Hi Sean, PyMOL is currently not capable of providing and "inset"-like image or grid-mode with independent motions. Programming this at the Python level wouldn't be very easy.
Cheers, -- Jason On Wed, Jan 26, 2011 at 9:39 AM, Sean Law <magic...@hotmail.com> wrote: > Hi PyMOLers, > > I was wondering if anybody had a solution for independent when using > grid_mode=on. I want to be able to show, side-by-side, the same structure > where one structure is "zoomed in" on a specific part on the biomolecule and > the other object is "zoomed out" (viewing the entire molecule). And as I > turn one of the two structures, the other one turns accordingly. I think > this would be useful when trying to keep track of the orientation of the > biomolecule or for docking. > > Any suggestions would be greatly appreciated. > > Sean > >> From: pymol-users-requ...@lists.sourceforge.net >> Subject: PyMOL-users Digest, Vol 56, Issue 9 >> To: pymol-users@lists.sourceforge.net >> Date: Mon, 24 Jan 2011 22:11:17 +0000 >> >> 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. Re: Faster way to find polymer chains? (Tsjerk Wassenaar) >> 2. Re: Faster way to find polymer chains? (Thomas Holder) >> 3. unable to open the file (wang_qi) >> 4. Re: unable to open the file (Christoph Gohlke) >> 5. Re: Faster way to find polymer chains? (Seth Harris) >> 6. dialogs in pyMOL (rv...@libero.it) >> >> >> ---------------------------------------------------------------------- >> >> Message: 1 >> Date: Sun, 23 Jan 2011 10:48:20 +0100 >> From: Tsjerk Wassenaar <tsje...@gmail.com> >> Subject: Re: [PyMOL] Faster way to find polymer chains? >> To: Seth Harris <set...@gmail.com> >> Cc: pymol-users@lists.sourceforge.net >> Message-ID: >> <AANLkTi=jdcwaci5n2jav_vqjybffatyb8cw5q0egq...@mail.gmail.com> >> Content-Type: text/plain; charset=ISO-8859-1 >> >> Oops... That should've been: >> >> polychains = set([i.chain for i in cmd.get_model('polymer').atom]) >> >> Sorry for that. :p >> >> Tsjerk >> >> On Sun, Jan 23, 2011 at 10:32 AM, Tsjerk Wassenaar <tsje...@gmail.com> >> wrote: >> > Hi Seth, >> > >> > So you just want to have all unique chain identifiers for the >> > 'polymer' selection? Does the following give what you want?: >> > >> > polychains = set([i.chain for i in cmd.get_model('polymer')]) >> > >> > Hope it helps, >> > >> > Tsjerk >> > >> > On Sun, Jan 23, 2011 at 10:04 AM, Seth Harris <set...@gmail.com> wrote: >> >> Hi All, >> >> I am script-plowing through PDB files and extracting unique chain >> >> identifiers only for "polymers" using PyMOL's polymer selection. Right >> >> now >> >> my code is a kind of brute force thing like this: >> >> <code> >> >> ??cmd.create ("justpolys","polymer") >> >> ??polymer_chains=[] >> >> ??for a in cmd.index("justpolys"): >> >> ?? ?q_sel = "%s`%d"%a >> >> ?? ?#print q_sel+":", >> >> ?? ?cmd.iterate(q_sel, "stored.qry_info = (chain,resn,resi,name)") >> >> ?? ?#cmd.iterate_state(1,q_sel, "stored.qry_xyz = (x,y,z)") >> >> ?? ?#print >> >> >> >> stored.qry_info[0],stored.qry_info[1],stored.qry_info[2],stored.qry_info[3] >> >> ?? ?# Track any unique chains by adding to polymer_chains list if not >> >> already there >> >> ?? ?# first reformat to get rid of flanking ' marks >> >> ?? ?thischain=`stored.qry_info[0]` >> >> ?? ?thischain=thischain.replace("'","") >> >> ?? ?if thischain not in polymer_chains: >> >> ?? ? ?polymer_chains.append(thischain) >> >> </code> >> >> This works, but is quite slow as it iterates over every atom in every >> >> pdb >> >> just to get out the chain so it is quite redundant. >> >> Is there any way to iterate in a 'chain by chain' fashion? This q_sel >> >> stuff >> >> is recycled from something Warren suggested for a different purpose >> >> years >> >> ago, and I only have a loose idea of how that is interacting with the >> >> cmd.index part. Maybe there's a way to get just the chain from the >> >> get-go >> >> instead of all the individual atoms? Any reminders on that one or >> >> better >> >> method suggestions? >> >> Thanks, >> >> Seth >> >> >> >> >> >> ------------------------------------------------------------------------------ >> >> Special Offer-- Download ArcSight Logger for FREE (a $49 USD value)! >> >> Finally, a world-class log management solution at an even better >> >> price-free! >> >> Download using promo code Free_Logger_4_Dev2Dev. Offer expires >> >> February 28th, so secure your free ArcSight Logger TODAY! >> >> http://p.sf.net/sfu/arcsight-sfd2d >> >> _______________________________________________ >> >> 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 >> >> >> > >> > >> > >> > -- >> > 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 >> > >> >> >> >> -- >> 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 >> >> >> >> ------------------------------ >> >> Message: 2 >> Date: Sun, 23 Jan 2011 14:58:17 +0100 >> From: Thomas Holder <spel...