Re: [PyMOL] pyMol executing python script: file path
Hi how do I determine the path of the script??? the answer is sys.argv[0] for more information see this page http://diveintopython.org/functional_programming/finding_the_path.html PS sorry for the mistake Jason Vertrees -- Yerko Ignacio Escalona Balboa Ingeniero en Biotecnología Molecular Universidad de Chile http://zeth.ciencias.uchile.cl/~yescalona/ -- Download Intel#174; Parallel Studio Eval Try the new software tools for yourself. Speed compiling, find bugs proactively, and fine-tune applications for parallel performance. See why Intel Parallel Studio got high marks during beta. http://p.sf.net/sfu/intel-sw-dev ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] pyMol executing python script: file path
I think you'll be saddened to discover that if you try what Petr (the original poster) was doing, sys.argv[0] won't work. $ cat test.py print sys.argv[0] $ pymol -qrc test.py PyMOLrun test.py,main /sw/lib/pymol-py26/modules/pymol/__init__.py This quite clearly gives the behavior that Petr had issues with. Instead, this is what is needed is a secret variable called pymol.__script__ e.g.: import pymol print pymol.__script__ which can be parsed to give the directory component and such. For example, to get the directory name reliably: import pymol from os import path print path.dirname(path.abspath(pymol.__script__)) I don't have the ability to test this on Windows, but it works on both Mac and Linux. -David On Thu, Apr 15, 2010 at 1:43 AM, Yerko Escalona yescal...@ug.uchile.cl wrote: Hi how do I determine the path of the script??? the answer is sys.argv[0] for more information see this page http://diveintopython.org/functional_programming/finding_the_path.html PS sorry for the mistake Jason Vertrees -- Yerko Ignacio Escalona Balboa Ingeniero en Biotecnología Molecular Universidad de Chile http://zeth.ciencias.uchile.cl/~yescalona/ -- Download Intel#174; Parallel Studio Eval Try the new software tools for yourself. Speed compiling, find bugs proactively, and fine-tune applications for parallel performance. See why Intel Parallel Studio got high marks during beta. http://p.sf.net/sfu/intel-sw-dev ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- Download Intel#174; Parallel Studio Eval Try the new software tools for yourself. Speed compiling, find bugs proactively, and fine-tune applications for parallel performance. See why Intel Parallel Studio got high marks during beta. http://p.sf.net/sfu/intel-sw-dev ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] feature request: supercell construction
Hi Nick, I noticed a few things: - when I run supercell 2, 1, 1 I get another cell outline along the a axis, but no atoms are shown in the second cell. Do I have to run another command for them to show up? the script does not create symmetry mates. The symexp command can create symmetry mates within a given radius (it will not just fill up the cell). - when I run the command again with other values for a, b, or c, nothing changes. I would expect that running the sequence supercell 2, 1, 1 and then supercell 2, 2, 1 would show me a 2x2x1 supercell at the end, but I see only the 2x1x1 supercell. the second call will create a new state for the same object. This is not convenient, so I changed it to replace the first state again. I put the modified script to the PyMOLWiki: http://www.pymolwiki.org/index.php/Supercell Cheers, Thomas -- Download Intel#174; Parallel Studio Eval Try the new software tools for yourself. Speed compiling, find bugs proactively, and fine-tune applications for parallel performance. See why Intel Parallel Studio got high marks during beta. http://p.sf.net/sfu/intel-sw-dev ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] pyMol executing python script: file path
Dear Mr. Hall, thank you very much for your help. This really works (I have tested it now on windows). Regards, Petr Benes 2010/4/15 David Hall li...@cowsandmilk.net: I think you'll be saddened to discover that if you try what Petr (the original poster) was doing, sys.argv[0] won't work. $ cat test.py print sys.argv[0] $ pymol -qrc test.py PyMOLrun test.py,main /sw/lib/pymol-py26/modules/pymol/__init__.py This quite clearly gives the behavior that Petr had issues with. Instead, this is what is needed is a secret variable called pymol.__script__ e.g.: import pymol print pymol.__script__ which can be parsed to give the directory component and such. For example, to get the directory name reliably: import pymol from os import path print path.dirname(path.abspath(pymol.__script__)) I don't have the ability to test this on Windows, but it works on both Mac and Linux. -David On Thu, Apr 15, 2010 at 1:43 AM, Yerko Escalona yescal...@ug.uchile.cl wrote: Hi how do I determine the path of the script??? the answer is sys.argv[0] for more information see this page http://diveintopython.org/functional_programming/finding_the_path.html PS sorry for the mistake Jason Vertrees -- Yerko Ignacio Escalona Balboa Ingeniero en Biotecnología Molecular Universidad de Chile http://zeth.ciencias.uchile.cl/~yescalona/ -- Download Intel#174; Parallel Studio Eval Try the new software tools for yourself. Speed compiling, find bugs proactively, and fine-tune applications for parallel performance. See why Intel Parallel Studio got high marks during beta. http://p.sf.net/sfu/intel-sw-dev ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- Download Intel#174; Parallel Studio Eval Try the new software tools for yourself. Speed compiling, find bugs proactively, and fine-tune applications for parallel performance. See why Intel Parallel Studio got high marks during beta. http://p.sf.net/sfu/intel-sw-dev ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
