From: Gregory R. <rs...@co...> - 2013-07-26 19:23:17
|
Hi, I'm a fairly new user to PyMol and am having some trouble with the sphere_scale command. I understand that if I want to draw a sphere around the x'th ca atom, I can use: /show spheres, ////X/ca/ However, what if I want that sphere to have a radius of 3 angstroms, or 6 angstroms, etc. I understand I can use set sphere_scale, 1, ///X/ca but what is the default scale of 1? Is it 1A, is it something else? Thank you for your help! Kind regards, Greg |
From: Sampson, J. <Jar...@ny...> - 2013-07-26 21:11:54
|
[Re-posting to the list because, as usual, I forgot to Reply All...] Hi Greg - If I understand correctly (and just on a quick visual inspection in PyMOL it looks like I'm at least close), the sphere_scale setting will scale the size of the sphere relative to the van der Waals radius of the atom. So at sphere_scale == 1, Carbon will be ~1.70Å, Oxygen will be ~1.52Å, Nitrogen ~1.55Å, and so forth. To have a CA atom of 3Å radius, you would use sphere_scale of ( 3.0 / 1.7 ) = 1.76. Hope that helps, Jared -- Jared Sampson Xiangpeng Kong Lab NYU Langone Medical Center Old Public Health Building, Room 610 341 East 25th Street New York, NY 10016 212-263-7898 http://kong.med.nyu.edu/ On Jul 26, 2013, at 3:23 PM, Gregory Ryslik <rs...@co...<mailto:rs...@co...>> wrote: Hi, I'm a fairly new user to PyMol and am having some trouble with the sphere_scale command. I understand that if I want to draw a sphere around the x'th ca atom, I can use: show spheres, ////X/ca However, what if I want that sphere to have a radius of 3 angstroms, or 6 angstroms, etc. I understand I can use set sphere_scale, 1, ///X/ca but what is the default scale of 1? Is it 1A, is it something else? Thank you for your help! Kind regards, Greg ------------------------------------------------------------------------------ See everything from the browser to the database with AppDynamics Get end-to-end visibility with application monitoring from AppDynamics Isolate bottlenecks and diagnose root cause in seconds. Start your free trial of AppDynamics Pro today! http://pubads.g.doubleclick.net/gampad/clk?id=48808831&iu=/4140/ostg.clktrk_______________________________________________ PyMOL-users mailing list (PyM...@li...) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pym...@li... |
From: White, M. <mawhite@UTMB.EDU> - 2013-07-27 13:34:28
|
Greg, You can also use the alter command to change the vdw to the value you want. This is often done with SAXS bead models so that they can then be surfaced. alter (n. ca), vdw= 3 If this is set after the show spheres command the rebuild the view rebuild Hope this helps. Best regards, Mark Sent from my iPhone On Jul 26, 2013, at 4:12 PM, "Sampson, Jared" <Jar...@ny...<mailto:Jar...@ny...>> wrote: [Re-posting to the list because, as usual, I forgot to Reply All...] Hi Greg - If I understand correctly (and just on a quick visual inspection in PyMOL it looks like I'm at least close), the sphere_scale setting will scale the size of the sphere relative to the van der Waals radius of the atom. So at sphere_scale == 1, Carbon will be ~1.70Å, Oxygen will be ~1.52Å, Nitrogen ~1.55Å, and so forth. To have a CA atom of 3Å radius, you would use sphere_scale of ( 3.0 / 1.7 ) = 1.76. Hope that helps, Jared -- Jared Sampson Xiangpeng Kong Lab NYU Langone Medical Center Old Public Health Building, Room 610 341 East 25th Street New York, NY 10016 212-263-7898 http://kong.med.nyu.edu/ On Jul 26, 2013, at 3:23 PM, Gregory Ryslik <rs...@co...<mailto:rs...@co...>> wrote: Hi, I'm a fairly new user to PyMol and am having some trouble with the sphere_scale command. I understand that if I want to draw a sphere around the x'th ca atom, I can use: show spheres, ////X/ca However, what if I want that sphere to have a radius of 3 angstroms, or 6 angstroms, etc. I understand I can use set sphere_scale, 1, ///X/ca but what is the default scale of 1? Is it 1A, is it something else? Thank you for your help! Kind regards, Greg ------------------------------------------------------------------------------ See everything from the browser to the database with AppDynamics Get end-to-end visibility with application monitoring from AppDynamics Isolate bottlenecks and diagnose root cause in seconds. Start your free trial of AppDynamics Pro today! http://pubads.g.doubleclick.net/gampad/clk?id=48808831&iu=/4140/ostg.clktrk_______________________________________________ PyMOL-users mailing list (PyM...@li...<mailto:PyM...@li...>) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pym...@li... ------------------------------------------------------------------------------ See everything from the browser to the database with AppDynamics Get end-to-end visibility with application monitoring from AppDynamics Isolate bottlenecks and diagnose root cause in seconds. Start your free trial of AppDynamics Pro today! http://pubads.g.doubleclick.net/gampad/clk?id=48808831&iu=/4140/ostg.clktrk _______________________________________________ PyMOL-users mailing list (PyM...@li...<mailto:PyM...@li...>) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pym...@li... |
