[PyMOL] Selecting ASP and GLU
Dear all What is the selection syntax to select all GLU and ASP residues within an object? I'm trying it the way its written on the wiki: remove resn hoh# remove water h_add # add hydrogens as surface color grey90 color slate, resn lys # lysines in light blue color paleyellow, resn cys # cysteines in light yellow *color tv_red, (resn asp or(resn glu)) # aspartic and glutamic acid in light red* but, the selection kind of does not work for me (I'm assuming the operator for the logical AND is 'and'). What is it that I need to do differently? Kind regards Martin -- Free Software Download: Index, Search Analyze Logs and other IT data in Real-Time with Splunk. Collect, index and harness all the fast moving IT data generated by your applications, servers and devices whether physical, virtual or in the cloud. Deliver compliance at lower cost and gain new business insights. http://p.sf.net/sfu/splunk-dev2dev ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] Selecting ASP and GLU
Hi Martin, The wiki way should work. The only thing I can think of is that you're not doing what you think you're doing :S Did you copy paste the commands from the wiki? Did you get an error? What version are you using? but, the selection kind of does not work for me (I'm assuming the operator for the logical AND is 'and'). That's correct, 'and' gives the intersection. What is it that I need to do differently? Can you provide an example that works using fetch and such? Just a simple script we can try. Cheers, Tsjerk -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group * Groningen Institute for Biomolecular Research and Biotechnology * Zernike Institute for Advanced Materials University of Groningen The Netherlands -- Free Software Download: Index, Search Analyze Logs and other IT data in Real-Time with Splunk. Collect, index and harness all the fast moving IT data generated by your applications, servers and devices whether physical, virtual or in the cloud. Deliver compliance at lower cost and gain new business insights. http://p.sf.net/sfu/splunk-dev2dev ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] Selecting ASP and GLU
Hi Martin, Try the following: color tv_red, resn asp+glu or color tv_red, resn asp or resn glu Cheers, 2011/3/1 Martin Hediger ma@bluewin.ch Dear all What is the selection syntax to select all GLU and ASP residues within an object? I'm trying it the way its written on the wiki: remove resn hoh# remove water h_add # add hydrogens as surface color grey90 color slate, resn lys # lysines in light blue color paleyellow, resn cys # cysteines in light yellow*color tv_red, (resn asp or(resn glu)) # aspartic and glutamic acid in light red* but, the selection kind of does not work for me (I'm assuming the operator for the logical AND is 'and'). What is it that I need to do differently? Kind regards Martin -- Free Software Download: Index, Search Analyze Logs and other IT data in Real-Time with Splunk. Collect, index and harness all the fast moving IT data generated by your applications, servers and devices whether physical, virtual or in the cloud. Deliver compliance at lower cost and gain new business insights. http://p.sf.net/sfu/splunk-dev2dev ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- David Rodríguez Díaz, PhD Student Fundación Pública Galega de Medicina Xenómica (SERGAS) Santiago de Compostela (Spain) http://webspersoais.usc.es/persoais/david.rodriguez.diaz http://webspersoais.usc.es/persoais/david.rodriguez.diaz -- Free Software Download: Index, Search Analyze Logs and other IT data in Real-Time with Splunk. Collect, index and harness all the fast moving IT data generated by your applications, servers and devices whether physical, virtual or in the cloud. Deliver compliance at lower cost and gain new business insights. http://p.sf.net/sfu/splunk-dev2dev ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] Selecting ASP and GLU
Hi Martin - ** Short answer: Use `resn asp+glu` (although your original command actually works for me). ** Not-so-short answer, with a bonus question about comment syntax: The Asp/Glu line of your script can be condensed slightly using a plus sign, but the original syntax of that line actually works fine for me (PyMOL v.1.3, Fink/X11 build on Mac OS 10.6.6). However, for me, the lines to remove waters and add hydrogens fail. To elaborate, I've found that, with certain commands (but oddly not all of them -- for example, the `color` statements in your original script handle this just fine), adding a comment on the same line returns a Malformed selection error. I don't know if this is by design or an unintended feature. I would expect these comments to be handled the same way as in Python code, but for whatever reason, they are not. (Query for the developers: Is there a specific reason some PyMOL functions attempt to include the hash mark and comment in the selection, rather than ignoring everything after the #? Perhaps it has something to do with the number of arguments--both the commands below that fail with an inline comment take only a single selection argument.) If you really want to keep the comment on the same line, add a semicolon between the command and the comment. The other option, of course, is to place the comment on the previous line. Also, you can use `remove solvent` to cover all the different ways of describing water (HOH, WAT, H2O). Try this: # remove water remove solvent; # or put the comment on the same line after a semicolon # add hydrogens h_add; # this one also requires a semicolon # basic view as surface color grey90 # color lys blue, cys yellow, asp/glu red color slate, resn lys# comments here seem to work without the semicolon color paleyellow, resn cys color tv_red, resn asp+glu Hope that