[Chimera-users] Fwd: Problem running chimera through a command script

Tue Feb 17 08:30:11 PST 2015

That fixed it! The python script now runs chimera through the command
script just fine! Thank you Tom,

Christos Deligkaris, PhD
Assistant Professor of Physics, Drury University
900 N Benton Ave, Springfield MO, 65802
Office Phone: (417) 873-7234
www2.drury.edu/christos <http://www2.drury.edu/christos/index.html>
@DeligkarisGroup <https://twitter.com/DeligkarisGroup> +ChristosDeligkaris
<http://google.com/+ChristosDeligkaris>

On Tue, Feb 17, 2015 at 10:28 AM, Tom Goddard <goddard at sonic.net> wrote:

> Hi Christos,
>
>   Now I think your problem is the line
>
>     script_file.close
>
> You need
>
>     script_file.close()
>
> with parentheses since close is a function.  Without that the command file
> you wrote is not closed before running chimera, and probably the file will
> not be written until closed because of buffering.
>
>   The spaces in the --nogui option is not a Chimera bug.  When you use
> subprocess.call() the arguments
>
> On Feb 17, 2015, at 6:44 AM, Christos Deligkaris <deligkaris at gmail.com>
> wrote:
>
> Thank you Tom. If I take out the spaces, those error messages disappear.
> It seems that that was a chimera issue.
>
> However, the chimera .com script is still not being executed with the
> subprocess.call command. I am not sure now whether this is a chimera issue
> or a python issue....
>
> Christos Deligkaris, PhD
> Assistant Professor of Physics, Drury University
> 900 N Benton Ave, Springfield MO, 65802
> Office Phone: (417) 873-7234
> www2.drury.edu/christos <http://www2.drury.edu/christos/index.html>
> @DeligkarisGroup <https://twitter.com/DeligkarisGroup> +ChristosDeligkaris
> <http://google.com/+ChristosDeligkaris>
>
>
>
> On Mon, Feb 16, 2015 at 11:02 PM, Tom Goddard <goddard at sonic.net> wrote:
>
>> Hi Christos,
>>
>>   I think your error is because the “—nogui” option in your
>> subprocess.call() has spaces before and after inside the quote marks.  Take
>> those spaces out and I bet it will work.  The error seems to be trying to
>> create the Chimera splash screen which would not happen in nogui mode.
>>
>> Tom
>>
>>
>> On Feb 16, 2015, at 8:30 PM, Christos Deligkaris wrote:
>>
>> Dear all,
>>
>> I have a python script that creates a .com command script for chimera and
>> then attempts to run the chimera script. Here is the python script:
>>
>> **************
>>
>> #!/usr/bin/env python
>> import re,os,sys,math, decimal, subprocess
>> from copy import deepcopy
>> from openeye.oechem import *
>> from decimal import *
>>
>> script_file=open("chimera_script_for_" + "ligand" +".com", 'w')
>> script_file.write("open "+ "127D" +"\n")
>> script_file.write("open " + "127D" +"\n")
>> script_file.write("open "+ "ligand.pdb" +"\n")
>> script_file.write("match #0:"+ "6" + " " + "#1:"+ "18" +"\n")
>> script_file.write("write format pdb 2 "+ "flipped_" + "ligand" + "\n")
>> script_file.write("stop")
>> script_file.close
>> print script_file.name
>> chimera=subprocess.call(["chimera", " --nogui ", "
>> chimera_script_for_ligand.com"])
>> print chimera
>> #delete the script, leaving just the flipped ligand
>> #os.remove(script_file.name)
>>
>> *******************
>>
>> When I run the script, it successfully generates the .com chimera script.