From: H. A. S. <h.a...@gm...> - 2013-07-29 15:05:19
|
It would be great if we could control PyMOL with a Leap Motion control <https://www.leapmotion.com>. I see it supports molecules. H. Adam Steinberg 7904 Bowman Rd Lodi, WI 53555 608/592-2366 |
From: David H. <li...@co...> - 2013-07-29 15:18:15
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Jason can fill you in if there's an update, but the latest status update I'm aware of was: http://www.mail-archive.com/pym...@li.../msg11572.html -David -David On Monday, July 29, 2013 at 11:04 AM, H. Adam Steinberg wrote: > It would be great if we could control PyMOL with a Leap Motion control <https://www.leapmotion.com>. > > I see it supports molecules. > > H. Adam Steinberg > 7904 Bowman Rd > Lodi, WI 53555 > 608/592-2366 > > > ------------------------------------------------------------------------------ > See everything from the browser to the database with AppDynamics > Get end-to-end visibility with application monitoring from AppDynamics > Isolate bottlenecks and diagnose root cause in seconds. > Start your free trial of AppDynamics Pro today! > http://pubads.g.doubleclick.net/gampad/clk?id=48808831&iu=/4140/ostg.clktrk > _______________________________________________ > PyMOL-users mailing list (PyM...@li... (mailto:PyM...@li...)) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > Archives: http://www.mail-archive.com/pym...@li... > > |
From: Thomas H. <tho...@sc...> - 2013-07-30 16:21:47
|
Hi, I put some instructions on the PyMOLWiki for those who want to play with the Leap Motion Controller. http://pymolwiki.org/index.php/Leap_Motion Cheers, Thomas David Hall wrote, On 07/29/13 17:18: > Jason can fill you in if there's an update, but the latest status update > I'm aware of was: > http://www.mail-archive.com/pym...@li.../msg11572.html > > -David > > On Monday, July 29, 2013 at 11:04 AM, H. Adam Steinberg wrote: > >> It would be great if we could control PyMOL with a Leap Motion control >> <https://www.leapmotion.com>. >> >> I see it supports molecules. >> >> H. Adam Steinberg >> 7904 Bowman Rd >> Lodi, WI 53555 >> 608/592-2366 -- Thomas Holder PyMOL Developer Schrödinger Contractor |
From: Martin H. <ma...@bl...> - 2013-07-30 12:40:23
|
Dear PyMOL users Sometimes PyMOL draws bonds between atoms which are not supposed to be connected. I know it is possible to unbond them using "unbond atom1, atom2", however this requires to always select the atoms and rename the selections to "atom1" and "atom2", respectively. It would be great if I could just click two atoms (using the "Atoms" selection quantifier) and then have them unbonded. How could I do that? Thanks a lot for any hints. Martin |
From: Thomas H. <tho...@sc...> - 2013-07-30 12:57:04
|
Hi Martin, that's what edit mode is for. Right-click on the mouse mode panel, choose "3-Button Editing", pick the two atoms and type "unbond". Cheers, Thomas Martin Hediger wrote, On 07/30/13 14:40: > Dear PyMOL users > > Sometimes PyMOL draws bonds between atoms which are not supposed to be > connected. I know it is possible to unbond them using "unbond atom1, > atom2", however this requires to always select the atoms and rename the > selections to "atom1" and "atom2", respectively. It would be great if I > could just click two atoms (using the "Atoms" selection quantifier) and > then have them unbonded. How could I do that? > > Thanks a lot for any hints. > Martin -- Thomas Holder PyMOL Developer Schrödinger Contractor |
From: Joel T. <joe...@ot...> - 2013-07-30 21:42:17
|
You can also use the builder module. Click on the two atoms and then delete bond button -----Original Message----- From: Martin Hediger [mailto:ma...@bl...] Sent: Wednesday, 31 July 2013 12:40 a.m. To: pym...@li... Subject: [PyMOL] Unbond two atoms Dear PyMOL users Sometimes PyMOL draws bonds between atoms which are not supposed to be connected. I know it is possible to unbond them using "unbond atom1, atom2", however this requires to always select the atoms and rename the selections to "atom1" and "atom2", respectively. It would be great if I could just click two atoms (using the "Atoms" selection quantifier) and then have them unbonded. How could I do that? Thanks a lot for any hints. Martin ------------------------------------------------------------------------------ Get your SQL database under version control now! Version control is standard for application code, but databases havent caught up. So what steps can you take to put your SQL databases under version control? Why should you start doing it? Read more to find out. http://pubads.g.doubleclick.net/gampad/clk?id=49501711&iu=/4140/ostg.clktrk _______________________________________________ PyMOL-users mailing list (PyM...@li...) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pym...@li... |