@users.sourceforge.net> >> Subject: Re: [PyMOL] Faster way to find polymer chains? >> To: Seth Harris <set...@gmail.com> >> Cc: pymol-users@lists.sourceforge.net >> Message-ID: <4d3c33f9.8010...@users.sourceforge.net> >> Content-Type: text/plain; charset=ISO-8859-1; format=flowed >> >> Hi Seth, >> >> I think this one-liner will do the job for you: >> >> print cmd.get_chains('polymer') >> >> Cheers, >> Thomas >> >> Seth Harris wrote, On 01/23/11 10:04: >> > Hi All, >> > >> > I am script-plowing through PDB files and extracting unique chain >> > identifiers only for "polymers" using PyMOL's polymer selection. Right >> > now my code is a kind of brute force thing like this: >> > <code> >> > >> > cmd.create ("justpolys","polymer") >> > >> > polymer_chains=[] >> > >> > for a in cmd.index("justpolys"): >> > q_sel = "%s`%d"%a >> > #print q_sel+":", >> > cmd.iterate(q_sel, "stored.qry_info = (chain,resn,resi,name)") >> > #cmd.iterate_state(1,q_sel, "stored.qry_xyz = (x,y,z)") >> > #print >> > >> > stored.qry_info[0],stored.qry_info[1],stored.qry_info[2],stored.qry_info[3] >> > # Track any unique chains by adding to polymer_chains list if not >> > already there >> > # first reformat to get rid of flanking ' marks >> > thischain=`stored.qry_info[0]` >> > thischain=thischain.replace("'","") >> > if thischain not in polymer_chains: >> > polymer_chains.append(thischain) >> > </code> >> > >> > This works, but is quite slow as it iterates over every atom in every >> > pdb just to get out the chain so it is quite redundant. >> > >> > Is there any way to iterate in a 'chain by chain' fashion? This q_sel >> > stuff is recycled from something Warren suggested for a different >> > purpose years ago, and I only have a loose idea of how that is >> > interacting with the cmd.index part. Maybe there's a way to get just the >> > chain from the get-go instead of all the individual atoms? Any reminders >> > on that one or better method suggestions? >> > >> > Thanks, >> > Seth >> >> >> >> ------------------------------ >> >> Message: 3 >> Date: Sun, 23 Jan 2011 23:02:17 +0800 >> From: "wang_qi" <wangqiu...@gmail.com> >> Subject: [PyMOL] unable to open the file >> To: "pymol-users" <pymol-users@lists.sourceforge.net> >> Message-ID: <201101232302123288...@gmail.com> >> Content-Type: text/plain; charset="us-ascii" >> >> Hello, everyone, >> >> I have downloaded the pymol of version 1.3. and installed it on windows XP >> successfully. But when selecting "file-open" to load my file, it doesn't >> work and displays that the file is unable to be opend. Dose anyone meet this >> problem? Ana how how can i solve it? >> >> Thanks. >> >> Qi Wang >> >> 2011-01-23 >> >> >> >> wang_qi >> -------------- next part -------------- >> An HTML attachment was scrubbed... >> >> ------------------------------ >> >> Message: 4 >> Date: Sun, 23 Jan 2011 08:27:33 -0800 >> From: Christoph Gohlke <cgoh...@uci.edu> >> Subject: Re: [PyMOL] unable to open the file >> To: pymol-users@lists.sourceforge.net >> Message-ID: <4d3c56f5.6020...@uci.edu> >> Content-Type: text/plain; charset="iso-8859-1" >> >> You can try the attached patch. It fixes three issues: >> >> * is_string() returns False in case of unicode filenames >> * Python/Tk bug http://bugs.python.org/issue5712 >> * filenames containing whitespace >> >> Christoph >> >> On 1/23/2011 7:02 AM, wang_qi wrote: >> > Hello, everyone, >> > I have downloaded the pymol of version 1.3. and installed it on windows >> > XP successfully. But when selecting "file-open" to load my file, it >> > doesn't work and displays that the file is unable to be opend. Dose >> > anyone meet this problem? Ana how how can i solve it? >> > Thanks. >> > Qi Wang >> > 2011-01-23 >> > wang_qi >> > >> > >> >> >> -------------- next part -------------- >> An embedded and charset-unspecified text was scrubbed... >> Name: pymol-fileopen.diff >> >> ------------------------------ >> >> Message: 5 >> Date: Sun, 23 Jan 2011 12:14:17 -0800 >> From: Seth Harris <set...