS]=readFortran(f,fmt)

#Read COORDINATES

f.close()
return
cmd.extend("readtraj",readtraj)

def writeFortran (f,buffer,fmt,length=0):

if (length == 0):
length=len(buffer)*4
f.write(struct.pack('i',length)) #Fortran unformatted
f.write(struct.pack(fmt,*(buffer)))
f.write(struct.pack('i',length)) #Fortran unformatted

return
cmd.extend("writeFortran",writeFortran)

def readFortran (f,fmt):
[bytes]=struct.unpack('i',f.read(4))
buffer=struct.unpack(fmt,f.read(bytes))
[bytes]=struct.unpack('i',f.read(4))

return buffer
cmd.extend("readFortran",readFortran)

def readCHARMMtitle(f):
[bytes]=struct.unpack('i',f.read(4))
[lines]=struct.unpack('i',f.read(4))
fmt=''
for line in range(lines):
fmt=fmt+'80s'
buffer=(struct.unpack(fmt,f.read(80*lines)))
[bytes]=struct.unpack('i',f.read(4))
#print buffer
return
cmd.extend("readCHARMMtitle",readCHARMMtitle)

</source>

← Older revision		Revision as of 11:20, 25 February 2019
Line 1:		Line 1:
		+	<div style="background-color: #9f9; padding: 10px; margin-bottom: 20px; text-align: center">
		+	'''Note:''' See [[save_traj]] for an improved version of this script.
		+	</div>
		+
	===Description===		===Description===

@@ Line 149: / Line 149: @@
      #Read COORDINATES
-     for frames in range(frames):
+     for frame in range(frames):
          fmt=str(NATOMS)+'f'
          x=readFortran(f,fmt)

← Older revision		Revision as of 20:25, 23 October 2009
Line 16:		Line 16:

	"name" corresponds to the output name and ".dcd" will be appended to the end of the name automatically.		"name" corresponds to the output name and ".dcd" will be appended to the end of the name automatically.
		+
		+	The trajectory file that is generated could be numbered differently than your PDB file since PyMOL modifies the RESID values. Thus, it may be necessary to open your original PDB file and save the molecule (with modified RESIDs) to a new file. Then, load the trajectory into that new file. Alternatively, one could retain the RESIDs as well before importing a PDB structure.

	===EXAMPLES===		===EXAMPLES===

← Older revision	Revision as of 03:58, 4 March 2019
(No difference)

← Older revision	Revision as of 03:09, 28 March 2014
(No difference)

@@ Line 137: / Line 137: @@
      fmt='4s9i1f10i'
      header=readFortran(f,fmt)
      #Read Title
@@ Line 146: / Line 147: @@
      #Read COORDINATES
+     for frames in range(frames):
      f.close()
@@ Line 182: / Line 187: @@
      return
 cmd.extend("readCHARMMtitle",readCHARMMtitle)
 </source>

@@ Line 1: / Line 1: @@
-==Description==
+===Description===
 WARNING: This script is still under development so please use at your own risk!
@@ Line 184: / Line 184: @@
 </source>

@@ Line 25: / Line 25: @@
 ===Script===
-#WARNING: This script is still under development so please use at your own risk!
+<b>WARNING: This script is still under development so please use at your own risk!</b>
 <source lang="python">