[PyMOL] distance atom-protein surface
Dear Pymol users, I would like to measure the distance between an atom and a specific point (not another atom) in the surface of the protein. Is it possible with pymol? do I need additional scripts? Thanks in advance, Giacomo Bastianelli
Re: [PyMOL] distance atom-protein surface
Hi Giacomo, you can either create an atom at that position (see eg. http://www.rubor.de/bioinf/tips_python.html#chempy) and than use the distance command (or wizard). Or you can get the position of your first atom and simply calculate the distance of the two positions, sth. like: class MyAtom: def __init__(self, selection = /1lov//A/1/CA): model = cmd.get_model(selection) self.coordinates = self.model.atom[0].coord ## requires at least one atom in the model def distance(self, coords): ## given some coordinates (list of three), from numarray import * distanceVector=array(self.coordinates)-array(coords) return sqrt(dot(distanceVector, distanceVector)) Hope, that's what you wanted! Cheers, Andreas Giacomo Bastianelli wrote: Dear Pymol users, I would like to measure the distance between an atom and a specific point (not another atom) in the surface of the protein. Is it possible with pymol? do I need additional scripts? Thanks in advance, Giacomo Bastianelli - Take Surveys. Earn Cash. Influence the Future of IT Join SourceForge.net's Techsay panel and you'll get the chance to share your opinions on IT business topics through brief surveys - and earn cash http://www.techsay.com/default.php?page=join.phpp=sourceforgeCID=DEVDEV ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users -- Andreas Henschel Bioinformatics Group TU Dresden Tatzberg 47-51 01307 Dresden, Germany Phone: +49 351 463 40063 EMail: a...@biotec.tu-dresden.de
[PyMOL] change the sphere size of a chosen atom ?
Hi All: A quick question. When I select one particular atom, say, a sulfur atom, and represented with sphere. Does any know how to resize the sphere? It appears too big to reflect the real sense in the space. Thanks and Happy New Year! Feng. pymol-users-requ...@lists.sourceforge.net wrote: Send PyMOL-users mailing list submissions to pymol-users@lists.sourceforge.net To subscribe or unsubscribe via the World Wide Web, visit https://lists.sourceforge.net/lists/listinfo/pymol-users or, via email, send a message with subject or body 'help' to pymol-users-requ...@lists.sourceforge.net You can reach the person managing the list at pymol-users-ow...@lists.sourceforge.net When replying, please edit your Subject line so it is more specific than Re: Contents of PyMOL-users digest... Today's Topics: 1. Kabsch CE Align (Jason Vertrees) 2. New plugin and Doubt with APBS Tools (Ra?l Mera) 3. red-blue, red-cyan stereo (Evan Kantrowitz) 4. Re: New plugin and Doubt with APBS Tools (Michael Lerner) 5. protein peptide interaction (Jamaine Saydu C. Davis) 6. Selecting nearby atoms (Jonathan Arthur) -- Message: 1 Date: Thu, 4 Jan 2007 00:37:46 -0600 From: Jason Vertrees Subject: [PyMOL] Kabsch CE Align To: pymol-users@lists.sourceforge.net Message-ID: 200701040037.47002.javer...@utmb.edu Content-Type: text/plain; charset=iso-8859-1 Howdy, Just a quick note to those who used my implementation of the Kabsch algorithm for alignments: I have uploaded another version to the wiki http://www.pymolwiki.org/index.php/Kabsch that uses, what I consider, an elegant solution to the problem --- SVD. Also, the new code fixes a small bug I had in the last code and you'll need Numpy for it. Lastly, I've implemented the CE (structure-based) alignment algorithm as a plugin for PyMol. Details can also be found on the wiki at http://www.pymolwiki.org/index.php/Cealign I'll release the code if I can make the Python code fast or whenever I get the C/C++ code properly plugged into PyMol. (The C++ code on my machine aligns two 400+ residue proteins in about 0.250 seconds; the Python code for 167 residue proteins, 35 seconds!) Please forward bugs/comments to me, address below. Cheers, -- Jason -- Jason Vertrees javer...@utmb.edu -- Message: 2 Date: Sun, 7 Jan 2007 12:17:53 -0600 (CST) From: Ra?l Mera Subject: [PyMOL] New plugin and Doubt with APBS Tools To: pymol-users@lists.sourceforge.net Message-ID: 802526.3909...@web52401.mail.yahoo.com Content-Type: text/plain; charset=iso-8859-1 Dear all, Two things. First, I just written a small plugin that uses the program reduce to add hydrogens to a molecule or to a trajectory loaded in Pymol.(since each frame of the trajectory is hydrogenated by reduce, I think that protonation states could vary between frames) This allow us to have a reliable protonation method in PyMOL, without having to save the structure as PDB and hydrogenate with another app, and using an open-source (as far as I know) and easy to install application. Since I don't have any website right now, I will try to make it available from the Pymol Wiki. If you want the plugin right now, just e-mail me. The other thing is a doubt in using the APBS Tools. When I use it to calculate electrostatics potentialsof a trajectory (but the PQR is made by PDB2PQR from a PDB made with PyMOL, i.e, only from the first snapshot) I get a .dx map that I think has the potentials only for the first frame. When I display the potential surface in the trajectory, the potentials seems to change between frames, which I wouldn't expect since I think that the calculation was performed only for the first frame. My doubt is: Are these changes alleatory due to a change of the structure's position changes on the grid, or they have some significance?, if the latter, what significance? (maybe the changes are produced by the motion of polar groups?) Thanks in advance, Raul __ Correo Yahoo! Espacio para todos tus mensajes, antivirus y antispam ?gratis! Reg?strate ya - http://correo.espanol.yahoo.com/ -- Message: 3 Date: Tue, 9 Jan 2007 10:01:09 -0500 From: Evan Kantrowitz Subject: [PyMOL] red-blue, red-cyan stereo To: pymol-users@lists.sourceforge.net Message-ID: 81b9f413-ed06-4c29-91f2-052174d39...@bc.edu Content-Type: text/plain; charset=us-ascii Anyone have an idea about how to write a script to do red-blue or red- cyan stereo with pymol --- Evan R. Kantrowitz, Ph.D e van.kantrow...@bc.edu Boston College Tel.617-552-4558 Department of Chemistry
Re: [PyMOL] change the sphere size of a chosen atom ?