[PyMOL] Pymol and APBS
Hi all, I've been trying to get APBS Tools and/or APBSTools2 running for a few weeks now on multiple linux systems (RedHat and Fedora). I've Installed MALOC and APBS Tools. I can start up Pymol through Phenix, load a .pqr generated from a PDB2PQR server, start APBS Tools, set the grid, but when I click on Run APBS I get: ObjectMapLoadDXFile-Error: Unable to open file! If I use the pymol generated PQR option with my .pqr even though it is a PDB2PQR server generated file APBS runs and states X atoms did not have properties assigned and to either remove or fix the atoms. How can I fix them? The problem residues are just regular amino acids; no split confrimations etc. I've also tried editing out the PDBs chain name before converting to the PDB to PQR but that didn't work. Another things I've tried is using APBSTools 2 but it errors as soon as I click set grid with: Error: 2 ... Attribute Error: elec_radius. I really need to get this to work but I have no clue what to try next. Thanks in advance for any thoughts. -Jon -- Download Intel#174; Parallel Studio Eval Try the new software tools for yourself. Speed compiling, find bugs proactively, and fine-tune applications for parallel performance. See why Intel Parallel Studio got high marks during beta. http://p.sf.net/sfu/intel-sw-dev ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] Pymol and APBS
Hi Jon, Perhaps you could look at VASCo http://genome.tugraz.at/VASCo/ I have found it to work extremely well on Windows and Linux platforms. You not only get electrostatics but also hydrophobic surface coloring, and all without the APBS and Python hassles and headaches. Sorry to be knocking down APBS+PyMOL integration like this, but IMHO VASCo does a stellar job as far as integrating outside programs with PyMOL goes. Good luck! Best, Shiven On Thu, Apr 15, 2010 at 12:01 AM, J. Fleming moloch...@gmail.com wrote: Hi all, I've been trying to get APBS Tools and/or APBSTools2 running for a few weeks now on multiple linux systems (RedHat and Fedora). I've Installed MALOC and APBS Tools. I can start up Pymol through Phenix, load a .pqr generated from a PDB2PQR server, start APBS Tools, set the grid, but when I click on Run APBS I get: ObjectMapLoadDXFile-Error: Unable to open file! If I use the pymol generated PQR option with my .pqr even though it is a PDB2PQR server generated file APBS runs and states X atoms did not have properties assigned and to either remove or fix the atoms. How can I fix them? The problem residues are just regular amino acids; no split confrimations etc. I've also tried editing out the PDBs chain name before converting to the PDB to PQR but that didn't work. Another things I've tried is using APBSTools 2 but it errors as soon as I click set grid with: Error: 2 ... Attribute Error: elec_radius. I really need to get this to work but I have no clue what to try next. Thanks in advance for any thoughts. -Jon -- Download Intel#174; Parallel Studio Eval Try the new software tools for yourself. Speed compiling, find bugs proactively, and fine-tune applications for parallel performance. See why Intel Parallel Studio got high marks during beta. http://p.sf.net/sfu/intel-sw-dev ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- Download Intel#174; Parallel Studio Eval Try the new software tools for yourself. Speed compiling, find bugs proactively, and fine-tune applications for parallel performance. See why Intel Parallel Studio got high marks during beta. http://p.sf.net/sfu/intel-sw-dev___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
[PyMOL] psw full screen , on screen menu and see typed commands in full screen mode
Hi I can get the animations launched from inside powerpoint to show up and go between my stored scenes. Is there some way to toggle on the internal_gui display from this full screen mode. I know the command set internal_gui,1 But when I type it on the full screen molecule, nothing happens. Other commands typed without seeing what I am typing - do the right thing Also is there some way to see typed commands in the full screen mode . Thanks Hari -- Download Intel#174; Parallel Studio Eval Try the new software tools for yourself. Speed compiling, find bugs proactively, and fine-tune applications for parallel performance. See why Intel Parallel Studio got high marks during beta. http://p.sf.net/sfu/intel-sw-dev ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
[PyMOL] how to install pymol in Mac?
