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[PyMOL] change the sphere size of a chosen atom ?
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From: GAO F. <mc...@ya...> - 2007-01-10 17:00:23
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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. pym...@li... wrote: Send PyMOL-users mailing list submissions to pym...@li... 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 pym...@li... You can reach the person managing the list at pym...@li... 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: pym...@li... Message-ID: <200...@ut...> 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 jav...@ut... ------------------------------ 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: pym...@li... Message-ID: <802...@we...> 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: pym...@li... Message-ID: <81B...@bc...> 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...@bc... Boston College Tel.617-552-4558 Department of Chemistry FAX 617-552-2705 Merkert Chemistry Center, Rm 239 Chestnut Hill, MA 02467 ------------------------------------------------------------------- -------------- next part -------------- An HTML attachment was scrubbed... URL: http://sourceforge.net/mailarchive/forum.php?forum=pymol-users/attachments/20070109/0b9fa285/attachment.html ------------------------------ Message: 4 Date: Tue, 9 Jan 2007 11:53:18 -0500 From: "Michael Lerner" Subject: Re: [PyMOL] New plugin and Doubt with APBS Tools To: " Ra?l Mera " Cc: pym...@li... Message-ID: Content-Type: text/plain; charset=ISO-8859-1; format=flowed Ra?l, 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, Ra?l Mera 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! > Reg?strate 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.php&p=sourceforge&CID=DEVDEV > _______________________________________________ > PyMOL-users mailing list > PyM...@li... > https://lists.sourceforge.net/lists/listinfo/pymol-users > -- Biophysics Graduate Student Carlson Lab, University of Michigan http://www.umich.edu/~mlerner http://lernerclan.net ------------------------------ Message: 5 Date: Tue, 9 Jan 2007 12:16:05 -0500 From: "Jamaine Saydu C. Davis" Subject: [PyMOL] protein peptide interaction To: Message-ID: <001801c73411$d953e1b0$501b5b80@JSD> Content-Type: text/plain; charset="us-ascii" I would like to compare interactions between a protein and two peptides with different charges. Is there a way to do this in pymol? Once I build the peptide, I can not dock into the protein binding site. Best, JSD -------------- next part -------------- An HTML attachment was scrubbed... URL: http://sourceforge.net/mailarchive/forum.php?forum=pymol-users/attachments/20070109/df1a9727/attachment.html ------------------------------ Message: 6 Date: Wed, 10 Jan 2007 14:32:09 +1100 From: Jonathan Arthur Subject: [PyMOL] Selecting nearby atoms To: pym...@li... Message-ID: <45A...@me...> Content-Type: text/plain; charset=ISO-8859-1; format=flowed Hello all, I am trying to select all atoms with 4 Angstroms from a particular atom, in this case the O of the OH group in a tyrosine residue. I executed the following commands select oh, id 341 select close, all within 4 of oh where the first command creates a named selection for the particular atom I am interested in and the second selects the nearby atoms. My problem is, there seems to be too many atoms selected and, when I check a few bond distances, I definitely have atoms selected further than 4 Angstroms away. What am I doing wrong? Also, once the selection is correct, is there any easy way to get a text list of all of these nearby atoms? Thanks for your help. Regards, Jonathan -- Dr Jonathan Arthur Sydney Bioinformatics Medical Foundation Building, K25 University of Sydney NSW 2006 Phone: +61 2 9036 3132 Fax: +61 2 9036 3233 Email: ja...@me... ------------------------------ ------------------------------------------------------------------------- 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.php&p=sourceforge&CID=DEVDEV ------------------------------ _______________________________________________ PyMOL-users mailing list PyM...@li... https://lists.sourceforge.net/lists/listinfo/pymol-users End of PyMOL-users Digest, Vol 8, Issue 2 ***************************************** --------------------------------- Access over 1 million songs - Yahoo! Music Unlimited. |
