Re: [PyMOL] How to find RMSD values using fitting.py using Shell script

http://www.pymolwiki.org/index.php/Command_Line_Options see the -c and -r options. I also use -q pymol -qcr script.py — arg1 arg2 arg3 > On Jul 10, 2015, at 8:44 AM, Gazal wrote: > > Hi, > > I'm trying to find the RMSD values for bat

Re: [PyMOL] Problem with loadBfact.py on windows

This is the problem. Pymol’s working directory is not where you have this file. So, the script never loads. > On Jul 10, 2015, at 12:20 PM, ABEL Stephane 175950 > wrote: > > No such file or directory: './loadB2Fact.py'

Re: [PyMOL] How to find RMSD values using fitting.py using Shell script

Hi Gazal, Generally when I want to do batch operations using PyMOL I wrote a Python script and I call PyMOL from within that script. I prefer this way because I think is more flexible and simple than using PyMOL from the command line. In those cases I start the Python script with the following imp

[PyMOL] TR : Problem with loadBfact.py on windows - FIXED

De : ABEL Stephane 175950 Envoyé : vendredi 10 juillet 2015 18:39 À : pymol-users@lists.sourceforge.net Objet : Problem with loadBfact.py on windows (ABEL Stephane 175950 I have re installed the program and removed an old version of Pymol and now my script

[PyMOL] Problem with loadBfact.py on windows (ABEL Stephane 175950

I have reinstall the program and removed an old version of Pymol. Now the script works Thanks -- Message: 2 Date: Fri, 10 Jul 2015 12:44:40 + From: ABEL Stephane 175950 Subject: [PyMOL] Problem with loadBfact.py on windows To: "pymol-users@lists.sourceforge.net

[PyMOL] Problem with loadBfact.py on windows

>> Stéphane, >>It looks like a slash/backslash issue between windows and linux: >>C:\Program Files (x86)\PyMOL_v13\PyMOL/modules\pymol\parser.py Thanks Jed, How to change it, since I can not to modify it with text editor (it seems to be used by another pr

Re: [PyMOL] Optimize Geometry {rpblem

I Stephen I am confused, the problem is with Avogadro, or with the PyMOL's optimize plugin ? I tried to replicate the problem (with the plugin) and I get the correct answer (the chair conformation) Cheers, Osvaldo On Fri, Jul 10, 2015 at 11:04 AM, S

[PyMOL] Optimize Geometry {rpblem

I have a bit of a strange problem. I have evaluated a number of Linux distributions in a VMware Player environment on my 64 bit laptop. I compile PyMol using the attached protocol. The OS is BioLinux v-8.0.5 with Avogadro Version 1.1.1 Library V

[PyMOL] Problem with loadBfact.py on windows

Hi Pymol users I use Pymol v1.3 on Windows and I would like to use the loadBfacts.py (http://www.pymolwiki.org/index.php/Load_new_B-factors) (renamed, here, loadB2Fact.py) to change the B factor value according to other values stored in an external txt file. On my linux machine, I use the follo

[PyMOL] How to find RMSD values using fitting.py using Shell script

Hi, I'm trying to find the RMSD values for batch purposes. The command which I found works for the Pymol-command line. I was hoping if I could get an idea about using the python script fitting.py in my shell script without triggering the Pymol GUI. Thanks in advance. Gazal --