Dear pymol users, I had to install pymol on my Macbook. I downloaded the files from SouceForge.net. When I typed as following I got error messages: python setup.py build install running build running build_py running build_ext building 'pymol._cmd' extension gcc -fno-strict-aliasing -Wno-long-double -no-cpp-precomp -mno-fused-madd -fno-common -dynamic -DNDEBUG -g -Os -Wall -Wstrict-prototypes -DMACOSX -I/usr/include/ffi -DENABLE_DTRACE -arch i386 -arch ppc -pipe -D_PYMOL_MODULE -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -I/usr/X11R6/include -I/Users/youngjin25/Downloads/trunk/pymol/ext/include -I/Users/youngjin25/Downloads/trunk/pymol/ext/include/GL -I/Users/youngjin25/Downloads/trunk/pymol/ext/include/freetype2 -Imodules/cealign/src -Imodules/cealign/src/tnt -I/System/Library/Frameworks/Python.framework/Versions/2.5/include/python2.5 -c modules/cealign/src/ccealignmodule.cpp -o build/temp.macosx-10.5-i386-2.5/modules/cealign/src/ccealignmodule.o unable to execute gcc: No such file or directory error: command 'gcc' failed with exit status 1 Could you tell me how I can handle this problem? Thanks in advance, Young-Jin -- Download Intel#174; Parallel Studio Eval Try the new software tools for yourself. Speed compiling, find bugs proactively, and fine-tune applications for parallel performance. See why Intel Parallel Studio got high marks during beta. http://p.sf.net/sfu/intel-sw-dev ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] Pymol and APBS
Hi, Which version of PyMOL, APBS and PDB2PQR are you using? If you send me a PQR file off-list, I can take a closer look at what's going on. Thanks, -Michael On Thu, Apr 15, 2010 at 12:01 AM, J. Fleming moloch...@gmail.com wrote: Hi all, I've been trying to get APBS Tools and/or APBSTools2 running for a few weeks now on multiple linux systems (RedHat and Fedora). I've Installed MALOC and APBS Tools. I can start up Pymol through Phenix, load a .pqr generated from a PDB2PQR server, start APBS Tools, set the grid, but when I click on Run APBS I get: ObjectMapLoadDXFile-Error: Unable to open file! If I use the pymol generated PQR option with my .pqr even though it is a PDB2PQR server generated file APBS runs and states X atoms did not have properties assigned and to either remove or fix the atoms. How can I fix them? The problem residues are just regular amino acids; no split confrimations etc. I've also tried editing out the PDBs chain name before converting to the PDB to PQR but that didn't work. Another things I've tried is using APBSTools 2 but it errors as soon as I click set grid with: Error: 2 ... Attribute Error: elec_radius. I really need to get this to work but I have no clue what to try next. Thanks in advance for any thoughts. -Jon -- Download Intel#174; Parallel Studio Eval Try the new software tools for yourself. Speed compiling, find bugs proactively, and fine-tune applications for parallel performance. See why Intel Parallel Studio got high marks during beta. http://p.sf.net/sfu/intel-sw-dev ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- Michael Lerner, Ph.D. IRTA Postdoctoral Fellow Laboratory of Computational Biology NIH/NHLBI 5635 Fishers Lane, Room T909, MSC 9314 Rockville, MD 20852 (UPS/FedEx/Reality) Bethesda MD 20892-9314 (USPS) -- Download Intel#174; Parallel Studio Eval Try the new software tools for yourself. Speed compiling, find bugs proactively, and fine-tune applications for parallel performance. See why Intel Parallel Studio got high marks during beta. http://p.sf.net/sfu/intel-sw-dev___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] Pymol and APBS
