Right. Without looking that much at the python code I have a hard
time understanding why one would need to make ones own program for
this task when g_dist does the job for you.
/Erik
11 sep 2007 kl. 18.44 skrev Arthur Roberts:
Hello,
I wrote a python script to do this. I would used pymol. Number
each of the pdb files 00000ps.pdb 00250ps.pdb, etc. Also, remove
the water. Just save the file as distances.py and run in pymol.
from pymol import cmd
cmd.reinitialize()
Distances=[]
Line=''
TimeMax=11500
TimeIncr=0
AA=1
AAMax=477
Distances.append([]) ## This is for amino acid 0
while AA <= AAMax:
Message = "Amino Acid Number "+ str(AA)+'\n'
print Message
Distances.append([])
TimeIncr=0
while TimeIncr <= TimeMax:
PDBTime=str("%05d"%TimeIncr)
PDBFile = PDBTime + 'ps.pdb'
Message = PDBTime + '\n'
print Message
cmd.load(PDBFile)
## hide everything
## dist=cmd.distance('tmp', PDBTime+'ps///91/CA',PDBTime
+'ps///478/FE')
dist=cmd.distance('tmp', PDBTime+'ps///'+str(AA)+'/
CA',PDBTime+'ps///478/FE')
if AA==1:
## print "OK"
Distances[0].append(PDBTime)
Line=str("%8.3f"%dist)
Distances[1].append(Line)
else:
Line=str("%8.3f"%dist)
Distances[AA].append(Line)
TimeIncr=TimeIncr+250
cmd.reinitialize()
AA=AA+1
DistancesTranspose=[]
Increment=0
Line = 'Time\t'
while Increment < AAMax-1:
Line = Line + 'aa'+str(Increment+18)+'\t'
Increment=Increment+1
Line = Line + 'aa'+str(Increment+18)+'\r\n'
DistancesTranspose.append(Line)
Increment=0
while Increment <= len(Distances[0])-1:
NestedIncrement=0
Line=''
while NestedIncrement <= len(Distances)-1:
if NestedIncrement >=1:
DistanceDifference = str(float(Distances[NestedIncrement]
[Increment])-float(Distances[NestedIncrement][0]))
else:
DistanceDifference = str(Distances[NestedIncrement][Increment])
if NestedIncrement == (len(Distances)-1):
Line = Line + DistanceDifference + '\r\n' ##
DistFile.write("%s\t" % Test)
else:
Line = Line + DistanceDifference + '\t'
NestedIncrement=NestedIncrement+1
DistancesTranspose.append(Line)
Increment=Increment +1
Message = "Writing File ...\n"
print Message
file('distances.dat', 'w').writelines(DistancesTranspose)
Best wishes,
Art
On Sep 10, 2007, at 8:36 PM, Rui Li wrote:
Hi all,
I want to get the plot of Change in distances between two atom
during MD
simulation.
what program can I use?
Thank you in advance
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_______________________________________________
Erik Marklund, PhD student
Laboratory of Molecular Biophysics,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: +46 18 471 4537 fax: +46 18 511 755
[EMAIL PROTECTED] http://xray.bmc.uu.se/molbiophys
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