helps, -- Jared Sampson Xiangpeng Kong Lab NYU Langone Medical Center New York, NY 10016 212-263-7898 On Mar 1, 2011, at 7:44 AM, Martin Hediger wrote: Dear all What is the selection syntax to select all GLU and ASP residues within an object? I'm trying it the way its written on the wiki: remove resn hoh# remove water h_add # add hydrogens as surface color grey90 color slate, resn lys # lysines in light blue color paleyellow, resn cys # cysteines in light yellow color tv_red, (resn asp or(resn glu)) # aspartic and glutamic acid in light red but, the selection kind of does not work for me (I'm assuming the operator for the logical AND is 'and'). What is it that I need to do differently? Kind regards Martin -- Free Software Download: Index, Search Analyze Logs and other IT data in Real-Time with Splunk. Collect, index and harness all the fast moving IT data generated by your applications, servers and devices whether physical, virtual or in the cloud. Deliver compliance at lower cost and gain new business insights. http://p.sf.net/sfu/splunk-dev2dev ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.netmailto:PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net This email message, including any attachments, is for the sole use of the intended recipient(s) and may contain information that is proprietary, confidential, and exempt from disclosure under applicable law. Any unauthorized review, use, disclosure, or distribution is prohibited. If you have received this email in error please notify the sender by return email and delete the original message. Please note, the recipient should check this email and any attachments for the presence of viruses. The organization accepts no liability for any damage caused by any virus transmitted by this email. = -- Free Software Download: Index, Search Analyze Logs and other IT data in Real-Time with Splunk. Collect, index and harness all the fast moving IT data generated by your applications, servers and devices whether physical, virtual or in the cloud. Deliver compliance at lower cost and gain new business insights. http://p.sf.net/sfu/splunk-dev2dev ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] Selecting ASP and GLU
Hi Martin, To select all ASPs and GLUs just type, select resn GLU+ASP or select resn GLU or resn ASP or, if you need parentheses, select ((resn GLU) or (resn ASP)) Maybe this will help: # fetch a test protein fetch 1rsy, async=0 # color all ASPs and GLUs red color tv_red, (resn ASP or resn GLU) While the boolean 'and' works, the following will fail to select and color any atoms: color tv_red, (resn ASP and resn GLU) because there will be no _single atom_ in both an ASP and a GLU. The boolean 'and' in (resn ASP and resn GLU) requests an atom that is in any ASP _and_ in any GLU--which is impossible. Cheers, -- Jason On Tue, Mar 1, 2011 at 7:44 AM, Martin Hediger ma@bluewin.ch wrote: Dear all What is the selection syntax to select all GLU and ASP residues within an object? I'm trying it the way its written on the wiki: remove resn hoh# remove water h_add # add hydrogens as surface color grey90 color slate, resn lys # lysines in light blue color paleyellow, resn cys # cysteines in light yellow color tv_red, (resn asp or(resn glu)) # aspartic and glutamic acid in light red but, the selection kind of does not work for me (I'm assuming the operator for the logical AND is 'and'). What is it that I need to do differently? Kind regards Martin -- Free Software Download: Index, Search Analyze Logs and other IT data in Real-Time with Splunk. Collect, index and harness all the fast moving IT data generated by your applications, servers and devices whether physical, virtual or in the cloud. Deliver compliance at lower cost and gain new business insights. http://p.sf.net/sfu/splunk-dev2dev ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- Jason Vertrees, PhD PyMOL Product Manager Schrodinger, LLC (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- Free Software Download: Index, Search Analyze Logs and other IT data in Real-Time with Splunk. Collect, index and harness all the fast moving IT data generated by your applications, servers and devices whether physical, virtual or in the cloud. Deliver compliance at lower cost and gain new business insights. http://p.sf.net/sfu/splunk-dev2dev ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] Selecting ASP and GLU
Hi Martin, On Tue, 01 Mar 2011 13:44:36 +0100 Martin Hediger ma@bluewin.ch wrote: Dear all What is the selection syntax to select all GLU and ASP residues within an object? I'm trying it the way its written on the wiki: remove resn hoh# remove water h_add # add hydrogens as surface color grey90 color slate, resn lys # lysines in light blue color paleyellow, resn cys # cysteines in light yellow *color tv_red, (resn asp or(resn glu)) # aspartic and glutamic acid in light red* The easier way to write that is: color tv_red, resn asp+glu You can string several sorts of selections together that way, for example: select actsite, resi 105+262+286 select aliphatic, resn ala+val+leu+ile Cheers, Rob -- Robert L. Campbell, Ph.D. Senior Research Associate/Adjunct Assistant Professor Botterell Hall Rm 644 Department of Biochemistry, Queen's University, Kingston, ON K7L 3N6 Canada Tel: 613-533-6821Fax: 613-533-2497 robert.campb...@queensu.cahttp://pldserver1.biochem.queensu.ca/~rlc -- Free Software Download: Index, Search Analyze Logs and other IT data in Real-Time with Splunk. Collect, index and harness all the fast moving IT data generated by your applications, servers and devices whether physical, virtual or in the cloud. Deliver compliance at lower cost and gain new business insights. http://p.sf.net/sfu/splunk-dev2dev ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