On Thu, Apr 15, 2010 at 10:30 AM, Shiven Shandilya shiven.shandi...@gmail.com wrote: Sorry to be knocking down APBS+PyMOL integration like this, but IMHO VASCo does a stellar job as far as integrating outside programs with PyMOL goes. I initially wrote the PyMOL/APBS plugin for my own use and I now maintain/develop it as a community resource in my limited free time. Despite this, several hundred users (at least) have found it quite helpful in their research, and I've included many newer features based on their feedback. The plugin is certainly not perfect, and I don't mind people knocking it down, but I appreciate it when that knocking down comes with constructive feedback. Additionally, unlike VASCo, the PyMOL/APBS/PDB2PQR toolchain is provided as completely free and open source suite of programs. For many reasons, I believe that free and open source software is vital to to good science. I would strongly urge users to consider such issues before settling on a suite of software products, especially when you're already working with programs like PyMOL and APBS. Cheers, -Michael Good luck! Best, Shiven On Thu, Apr 15, 2010 at 12:01 AM, J. Fleming moloch...@gmail.com wrote: Hi all, I've been trying to get APBS Tools and/or APBSTools2 running for a few weeks now on multiple linux systems (RedHat and Fedora). I've Installed MALOC and APBS Tools. I can start up Pymol through Phenix, load a .pqr generated from a PDB2PQR server, start APBS Tools, set the grid, but when I click on Run APBS I get: ObjectMapLoadDXFile-Error: Unable to open file! If I use the pymol generated PQR option with my .pqr even though it is a PDB2PQR server generated file APBS runs and states X atoms did not have properties assigned and to either remove or fix the atoms. How can I fix them? The problem residues are just regular amino acids; no split confrimations etc. I've also tried editing out the PDBs chain name before converting to the PDB to PQR but that didn't work. Another things I've tried is using APBSTools 2 but it errors as soon as I click set grid with: Error: 2 ... Attribute Error: elec_radius. I really need to get this to work but I have no clue what to try next. Thanks in advance for any thoughts. -Jon -- Download Intel#174; Parallel Studio Eval Try the new software tools for yourself. Speed compiling, find bugs proactively, and fine-tune applications for parallel performance. See why Intel Parallel Studio got high marks during beta. http://p.sf.net/sfu/intel-sw-dev ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- Download Intel#174; Parallel Studio Eval Try the new software tools for yourself. Speed compiling, find bugs proactively, and fine-tune applications for parallel performance. See why Intel Parallel Studio got high marks during beta. http://p.sf.net/sfu/intel-sw-dev ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- Michael Lerner, Ph.D. IRTA Postdoctoral Fellow Laboratory of Computational Biology NIH/NHLBI 5635 Fishers Lane, Room T909, MSC 9314 Rockville, MD 20852 (UPS/FedEx/Reality) Bethesda MD 20892-9314 (USPS) -- Download Intel#174; Parallel Studio Eval Try the new software tools for yourself. Speed compiling, find bugs proactively, and fine-tune applications for parallel performance. See why Intel Parallel Studio got high marks during beta. http://p.sf.net/sfu/intel-sw-dev___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] pymol and freemol
Hi David, I downloaded apbs and pdb2pqr, but I don't know how to install them on my ubuntu 9.04. Is it possible to make an easy to install release? For now, could you please send me the instruction. Maia David Hall wrote: In my incentive build, freemol is present with the following readme: This is a binary distribution of the FreeMOL Open-Source Compilation. The FreeMOL project home page can be found at: http://bioinformatics.org/freemol Complete source code for building FreeMOL and its various components can be browsed via: http://www.bioinformatics.org/websvn/listing.php?repname=freemol and fetched via: svn co svn://bioinformatics.org/svnroot/freemol/trunk Licensing information can be found in LICENSE.txt If you have any questions about FreeMOL, please contact: Warren L. DeLano, Ph.D. DeLano Scientific LLC war...