Re: [PyMOL] Conformation Editing
Yu, The conformational editing features are not fully designed nor well tested, and the documentation is still incomplete. Until the PyMOL user interface is a bit more stabilized, documentation seems premature. I am resistant to the idea of committing to a user interface which hasn't really been evaluated or optimized for usability. However it is quite frustrating for all of us knowing that there is considerable power under the hood which can't yet be accessed by users : ( . However, you should at least be able to do a few basic things, such as manually adjusting bond torsions: 1. put the mouse into editing mode (Mouse menu) 2. ctrl-right click on a bond 3. ctrl-left click and drag atoms on either side of the bond. Other mouse combinations allow you to move fragments in different ways...just play around with the different combinations on the mouse "matrix". Sculpting is a bit less obvious: PyMOL will take a snapshot of bond lenths, angles, and stereochemistry inside a molecule the first time sculpting is activated on an object. From then on, no matter what you do, PyMOL will labor to maintain those constraints while you drag atoms around or make other conformational changes. The Sculpting Wizard can help you out in getting started with this feature. However, the bottom line is that more work needs to be done on these aspects of PyMOL, and that's why increasing funding for PyMOL is essential. Until I can afford to start paying people to help me with development and documentation, progress will cotinue to be slow. So in closing, I wouldn't look to PyMOL as a workhorse conformational editing tool just yet -- give it another year or so. Cheers, Warren On Thu, 26 Sep 2002, Yu Shao wrote: > Hello everyone, > > Does anyone know how to use the conformation editing of PyMol, or has it > been implemented? It's unclear from the menual, which just said that > "Sorry, no documentation yet -- these features won't be too useful until > PyMOL is coupled up with an energy minimiation engine." Any infomation > will be highly appreciated. > > Best wishes, > Yu Shao > R.P.I. > > > > > --- > This sf.net email is sponsored by:ThinkGeek > Welcome to geek heaven. > http://thinkgeek.com/sf > ___ > PyMOL-users mailing list > PyMOL-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/pymol-users >
[PyMOL] Conformation Editing
Hello everyone, Does anyone know how to use the conformation editing of PyMol, or has it been implemented? It's unclear from the menual, which just said that "Sorry, no documentation yet -- these features won't be too useful until PyMOL is coupled up with an energy minimiation engine." Any infomation will be highly appreciated. Best wishes, Yu Shao R.P.I.
[PyMOL] Stereo3D hardware recommendation
Hello there, I plan to purchase a new graphics card and a pair of stereo glasses to be used with PyMOL. My current system: Dual Althlon 1900XP / 1GB DDR memory / Geforce4 video card. Could anyone please give me some suggestions/recommendations on the following questions? Because of the mono-performance issue, I decide to change my graphics card to ATI Fire GL2 (or 3 / 4). The current price I found: GL2: $800 GL3: $1300 GL4: $1700 My first question is: how will the different cards affect the stereo-viewing performance (at 1280x1024)? Is it necessary to go for a high-end card (and pay extra cash)? For the stereo glasses, I called Stereo Graphics and their CrystalEyes3 + Emitter boundle costs about $900. I also called NuVision and their 60GX + Emitter cost about $300. My second question is: what's the difference between these two? Can the difference justify the extra $600? Thanks a lot! Jiye Shi __ Do you Yahoo!? New DSL Internet Access from SBC & Yahoo! http://sbc.yahoo.com
RE: [PyMOL] pair_fit crashes
Hi Jeremy, If the proteins have significant homology, then you can use the align command: align prot1ca,prot2 which will perform a sequence alignment of prot1 against prot2, and then an optimizing fit using the CA positions. I'm not sure if the help text for align got into 0.82, but the next version will definitely have it. PyMOL's command length is limit to about 1000 characters, which is probably what is causing pair_fit to crash. However, ideally it should complain gracefully instead of crashing, so if you have a sample script & input PDB files which cause it to crash, please send them to me as attachments. As far as script options go, you've pointed out a hole which I had forgotten about, but Robert's suggestion on defining a function call in the script is definitely the way to go for now. Cheers, Warren -- mailto:war...@sunesis.com Warren L. DeLano, Ph.D. Informatics Manager Sunesis Pharmaceuticals, Inc. 341 Oyster Point Blvd. S. San Francisco, CA 94080 (650)-266-3606 FAX:(650)-266-3501 -Original Message- From: Jeremy Craven [mailto:c.j.cra...@sheffield.ac.uk] Sent: Thursday, September 26, 2002 2:00 AM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] pair_fit crashes I have been trying to write a script to overlay two arbitrary proteins via my own alignment and the 'pair_fit' command. 1) After running into the problem I described below I looked through the pymol-users mailing list as hard as I could and found a statment that such arbitrary alignment should be in pymol anyhow from vsn 0.80. I am using 0.82 but cannot find it. Is it there ? 