You can go to settings edit all sphere scale. Default is set to one, I have found that 0.3-0.4 works best. Bob _ From: pymol-users-boun...@lists.sourceforge.net [mailto:pymol-users-boun...@lists.sourceforge.net] On Behalf Of GAO FENG Sent: Wednesday, January 10, 2007 12:00 PM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] change the sphere size of a chosen atom ? Hi All: A quick question. When I select one particular atom, say, a sulfur atom, and represented with sphere. Does any know how to resize the sphere? It appears too big to reflect the real sense in the space. Thanks and Happy New Year! Feng. pymol-users-requ...@lists.sourceforge.net wrote: Send PyMOL-users mailing list submissions to pymol-users@lists.sourceforge.net To subscribe or unsubscribe via the World Wide Web, visit https://lists.sourceforge.net/lists/listinfo/pymol-users or, via email, send a message with subject or body 'help' to pymol-users-requ...@lists.sourceforge.net You can reach the person managing the list at pymol-users-ow...@lists.sourceforge.net When replying, please edit your Subject line so it is more specific than Re: Contents of PyMOL-users digest... Today's Topics: 1. Kabsch CE Align (Jason Vertrees) 2. New plugin and Doubt with APBS Tools (Ra?l Mera) 3. red-blue, red-cyan stereo (Evan Kantrowitz) 4. Re: New plugin and Doubt with APBS Tools (Michael Lerner) 5. protein peptide interaction (Jamaine Saydu C. Davis) 6. Selecting nearby atoms (Jonathan Arthur) -- Message: 1 Date: Thu, 4 Jan 2007 00:37:46 -0600 From: Jason Vertrees Subject: [PyMOL] Kabsch CE Align To: pymol-users@lists.sourceforge.net Message-ID: 200701040037.47002.javer...@utmb.edu Content-Type: text/plain; charset=iso-8859-1 Howdy, Just a quick note to those who used my implementation of the Kabsch algorithm for alignments: I have uploaded another version to the wiki http://www.pymolwiki.org/index.php/Kabsch that uses, what I consider, an elegant solution to the problem --- SVD. Also, the new code fixes a small bug I had in the last code and you'll need Numpy for it. Lastly, I've implemented the CE (structure-based) alignment algorithm as a plugin for PyMol. Details can also be found on the wiki at http://www.pymolwiki.org/index.php/Cealign I'll release the code if I can make the Python code fast or whenever I get the C/C++ code properly plugged into PyMol. (The C++ code on my machine aligns two 400+ residue proteins in about 0.250 seconds; the Python code for 167 residue proteins, 35 seconds!) Please forward bugs/comments to me, address below. Cheers, -- Jason -- Jason Vertrees javer...@utmb.edu -- Message: 2 Date: Sun, 7 Jan 2007 12:17:53 -0600 (CST) From: Ra?l Mera Subject: [PyMOL] New plugin and Doubt with APBS Tools To: pymol-users@lists.sourceforge.net Message-ID: 802526.3909...@web52401.mail.yahoo.com Content-Type: text/plain; charset=iso-8859-1 Dear all, Two things. First, I just written a small plugin that uses the program reduce to add hydrogens to a molecule or to a trajectory loaded in Pymol.(since each frame of the trajectory is hydrogenated by reduce, I think that protonation states could vary between frames) This allow us to have a reliable protonation method in PyMOL, without having to save the structure as PDB and hydrogenate with another app, and using an open-source (as far as I know) and easy to install application. Since I don't have any website right now, I will try to make it available from the Pymol Wiki. If you want the plugin right now, just e-mail me. The other thing is a doubt in using the APBS Tools. When I use it to calculate electrostatics potentialsof a trajectory (but the PQR is made by PDB2PQR from a PDB made with PyMOL, i.e, only from the first snapshot) I get a .dx map that I think has the potentials only for the first frame. When I display the potential surface in the trajectory, the potentials seems to change between frames, which I wouldn't expect since I think that the calculation was performed only for the first frame. My doubt is: Are these changes alleatory due to a change of the structure's position changes on the grid, or they have some significance?, if the latter, what significance? (maybe the changes are produced by the motion of polar groups?) Thanks in advance, Raul __ Correo Yahoo! Espacio para todos tus mensajes, antivirus y antispam ?gratis! Reg?strate ya - http://correo.espanol.yahoo.com/ -- Message: 3 Date: Tue, 9 Jan 2007 10:01:09 -0500 From: Evan Kantrowitz Subject: [PyMOL] red-blue, red-cyan stereo To: pymol-users@lists.sourceforge.net Message-ID: 81b9f413-ed06-4c29-91f2-052174d39...@bc.edu Content-Type: text/plain; charset=us-ascii Anyone have an idea about how to write a script to do red-blue or red- cyan stereo with pymol
Re: [PyMOL] Pymol cone shape?