@delsci.com Thank You! I don't have any instructions how to incorporate this into building from pymol trunk necessarily though. In the incentive builds, the freemol folder is not inside ext or modules or anything, but instead is a top level directory like those. You will have to build the sources of the things that come with it (apbs, mengine, mpeg_encode, pdb2pqr). I think pymol autodetects the presence of freemol based on this grep output on the pymol source. modules/pymol/__init__.py:# auto-detect bundled FREEMOL (if present) modules/pymol/__init__.py:if not os.environ.has_key(FREEMOL): modules/pymol/__init__.py:test_path = os.path.join(os.environ['PYMOL_PATH'],freemol) modules/pymol/__init__.py:os.environ['FREEMOL'] = test_path modules/pymol/__init__.py:# include FREEMOL's libpy in sys.path (if present) modules/pymol/__init__.py:if os.environ.has_key(FREEMOL): modules/pymol/__init__.py:freemol_libpy = os.path.join(os.environ['FREEMOL'],libpy) modules/pymol/__init__.py:if os.path.isdir(freemol_libpy): modules/pymol/__init__.py:if freemol_libpy not in sys.path: modules/pymol/__init__.py:sys.path.append(freemol_libpy) Hopefully this all helps. -David - Original Message From: Maia Cherney ch...@ualberta.ca To: Jason Vertrees jason.vertr...@schrodinger.com Cc: pymol-users@lists.sourceforge.net Sent: Wed, January 20, 2010 9:37:46 PM Subject: Re: [PyMOL] new ideas Thanks, But I could not find the download site for FreeMol. Could somebody send me a link to FreeMol? Maia Jason Vertrees wrote: Maia, You can already move structures independently. If you install PyMOL+FreeMOL you can have access to the MMFF-enabled PyMOL that will allow you to do small molecule cleanup and editing. Try putting your mouse into Editing Mode and moving atoms around. It's not hard. Check this out: http://pymolwiki.org/index.php/Molecular_Sculpting for some help. Regards, -- Jason On Wed, Jan 20, 2010 at 11:52 AM, Maia Cherney wrote: Hi Jason I need such features. I open two different pdbs and I want to manually move one structure relative to another. I want to dock one structure into another or superpose 2 structures manually. Is it possible? Or I want to move a fragment of the molecule relative to the rest of the molecule. Is it possible? Maia -- Throughout its 18-year history, RSA Conference consistently attracts the world's best and brightest in the field, creating opportunities for Conference attendees to learn about information security's most important issues through interactions with peers, luminaries and emerging and established companies. http://p.sf.net/sfu/rsaconf-dev2dev ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- Download Intel#174; Parallel Studio Eval Try the new software tools for yourself. Speed compiling, find bugs proactively, and fine-tune applications for parallel performance. See why Intel Parallel Studio got high marks during beta. http://p.sf.net/sfu/intel-sw-dev ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] pymol and freemol
On Thu, Apr 15, 2010 at 11:53:06AM -0600, Maia Cherney wrote: I downloaded apbs and pdb2pqr, but I don't know how to install them on my ubuntu 9.04. Is it possible to make an easy to install release? For now, could you please send me the instruction. apbs is available in Ubuntu (via Debian) since at least hardy. We tried to get pdb2pqr into Debian (and thus, Ubuntu), but it was rejected due to unclear licensing/copyright status and other issues. We will hopefully try again, but it will obviously be too late for lucid. Michael -- Download Intel#174; Parallel Studio Eval Try the new software tools for yourself. Speed compiling, find bugs proactively, and fine-tune applications for parallel performance. See why Intel Parallel Studio got high marks during beta. http://p.sf.net/sfu/intel-sw-dev ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] Pymol and APBS
Dear Michael, First, let me thank you for your time and effort in providing the community with your contributions. I do sincerely appreciate your hard work and your willingness to share it with us all. Without the contributions of users such as yourself, PyMOL's stature and utility would be far less than what it is now. I have used the APBS plugin in the past, successfully and without problems. And yes, it has been helpful in solving the problem(s) at hand. As for the knocking down, it was more of a comparison with VASCo than a direct criticism of your work. I am no expert at programming PyMOL/python plugins but I have used quite a few over the years. All I speak is from my own user experience when I say that some plugins work better than others. VASCo, in my experience, happens to belong to the better category. Now why the better plugins work the way do may depend on many factors but some that I feel important are listed below (nothing specifically for/against the APBS plugin). I only speculate when I write the following, but in hopes that it may be considered constructive feedback: (1). Whenever possible, farm out the heavy lifting to external executables (apbs, python scripts, black magic shamans etc.)