2) Anyhow, (and assuming that I might want to do alignments my own way anyhow), I created a script which read in an alignment and created a big long pair_fit command of the form pair_fit (tbr and resi 187 and name ca),(bs and resi 170 and name ca), (tbr and resi 192 and name ca),(bs and resi 175 and name ca), etc The script then executed this string with cmd.do If I restricted this to about 10 atom pairs it worked fine. If I allow more atoms it crashes the program. On linux it gave segmentation violation. On irix it gave bus error. On irix it gave another message that implied that maybe the selections had got truncated. On linux it got as far as giving a sensible 'ExecutiveRMS' message (including a value for the rmsd and the number of atoms) and then froze and eventually core dumped. It therefore seems that the long selection has been accepted properly, but may it corrupts something else as a side effect ? Any ideas anyone ?? I wondered about doing all the selections invidually into named selections and then create a shorter pair_fit command, but decided I would ask here first. A second little quesion is how do you send command line arguments to a pymol python script. If I say PyMOL> run test1.py abcdef it says Traceback (most recent call last): File "/usr/lib/python1.5/site-packages/pymol/modules/pymol/parser.py", line 186, in parse execfile(args[nest][0],pymol_names,pymol_names) IOError: [Errno 2] No such file or directory whereas test1.py really does exist, and "run test1.py" works fine. Otherwise pymol is a great joy to have discovered in the last month or so, and a project that I hope I can support (e.g. by contributing scripts like this one once I can get it to work properly ...) Cheers Jeremy -- * Dr C. Jeremy Craven Department of Molecular Biology and Biotechnology University of Sheffield, Firth Court, Western Bank S10 2TN Sheffield UK e-mail: c.j.cra...@shef.ac.uk http://www.shef.ac.uk/uni/projects/nmr/CJC/CJC.html Phone: x24323 From outside Sheffield: 0114 222 4323 From outside UK: +44 114 2224323 Fax: 0114 272 8697 *
Re: [PyMOL] pair_fit crashes
* Jeremy Craven [2002-09-26 09:59] wrote: > 2) Anyhow, (and assuming that I might want to do alignments my own way > anyhow), > I created a script which read in an alignment and created a big long pair_fit > command of the form > > pair_fit (tbr and resi 187 and name ca),(bs and resi 170 and name ca), (tbr > and > resi 192 and name ca),(bs and resi 175 and name ca), etc > > The script then executed this string with cmd.do > I'll tackle the second question: > A second little quesion is how do you send command line arguments to a pymol > python script. > > If I say > > PyMOL> run test1.py abcdef > > it says > > Traceback (most recent call last): > File "/usr/lib/python1.5/site-packages/pymol/modules/pymol/parser.py", line > 186, in parse > execfile(args[nest][0],pymol_names,pymol_names) > IOError: [Errno 2] No such file or directory > > whereas test1.py really does exist, and "run test1.py" works fine. > If you write test1.py to be a function definition, e.g.: def make_pair_fit(arg1,arg2,arg3): Then "run test1.py" will read the python script to create the definition, but not actually run it. Then you can run it with: make_pair_fit(YourArg1,YourArg2,YourArg3,...) where you've filled in the appropriate values for the arguments. Hope that helps. Cheers, Robert -- Robert L. Campbell, Ph.D. http://biophysics.med.jhmi.edu/rlc r...@k2.med.jhmi.eduphone: 410-614-6313 Research Specialist/X-ray Facility Manager HHMI/Dept. of Biophysics & Biophysical Chem., The Johns Hopkins University PGP Fingerprint: 9B49 3D3F A489 05DC B35C 8E33 F238 A8F5 F635 C0E2
[PyMOL] pair_fit crashes
I have been trying to write a script to overlay two arbitrary proteins via my own alignment and the 'pair_fit' command. 1) After running into the problem I described below I looked through the pymol-users mailing list as hard as I could and found a statment that such arbitrary alignment should be in pymol anyhow from vsn 0.80. I am using 0.82 but cannot find it. Is it there ? 2) Anyhow, (and assuming that I might want to do alignments my own way anyhow), I created a script which read in an alignment and created a big long pair_fit command of the form pair_fit (tbr and resi 187 and name ca),(bs and resi 170 and name ca), (tbr and resi 192 and name ca),(bs and resi 175 and name ca), etc The script then executed this string with cmd.do If I restricted this to about 10 atom pairs it worked fine. If I allow more atoms it crashes the program. On linux it gave segmentation violation. On irix it gave bus error. On irix it gave another message that implied that maybe the selections had got truncated. On linux it got as far as giving a sensible 'ExecutiveRMS' message (including a value for the rmsd and the number of atoms) and then froze and eventually core dumped. It therefore seems that the long selection has been accepted properly, but may it corrupts something else as a side effect ? Any ideas anyone ?? I wondered about doing all the selections invidually into named selections and then create a shorter pair_fit command, but decided I would ask here first. A second little quesion is how do you send command line arguments to a pymol python script. If I say PyMOL> run test1.py abcdef it says Traceback (most recent call last): File "/usr/lib/python1.5/site-packages/pymol/modules/pymol/parser.py", line 186, in parse execfile(args[nest][0],pymol_names,pymol_names) IOError: [Errno 2] No such file or directory whereas test1.py really does exist, and "run test1.py" works fine. Otherwise pymol is a great joy to have discovered in the last month or so, and a project that I hope I can support (e.g. by contributing scripts like this one once I can get it to work properly ...) Cheers Jeremy -- * Dr C. Jeremy Craven Department of Molecular Biology and Biotechnology University of Sheffield, Firth Court, Western Bank S10 2TN Sheffield UK e-mail: c.j.cra...@shef.ac.uk http://www.shef.ac.uk/uni/projects/nmr/CJC/CJC.html Phone: x24323 From outside Sheffield: 0114 222 4323 From outside UK: +44 114 2224323 Fax: 0114 272 8697 *
