[PyMOL] depiction of ligands
Hi all I would like to know, how we can show the ligands in pymol. Although i can see the non-bonded atoms ( HOH) automatically, eacept other nonbonded atoms l;ike sulphate and metal ions. I will appreciate the suggestions. Thanks in advance Thomas
[PyMOL] Rosetta Academic Training Webinar
The Rosetta Design Group is proud to present the first webinar in the Rosetta Academic Workshop Series. For the first webinar, we have selected to focus on Protein-Protein Docking based on the answers to the interest poll. We hope this will be the first in a line of helpful and inspiring webinars to kick-off our Rosetta Academic Workshop Series. What: Protein-Protein Docking When: May 4th 2009, 0800-1000 AM EST Where: Your office! Click here for more details and registration (For non html emails: http://rosettadesigngroup.com/RDGLS/index.php?sid=54479lang=en) Pleas note: This is not a promotional webinar. Rosetta is open-source and freeware for academic and non-profit organizations and can be downloaded here from University of Washington's TechTransfer Digital Ventures. The majority of the webinar is concerned with Rosetta 2.3.0. Rosetta 3.0 is still a beta version. Hope to see you there, Nir London. Rosetta Design Group | http://rosettadesigngroup.com/
Re: [PyMOL] Rosetta Academic Training Webinar
On Wed, Mar 25, 2009 at 5:07 PM, Nir London n...@rosettadesigngroup.com wrote: Pleas note: This is not a promotional webinar. Rosetta is open-source and freeware for academic and non-profit organizations and can be downloaded here from University of Washington's TechTransfer Digital Ventures. The majority of the webinar is concerned with Rosetta 2.3.0. Rosetta 3.0 is still a beta version. I think you've got your wording confused. It looks like Rosetta is freely available to academics and non-profits (with a lot of restrictions on what they can do with it). It's certainly not open-source since source code is not available to the general community. The wikipedia article has a pretty nice description of the term: http://en.wikipedia.org/wiki/Open_source as does the web page of the open-source initiative: http://opensource.org/docs/osd Best Regards, -greg
[PyMOL] Showing only part of a surface around a ligand
Hi all, this question may be resolvable by sufficient RTFMing, but maybe there is someone out there to help me... I am trying to generate a figure in which I want to show only a part of the protein surface around a ligand - pretty much like preset -- ligand sites -- solid surface I have already tried some amateur solutions like splitting the ligand into parts, placing waters to generate pseudo-ligand atoms and the like. Somewhat unsatisfying. I have also realized that I can click on every atom of the protein and do a show surface, but this will drive me insane sooner than later. I guess it must be doable through some magic selection commands - if I could only see how the preset command works, I could probably work it out from there. Can somebody please point me in the right direction? Thanks in advance, Wulf
Re: [PyMOL] Showing only part of a surface around a ligand
Wulf, suppose you have this scenario: Protein in chain A Ligand in chain I Then create b-site, byres chain A within 5 of chain I show sticks, chain I show surface, b-site should get you close. HTH Carsten BTW If you replace the create command with select your surface will be scribed i.e. with frizzled ends. If this is what you want then you should use select. -Original Message- From: Wulf Blankenfeldt [mailto:wulf.blankenfe...@mpi-dortmund.mpg.de] Sent: Wednesday, March 25, 2009 1:31 PM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] Showing only part of a surface around a ligand Hi all, this question may be resolvable by sufficient RTFMing, but maybe there is someone out there to help me... I am trying to generate a figure in which I want to show only a part of the protein surface around a ligand - pretty much like preset -- ligand sites -- solid surface I have already tried some amateur solutions like splitting the ligand into parts, placing waters to generate pseudo-ligand atoms and the like. Somewhat unsatisfying. I have also realized that I can click on every atom of the protein and do a show surface, but this will drive me insane sooner than later. I guess it must be doable through some magic selection commands - if I could only see how the preset command works, I could probably work it out from there. Can somebody please point me in the right direction? Thanks in advance, Wulf -- ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
Re: [PyMOL] Showing only part of a surface around a ligand
Wulf, The source code for presets can be found in modules/pymol/preset.py, but there is object, method, and housekeeping stuff in there that distracts from its understandability. show surface, polymer within 5 of organic May be all that you really need. # example use load $TUT/1hpv.pdb hide show surface, polymer within 5 of organic set two_sided_lighting show lines, byres polymer within 5 of organic show sticks, organic color auto, organic and elem c set transparency, 0.3 Cheers, Warren -Original Message- From: Wulf Blankenfeldt [mailto:wulf.blankenfe...@mpi-dortmund.mpg.de] Sent: Wednesday, March 25, 2009 10:34 AM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] Showing only part of a surface around a ligand Hi all, this question may be resolvable by sufficient RTFMing, but maybe there is someone out there to help me... I am trying to generate a figure in which I want to show only a part of the protein surface around a ligand - pretty much like preset -- ligand sites -- solid surface I have already tried some amateur solutions like splitting the ligand into parts, placing waters to generate pseudo-ligand atoms and the like. Somewhat unsatisfying. I have also realized that I can click on every atom of the protein and do a show surface, but this will drive me insane sooner than later. I guess it must be doable through some magic selection commands - if I could only see how the preset command works, I could probably work it out from there. Can somebody please point me in the right direction? Thanks in advance, Wulf -- ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
Re: [PyMOL] depiction of ligands
Hi Thomas, You're not really specific here, so I'll give the most general reply: show spheres, hetatm By the way, these compounds will definitely be drawn either as sticks or as nonbonded upon loading of the structure. You may not easily see them, but if they're in the file, they'll be drawn. Hope it helps, Tsjerk On Wed, Mar 25, 2009 at 5:30 PM, Jhon Thomas jhon1.tho...@gmail.com wrote: Hi all I would like to know, how we can show the ligands in pymol. Although i can see the non-bonded atoms ( HOH) automatically, eacept other nonbonded atoms l;ike sulphate and metal ions. I will appreciate the suggestions. Thanks in advance Thomas -- ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users -- Tsjerk A. Wassenaar, Ph.D. Junior UD (post-doc) Biomolecular NMR, Bijvoet Center Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands P: +31-30-2539931 F: +31-30-2537623
Re: [PyMOL] depiction of ligands
Hi there, There are many ways to do this. You can also try Actionpresetligands. This will show the ligands (hetatms) and their interactions. Unfortunately this doesn't highlight metal ions everytime (unless it interacts with the ligands). You can usually view this using the sequence option. [show the sequence - S button bottom right, move the slider to the end of the protein (usually) and select the metal(s) show spheres of selection] Hope this helps J _ Joel Tyndall, PhD Senior Lecturer in Medicinal Chemistry National School of Pharmacy University of Otago PO Box 56 Dunedin 9054 New Zealand http://www.researcherid.com/rid/C-2803-2008 Pukeka Matua Te Kura Taiwhanga Putaiao Te Whare Wananga o Otago Pouaka Poutapeta 56 Otepoti 9054 Aotearoa Ph / Waea +64 3 4797293 Fax / Waeawhakaahua +64 3 4797034 From: Jhon Thomas [mailto:jhon1.tho...@gmail.com] Sent: Thursday, 26 March 2009 5:30 a.m. To: pymol-users@lists.sourceforge.net Subject: [PyMOL] depiction of ligands Hi all I would like to know, how we can show the ligands in pymol. Although i can see the non-bonded atoms ( HOH) automatically, eacept other nonbonded atoms l;ike sulphate and metal ions. I will appreciate the suggestions. Thanks in advance Thomas
