Hi Eric,

 

I managed to figure out something by pirating some python codes I found from chimera mailing list through googling. I want to use the code to save my reply log, which is going to be about 3.4 million lines (by the way, is there a maximum buffer for the number of lines reply log can take? I feared overrunning the buffer and losing my some part of the replylog)

 

Below is the code; I commented away the part I do not use from the original code.

 

I tried the code by opening it using the chimera gui, and it worked just fine, producing the log file I want. But when I tried opening the same code using command line the log file was produced, but empty.

I tried :

 

E:\Chimera\bin>chimera --nogui save_replylog.py   <- -  doesnot show anything, no popup command window, nothing.

E:\Chimera\bin>chimera --nogui --debug save_replylog.py <- - shows a new pop up window

 

Both commands created my log file, but were both empty files.

 

I would want to run the script later in nogui mode, but I need to retrieve the log for rmsd values, therefore I need to overcome this problem. Any advise..?

 

Thanks!

 

Cheers,

Sumitro

 

 

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from chimera import runCommand

from chimera.tkgui import saveReplyLog

 

#def rms2ref(ref, pose, no):

#    runCommand('open %s; open %s' % (ref, pose))

#    i = 1

#    while i <= no:

#       # only hetatms are included --> ~@/element=h

#       runCommand('sel #1.%i & ~@/element=h' % i)

#       runCommand('rmsd #0 sel')

#       i += 1

#

#rms2ref('lig_cryst.pdb', 'poses.sdf', 10)

 

runCommand('open noprefs E:\\D.combine\\receptor_models\\A-0101_1W72_A.pdb')

runCommand('open noprefs E:\\A.Model_receptor\\PDB_MODELS\\1DUZ.pdb')

runCommand('open noprefs E:\\D.combine\\chain_models\\A-0101_ITLVYKVYY_2CIK.pdb')

runCommand('rmsd #0:@ca #1:2-182.A@ca')

runCommand('match #0:@ca,n,c,o #1:2-182.A@ca,n,c,o')

runCommand('match #2:1-3.C,7-9.C@ca #1:1-3.C,7-9.C@ca ')

runCommand('match #2:1-3.C,7-9.C@ca,n,c,o #1:1-3.C,7-9.C@ca,n,c,o ')

runCommand('combine #0|#2:1-9.C name A-0101_ITLVYKVYY_2CIK.C.(1DUZ.C).A-0101_1W72_A modelId 5')

runCommand('write format pdb 5 E:\\D.combine\\complex\\A-0101_ITLVYKVYY_2CIK.C.(1DUZ.C).A-0101_1W72_A.pdb')

runCommand('close all')

 

# generate output from replyLog.txt

 

saveReplyLog('e:\\D.combine\\mylog.txt')

 

#rmsds = []

#for i in open('mylog2.txt').readlines():

#    if i.startswith('RMSD between'):

#       rmsds.append(i.split()[-2])

#

#print rmsds

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