>> However, I get the following error message:
>>
>> *******************
>>
>> [christos at biophysics Desktop]$ ./script.py
>> chimera_script_for_ligand.com
>> Traceback (most recent call last):
>>   File "/share/apps/PROGRAMS/CHIMERA/CHIMERA-1.9/share/__main__.py", line
>> 69, in <module>
>>     value = chimeraInit.init(sys.argv)
>>   File "/share/apps/PROGRAMS/CHIMERA/CHIMERA-1.9/share/chimeraInit.py",
>> line 638, in init
>>     splash.create()
>>   File
>> "/share/apps/PROGRAMS/CHIMERA/CHIMERA-1.9/share/chimera/splash.py", line
>> 25, in create
>>     sync=chimera.debug)
>>   File
>> "/share/apps/PROGRAMS/CHIMERA/CHIMERA-1.9/lib/python2.7/lib-tk/Tkinter.py",
>> line 1747, in __init__
>>     self.tk = _tkinter.create(screenName, baseName, className,
>> interactive, wantobjects, useTk, sync, use)
>> _tkinter.TclError: no display name and no $DISPLAY environment variable
>> 1
>>
>> **********************
>>
>> The python script successfully creates the .com script:
>>
>> ******************************
>>
>> [christos at biophysics Desktop]$ more chimera_script_for_ligand.com
>> open 127D
>> open 127D
>> open ligand.pdb
>> match #0:6 #1:18
>> write format pdb 2 flipped_ligand
>> stop
>>
>> ***************************
>>
>> and if I manually execute this chimera script, everything works out well:
>>
>> **************************
>>
>> [christos at biophysics Desktop]$ chimera --nogui
>> chimera_script_for_ligand.com
>> Fetching 127D from web site www.rcsb.org
>> 0 Kbytes received
>> Fetch 127D: finished
>> Done fetching 127D; verifying...
>> Opening 127D...
>> #0, chain A: dna (5'-D(*cp*gp*cp*gp*ap*ap*tp*tp*cp*gp*cp*G)- 3')
>>
>> #0, chain B: dna (5'-D(*cp*gp*cp*gp*ap*ap*tp*tp*cp*gp*cp*G)- 3')
>>
>> Opening VRML model in 127D - Nucleotides...
>> 127D opened
>> Opened VRML model in 127D - Nucleotides
>> Opened 127D containing 1 model, 639 atoms, and 146 residues
>> Fetching 127D from web site www.rcsb.org
>> 88 Kbytes received
>> 80 Kbytes received
>> Fetch 127D: finished
>> Done fetching 127D; verifying...
>> Opening 127D...
>> #1, chain A: dna (5'-D(*cp*gp*cp*gp*ap*ap*tp*tp*cp*gp*cp*G)- 3')
>>
>> #1, chain B: dna (5'-D(*cp*gp*cp*gp*ap*ap*tp*tp*cp*gp*cp*G)- 3')
>>
>> Opening VRML model in 127D - Nucleotides...
>> 127D opened
>> Opened VRML model in 127D - Nucleotides
>> Opened 127D containing 1 model, 639 atoms, and 146 residues
>> Opening ligand.pdb...
>> ligand.pdb opened
>> Opened ligand.pdb containing 1 model, 32 atoms, and 1 residues
>> Executing match ['#0:6', '#1:18'], no iteration
>>
>> RMSD between 21 atom pairs is 0.630 angstroms
>> Wrote flipped_ligand into /home/christos/Desktop
>>
>> *****************************
>>
>> Why do I get the error message when I attempt to run chimera through
>> script.py? Is this a python issue or a chimera issue? I appreciate any
>> thoughts on solving this problem....thank you,
>>
>> Christos Deligkaris, PhD
>> Assistant Professor of Physics, Drury University
>> 900 N Benton Ave, Springfield MO, 65802
>> Office Phone: (417) 873-7234
>> www2.drury.edu/christos <http://www2.drury.edu/christos/index.html>
>> @DeligkarisGroup <https://twitter.com/DeligkarisGroup>
>> +ChristosDeligkaris <http://google.com/+ChristosDeligkaris>
>>
>>
>>
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>>
>>
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