Package: pymol
Version: 1.7.2.1-1
Severity: normal
Hello,
I've been trying to make a small script that drives pymol completely
uninteractively using a pymol -c -p command.
Unfortunately, pymol is polling from stdin DURING the reading of
scripts from within a @ command, which leads to painful race
conditions, as I'm wrapping the call to scripts to a cd in/cd out
command.
For instance, I'm running
cd /home/vincent/Recherche/Proteines/CODH
@ CODH-clusters.pml
cd /home/vincent/tmp
The CODH-clusters.pml runs a series of pymol scripts by itself.
As you can see below, the cd /home/vincent/tmp comes between
select prot, ((all) and (not ((fes) or (nifes))))
and
select s, /////S3
Both of these commands are within the
"CODH-Chydrogenoformans-definitions.pml" script. This is really
painful, since one cannot assume that because one sends commands
sequentially, the previous one is finished before the next one starts.
============================================================
PyMOL>cd /home/vincent/Recherche/Proteines/CODH
cd: now in /home/vincent/Recherche/Proteines/CODH
PyMOL>@ CODH-clusters.pml
PyMOL>@ CODH-vue-generale.pml
PyMOL>@ CODH-Chydrogenoformans-definitions.pml
PyMOL>load ../PDB/1SU8.pdb.gz, Ch;
[...]
PyMOL>select prot, ((all) and (not ((fes) or (nifes))))
Selector: selection "prot" defined with 11466 atoms.
PyMOL>cd /home/vincent/tmp
PyMOL>select s, /////S3
============================================================
I'll try to see if this can be easily fixed...
Vincent
-- System Information:
Debian Release: jessie/sid
APT prefers unstable
APT policy: (500, 'unstable'), (500, 'stable'), (1, 'experimental')
Architecture: amd64 (x86_64)
Foreign Architectures: i386
Kernel: Linux 3.16.3+macbook (SMP w/8 CPU cores)
Locale: LANG=en_GB.utf8, LC_CTYPE=en_GB.utf8 (charmap=UTF-8)
Shell: /bin/sh linked to /bin/dash
Versions of packages pymol depends on:
ii freeglut3 2.8.1-2
ii libc6 2.19-11
ii libfreetype6 2.5.2-2
ii libgcc1 1:4.9.1-16
ii libgl1-mesa-glx [libgl1] 10.2.8-1
ii libglew1.10 1.10.0-3
ii libglu1-mesa [libglu1] 9.0.0-2
ii libpng12-0 1.2.50-2
ii libstdc++6 4.9.1-16
ii python 2.7.8-1
ii python-numpy [python-numpy-abi9] 1:1.8.2-2
ii python-pmw 1.3.2-6
ii python-tk 2.7.8-2
pn python2.7:any <none>
Versions of packages pymol recommends:
ii apbs 1.4-1
pymol suggests no packages.
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