... (2). Clearly ask for all the defaults a user must specify at first run (executable location, temporary directory, other knick-knacks your plugin requires) Do not allow execution to begin unless you are reasonably sure you have everything needed to properly finish the job. (3). And, for heaven's sake, save those user-specified defaults for the rest of posterity in a location (pymolrc, yourpluginrc) that your plugin can always find... never, ever make a user specify such mundane things over and over again... nothing kills the user experience quicker than that. (4). Overwrite result files only if you have to... create a new directory for every new run (and clearly display the location)... Remember, (storage) space is cheap and (a user's) time is expensive, respect that. (5). If possible, give the users a clear indication of the status of the back-end job doing the heavy lifting... (6). Once you are done running the back-end job(s), prompt the user immediately and (if agreed) automatically load the results. (7). If your back-end job fails, parse the error in your plugin and inform the user where in the entire process the error occurred, why it may have occurred and what the user should do to prevent this error from occurring again. If it is an error your plugin does not understand let the user know, clearly and loudly. If an error log file, hopefully text, was written, specify its location (full path) in your error prompts. Prefrably, display that error file in the system %editor% so that the user does not have to go hunting for it. ...and I'll leave it at that... ;-) I welcome your feedback and views of other community members on this. Thank you! With best regards, Shiven P.S. Apologies again if my criticism hit a personal note. Like everyone else writing to the list and answering questions, my aim was to help a fellow user get that job done. --- On Thu, Apr 15, 2010 at 12:00 PM, Michael Lerner mgler...@gmail.com wrote: On Thu, Apr 15, 2010 at 10:30 AM, Shiven Shandilya shiven.shandi...@gmail.com wrote: Sorry to be knocking down APBS+PyMOL integration like this, but IMHO VASCo does a stellar job as far as integrating outside programs with PyMOL goes. I initially wrote the PyMOL/APBS plugin for my own use and I now maintain/develop it as a community resource in my limited free time. Despite this, several hundred users (at least) have found it quite helpful in their research, and I've included many newer features based on their feedback. The plugin is certainly not perfect, and I don't mind people knocking it down, but I appreciate it when that knocking down comes with constructive feedback. Additionally, unlike VASCo, the PyMOL/APBS/PDB2PQR toolchain is provided as completely free and open source suite of programs. For many reasons, I believe that free and open source software is vital to to good science. I would strongly urge users to consider such issues before settling on a suite of software products, especially when you're already working with programs like PyMOL and APBS. Cheers, -Michael Good luck! Best, Shiven On Thu, Apr 15, 2010 at 12:01 AM, J. Fleming moloch...@gmail.com wrote: Hi all, I've been trying to get APBS Tools and/or APBSTools2 running for a few weeks now on multiple linux systems (RedHat and Fedora). I've Installed MALOC and APBS Tools. I can start up Pymol through Phenix, load a .pqr generated from a PDB2PQR server, start APBS Tools, set the grid, but when I click on Run APBS I get: ObjectMapLoadDXFile-Error: Unable to open file! If I use the pymol generated PQR option with my .pqr even though it is a PDB2PQR server generated file APBS runs and states X atoms did not have properties
Re: [PyMOL] how to install pymol in Mac?