Let's ask on the pymol mailing list... On Jan 10, 2007, at 11:02 AM, Martin.Laurberg wrote: Damn, I can convert my 1969 CNS base pair restraints into what they call CGO drawn lines, and thereby display enforced hydrogen bonds, but I wish to draw cones for the base pair ladder as ribbons can do it. Oh well, .. On Wed, 10 Jan 2007, William Scott wrote: I think it is possible, but I don't know how. On Jan 10, 2007, at 9:24 AM, Martin.Laurberg wrote: Hi Bill, is it possible to draw a cone-shape in pymol?
Re: [PyMOL] New plugin and Doubt with APBS Tools
We discussed this a bit off-list, and it looks like this was the answer: The potentials are assigned to points in space. That's why the isosurfaces don't change, and also why the surface coloring changes when you change the shape of the surface. Hope that helps anyone else who might have this question, -michael On 1/9/07, Michael Lerner mgler...@gmail.com wrote: Raúl, I don't have time to look at this in detail right now, but .. what exactly do you mean that the potentials change between frames? What happens if you draw isosurfaces? Do they change? -michael On 1/7/07, Raúl Mera butil_li...@yahoo.com wrote: Dear all, Two things. First, I just written a small plugin that uses the program reduce to add hydrogens to a molecule or to a trajectory loaded in Pymol.(since each frame of the trajectory is hydrogenated by reduce, I think that protonation states could vary between frames) This allow us to have a reliable protonation method in PyMOL, without having to save the structure as PDB and hydrogenate with another app, and using an open-source (as far as I know) and easy to install application. Since I don't have any website right now, I will try to make it available from the Pymol Wiki. If you want the plugin right now, just e-mail me. The other thing is a doubt in using the APBS Tools. When I use it to calculate electrostatics potentialsof a trajectory (but the PQR is made by PDB2PQR from a PDB made with PyMOL, i.e, only from the first snapshot) I get a .dx map that I think has the potentials only for the first frame. When I display the potential surface in the trajectory, the potentials seems to change between frames, which I wouldn't expect since I think that the calculation was performed only for the first frame. My doubt is: Are these changes alleatory due to a change of the structure's position changes on the grid, or they have some significance?, if the latter, what significance? (maybe the changes are produced by the motion of polar groups?) Thanks in advance, Raul __ Correo Yahoo! Espacio para todos tus mensajes, antivirus y antispam ¡gratis! Regístrate ya - http://correo.espanol.yahoo.com/ - Take Surveys. Earn Cash. Influence the Future of IT Join SourceForge.net's Techsay panel and you'll get the chance to share your opinions on IT business topics through brief surveys - and earn cash http://www.techsay.com/default.php?page=join.phpp=sourceforgeCID=DEVDEV ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users -- Biophysics Graduate Student Carlson Lab, University of Michigan http://www.umich.edu/~mlerner http://lernerclan.net -- Biophysics Graduate Student Carlson Lab, University of Michigan http://www.umich.edu/~mlerner http://lernerclan.net
Re: [PyMOL] Pymol cone shape?
Hi William You can do it, or something that's as close to a cone as you could wish for, by using a triangle fan. The apex of the fan is the top of the cone and then you just add points around the base of the cone at whatever granularity you like. That would take some programming though, but it's not too difficult if you know some Python, as the CGO interface is very simple. I wrote a pymol plugin to do something similar: it takes an input specification file, parses it, and draws many CGO objects as a result. It works just fine. Making the resulting cones smoothly colored or transparent would be more, and harder, work though. Without doing that, your cones may not play nicely with the rest of the stuff drawn by pymol (which in my case is nothing at all :-)). Terry | Let's ask on the pymol mailing list... | | On Jan 10, 2007, at 11:02 AM, Martin.Laurberg wrote: | | Damn, I can convert my 1969 CNS base pair restraints into what they call | CGO drawn lines, and thereby display enforced hydrogen bonds, but I wish | to draw cones for the base pair ladder as ribbons can do it. Oh well, .. | | On Wed, 10 Jan 2007, William Scott wrote: | | I think it is possible, but I don't know how. | | On Jan 10, 2007, at 9:24 AM, Martin.Laurberg wrote: | Hi Bill, is it possible to draw a cone-shape in pymol?
