From: Cartailler, Jean-P. <jp.cartailler@Vanderbilt.Edu> - 2003-10-08 15:46:13
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What has happened to alpha channel support in PNG output? I could have sworn it used to be there. I'm now working in version 0.9. thanks Jean-Philippe Cartailler -------------------------------------------- Vanderbilt University Medical Center S-3223 Medical Center North 1161 21st Avenue South Nashville, TN 37232-2372 Phone: 615.322.7729 FAX: 615.343.7156 email: jp....@va... www: http://www.cartailler.com -------------------------------------------- |
From: Warren L. D. <wa...@de...> - 2003-10-08 16:37:49
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Jean, Did you set ray_opaque_background, 0 ? Warren -- mailto:wa...@de... Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020 > -----Original Message----- > From: pym...@li... [mailto:pymol-users- > ad...@li...] On Behalf Of Cartailler, Jean-Philippe > Sent: Wednesday, October 08, 2003 7:46 AM > To: pym...@li... > Subject: [PyMOL] Alpha channel support gone? > > What has happened to alpha channel support in PNG output? I could have > sworn it used to be there. I'm now working in version 0.9. > > thanks > > Jean-Philippe Cartailler > > -------------------------------------------- > Vanderbilt University Medical Center > S-3223 Medical Center North > 1161 21st Avenue South > Nashville, TN 37232-2372 > > Phone: 615.322.7729 > FAX: 615.343.7156 > email: jp....@va... > www: http://www.cartailler.com > -------------------------------------------- > > > ------------------------------------------------------- > This SF.net email is sponsored by: SF.net Giveback Program. > SourceForge.net hosts over 70,000 Open Source Projects. > See the people who have HELPED US provide better services: > Click here: http://sourceforge.net/supporters.php > _______________________________________________ > PyMOL-users mailing list > PyM...@li... > https://lists.sourceforge.net/lists/listinfo/pymol-users |
From: Shu-Hsien S. <sheu@BU.EDU> - 2003-10-08 17:59:58
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Hi, This should be a trial question though I cannot find a way of doing it. I have a simple script that looks like this: (the original commands, rather than cmd.select......) select ligand, resn XYZ select protein, ! ligand select box, protein within 8 of ligand select box, box or byres box save box as box.pdb I don't need the viewer at all and would be even more efficient if I can call the PyMol API from the shell. Or, in a python script. For example, I would like to have something like: ./pymol select_box.py thanks! |
From: Warren L. D. <wa...@de...> - 2003-10-08 18:12:11
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Shu-hsien Sure, instead of cmd.select, use cmd.do("select ligand, resn XYZ") cmd.do("select protein, ! ligand ") etc. ./pymol -qc select_box.py Is the command line mode of PyMOL. "pymol -qc" can be used like "python" in most cases. Cheers, Warren -- mailto:wa...@de... Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020 > -----Original Message----- > From: pym...@li... [mailto:pymol-users- > ad...@li...] On Behalf Of Shu-Hsien Sheu > Sent: Saturday, November 08, 2003 10:58 AM > To: pym...@li... > Subject: [PyMOL] Accessing PyMol's commands from outside (or without > viewer) > > Hi, > > This should be a trial question though I cannot find a way of doing it. > I have a simple script that looks like this: > (the original commands, rather than cmd.select......) > select ligand, resn XYZ > select protein, ! ligand > select box, protein within 8 of ligand > select box, box or byres box > save box as box.pdb > > I don't need the viewer at all and would be even more efficient if I can > call the PyMol API from the shell. Or, in a python script. > For example, I would like to have something like: > ./pymol select_box.py > > thanks! > > > > ------------------------------------------------------- > This SF.net email is sponsored by: SF.net Giveback Program. > SourceForge.net hosts over 70,000 Open Source Projects. > See the people who have HELPED US provide better services: > Click here: http://sourceforge.net/supporters.php > _______________________________________________ > PyMOL-users mailing list > PyM...@li... > https://lists.sourceforge.net/lists/listinfo/pymol-users |
From: Shu-Hsien S. <sh...@bu...> - 2003-10-08 21:06:11
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Dear Dr.DeLano, Thanks! That really helps! Two more questions: Does the 'pymol -qc' takes command line variables (os.argv in python)? For example, the first line of my script would be: cmd.do('load %s' %os.argv[1]) Second question might be off a little bit. Is it possible to wrap PyMol as a module of Python? I know can be installed as a Python module, but that doesn't seem to be able to let me do things like: # Sample Python script import PyMol PyMol.cmd.do('......') distance = PyMol.cmd.do('distance ......') Does it make any difference whether or not I installed PyMol independant of Python? I am a bit confused with cmd.do vs cmd.select. So, if I am writing a script for running in PyMol(using @some_script.py), I should use: import PyMol cmd.select('...') If I am writing a script for running PyMol in command line, I should use: from PyMol import cmd cmd.do('...') Kind of confused... -shuhsien >Shu-hsien > >Sure, instead of cmd.select, use > >cmd.do("select ligand, resn XYZ") >cmd.do("select protein, ! ligand ") > >etc. > >./pymol -qc select_box.py > >Is the command line mode of PyMOL. "pymol -qc" can be used like >"python" in most cases. > >Cheers, >Warren > > |
From: Warren L. D. <wa...@de...> - 2003-10-09 01:56:42
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> Two more questions: > Does the 'pymol -qc' takes command line variables (os.argv in python)? > For example, the first line of my script would be: > cmd.do('load %s' %os.argv[1]) That's not possible. In order to get this behavior (for now) you need to treat PyMOL as a module (see below). > Second question might be off a little bit. > Is it possible to wrap PyMol as a module of Python? Yes, but to do this (in most cases), you'll have to recompile and install PyMOL as a standard "distutils" module. If you're not familiar with compilation, then this isn't for you... python setup.py build install python setup2.py install Then from python import pymol pymol.finish_launching() can work > I know can be > installed as a Python module, but that doesn't seem to be able to let me > do things like: > > # Sample Python script > import PyMol > PyMol.cmd.do('......') > distance = PyMol.cmd.do('distance ......') Close. from pymol import cmd distance = cmd.distance('tmp',sele1,sele2) > Does it make any difference whether or not I installed PyMol independant > of Python? > I am a bit confused with cmd.do vs cmd.select. cmd.do places string command to the PYMOL parser input queue and returns nothing. cmd.functionName calls the PyMOL API and returns the result (if any). > So, if I am writing a script for running in PyMol(using @some_script.py), > I should use: > import PyMol > cmd.select('...') > > If I am writing a script for running PyMol in command line, > I should use: > from PyMol import cmd > cmd.do('...') The only time you'd use cmd.do is for convenience... cmd.do("select cas, name ca") will always be substantially slower than cmd.select("cas","name ca") because an extra parsing step in involved. Cheers, Warren > Kind of confused... > > -shuhsien > > >Shu-hsien > > > >Sure, instead of cmd.select, use > > > >cmd.do("select ligand, resn XYZ") > >cmd.do("select protein, ! ligand ") > > > >etc. > > > >./pymol -qc select_box.py > > > >Is the command line mode of PyMOL. "pymol -qc" can be used like > >"python" in most cases. > > > >Cheers, > >Warren > > > > > > > > ------------------------------------------------------- > This SF.net email is sponsored by: SF.net Giveback Program. > SourceForge.net hosts over 70,000 Open Source Projects. > See the people who have HELPED US provide better services: > Click here: http://sourceforge.net/supporters.php > _______________________________________________ > PyMOL-users mailing list > PyM...@li... > https://lists.sourceforge.net/lists/listinfo/pymol-users |