The error below shows that you don't have gcc, which means you have to install Apple's Developer tools to compile pymol. That said, the easiest way right now is probably using macports. Follow the instructions at http://www.macports.org/install.php for installing macports, then you can run port install pymol and you should be good to go. -David On Thu, Apr 15, 2010 at 10:54 AM, Young-Jin Cho youngji...@gmail.com wrote: Dear pymol users, I had to install pymol on my Macbook. I downloaded the files from SouceForge.net. When I typed as following I got error messages: python setup.py build install running build running build_py running build_ext building 'pymol._cmd' extension gcc -fno-strict-aliasing -Wno-long-double -no-cpp-precomp -mno-fused-madd -fno-common -dynamic -DNDEBUG -g -Os -Wall -Wstrict-prototypes -DMACOSX -I/usr/include/ffi -DENABLE_DTRACE -arch i386 -arch ppc -pipe -D_PYMOL_MODULE -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -I/usr/X11R6/include -I/Users/youngjin25/Downloads/trunk/pymol/ext/include -I/Users/youngjin25/Downloads/trunk/pymol/ext/include/GL -I/Users/youngjin25/Downloads/trunk/pymol/ext/include/freetype2 -Imodules/cealign/src -Imodules/cealign/src/tnt -I/System/Library/Frameworks/Python.framework/Versions/2.5/include/python2.5 -c modules/cealign/src/ccealignmodule.cpp -o build/temp.macosx-10.5-i386-2.5/modules/cealign/src/ccealignmodule.o unable to execute gcc: No such file or directory error: command 'gcc' failed with exit status 1 Could you tell me how I can handle this problem? Thanks in advance, Young-Jin -- Download Intel#174; Parallel Studio Eval Try the new software tools for yourself. Speed compiling, find bugs proactively, and fine-tune applications for parallel performance. See why Intel Parallel Studio got high marks during beta. http://p.sf.net/sfu/intel-sw-dev ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- Download Intel#174; Parallel Studio Eval Try the new software tools for yourself. Speed compiling, find bugs proactively, and fine-tune applications for parallel performance. See why Intel Parallel Studio got high marks during beta. http://p.sf.net/sfu/intel-sw-dev ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
[PyMOL] Fwd: feature request: supercell construction
forgot to also send to the list. -- Forwarded message -- From: Nicolas Bock nicolasb...@gmail.com Date: Thu, Apr 15, 2010 at 15:46 Subject: Re: [PyMOL] feature request: supercell construction To: Thomas Holder spel...@users.sourceforge.net Hi Thomas, On Thu, Apr 15, 2010 at 03:42, Thomas Holder spel...@users.sourceforge.netwrote: Hi Nick, I noticed a few things: - when I run supercell 2, 1, 1 I get another cell outline along the a axis, but no atoms are shown in the second cell. Do I have to run another command for them to show up? the script does not create symmetry mates. The symexp command can create symmetry mates within a given radius (it will not just fill up the cell). Maybe I just don't understand the symexp command, but how would it help me in constructing a 2x2x2 supercell from a unit cell with atom positions? Isn't the radius meaningless in this context since it implies a radial cutoff, whereas a simple cubic unit cell has a cubic cutoff? When I look at a crystal I would want the supercell construction to get a better idea of how the bulk crystal looks like. With small unit cells this is sometimes tricky without explicitly constructing a supercell. Also, in the case of a triclinic unit cell, for example, finding the correct symmetry operation for the symexp command might be rather tricky. - when I run the command again with other values for a, b, or c, nothing changes. I would expect that running the sequence supercell 2, 1, 1 and then supercell 2, 2, 1 would show me a 2x2x1 supercell at the end, but I see only the 2x1x1 supercell. the second call will create a new state for the same object. This is not convenient, so I changed it to replace the first state again. I put the modified script to the PyMOLWiki: http://www.pymolwiki.org/index.php/Supercell Thanks! Cheers, Thomas -- Download Intel#174; Parallel Studio Eval Try the new software tools for yourself. Speed compiling, find bugs proactively, and fine-tune applications for parallel performance. See why Intel Parallel Studio got high marks during beta. http://p.sf.net/sfu/intel-sw-dev___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
[PyMOL] Symmetry Expansion
PyMOLers, A bug was brought to my attention to day in the symmetry expansion command (try it on 2bop). If you have issues with the symexp command in your work, please check out the hastily-written and really-slow, but correct (for my test cases), manual symmetry expansion script: http://pymolwiki.org/index.php/ManualSymExp. I am working on a fix. Last, PyMOLers wrote three other cool scripts and deposited them on the wiki this week--check those out, too. Cheers, -- Jason -- Jason Vertrees, PhD PyMOL Product Manager Schrodinger, LLC (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- Download Intel#174; Parallel Studio Eval Try the new software tools for yourself. Speed compiling, find bugs proactively, and fine-tune applications for parallel performance. See why Intel Parallel Studio got high marks during beta. http://p.sf.net/sfu/intel-sw-dev ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