@gmail.com> >> Subject: Re: [PyMOL] Faster way to find polymer chains? >> To: Thomas Holder <spel...@users.sourceforge.net> >> Cc: pymol-users@lists.sourceforge.net >> Message-ID: >> <AANLkTi=9d7uo4s3msl56tehhwnyzcdh6ofpo+ybtd...@mail.gmail.com> >> Content-Type: text/plain; charset="iso-8859-1" >> >> Thanks Thomas and Tsjerk for pointing me back to the path...from my >> quicksand and brambles where I knew I was off! Brilliant. Seems to be an >> unfortunate habit I have in scripting where it's like "Why use a simple, >> elegant one-liner when a mess of impenetrable hack-arounds would do?" I >> had >> forgotten about those get_<goodstuff> commands. >> >> Much appreciated! >> -Seth >> >> >> >> On Sun, Jan 23, 2011 at 5:58 AM, Thomas Holder < >> spel...@users.sourceforge.net> wrote: >> >> > Hi Seth, >> > >> > I think this one-liner will do the job for you: >> > >> > print cmd.get_chains('polymer') >> > >> > Cheers, >> > Thomas >> > >> > Seth Harris wrote, On 01/23/11 10:04: >> > >> > Hi All, >> >> >> >> I am script-plowing through PDB files and extracting unique chain >> >> identifiers only for "polymers" using PyMOL's polymer selection. Right >> >> now >> >> my code is a kind of brute force thing like this: >> >> <code> >> >> >> >> cmd.create ("justpolys","polymer") >> >> >> >> polymer_chains=[] >> >> >> >> for a in cmd.index("justpolys"): >> >> q_sel = "%s`%d"%a >> >> #print q_sel+":", >> >> cmd.iterate(q_sel, "stored.qry_info = (chain,resn,resi,name)") >> >> #cmd.iterate_state(1,q_sel, "stored.qry_xyz = (x,y,z)") >> >> #print >> >> >> >> stored.qry_info[0],stored.qry_info[1],stored.qry_info[2],stored.qry_info[3] >> >> # Track any unique chains by adding to polymer_chains list if not >> >> already there >> >> # first reformat to get rid of flanking ' marks >> >> thischain=`stored.qry_info[0]` >> >> thischain=thischain.replace("'","") >> >> if thischain not in polymer_chains: >> >> polymer_chains.append(thischain) >> >> </code> >> >> >> >> This works, but is quite slow as it iterates over every atom in every >> >> pdb >> >> just to get out the chain so it is quite redundant. >> >> Is there any way to iterate in a 'chain by chain' fashion? This q_sel >> >> stuff is recycled from something Warren suggested for a different >> >> purpose >> >> years ago, and I only have a loose idea of how that is interacting with >> >> the >> >> cmd.index part. Maybe there's a way to get just the chain from the >> >> get-go >> >> instead of all the individual atoms? Any reminders on that one or >> >> better >> >> method suggestions? >> >> >> >> Thanks, >> >> Seth >> >> >> > >> -------------- next part -------------- >> An HTML attachment was scrubbed... >> >> ------------------------------ >> >> Message: 6 >> Date: Mon, 24 Jan 2011 23:11:09 +0100 (CET) >> From: "rv...@libero.it" <rv...@libero.it> >> Subject: [PyMOL] dialogs in pyMOL >> To: pymol-users@lists.sourceforge.net >> Message-ID: >> <10798172.456681295907069292.JavaMail.defaultUser@defaultHost> >> Content-Type: text/plain;charset="UTF-8" >> >> Hi to all, >> I need to open a message box dialog inside a pyMOL plug-in. >> >> When I try the code: >> >> import tkMessageBox >> tkMessageBox.showinfo(?title?, ?msg?) >> >> pyMOL crashes (the window doesn?t appear and pyMOL blocks). >> >> I am just entering pyMOL and python. I never used Tkinter before. >> >> Could anyone help me? >> Thanks >> >> >> >> ------------------------------ >> >> >> ------------------------------------------------------------------------------ >> Special Offer-- Download ArcSight Logger for FREE (a $49 USD value)! >> Finally, a world-class log management solution at an even better >> price-free! >> Download using promo code Free_Logger_4_Dev2Dev. Offer expires >> February 28th, so secure your free ArcSight Logger TODAY! >> http://p.sf.net/sfu/arcsight-sfd2d >> >> ------------------------------ >> >> _______________________________________________ >> PyMOL-users mailing list >> PyMOL-users@lists.sourceforge.net >> https://lists.sourceforge.net/lists/listinfo/pymol-users >> >> >> End of PyMOL-users Digest, Vol 56, Issue 9 >> ****************************************** > > ------------------------------------------------------------------------------ > Special Offer-- Download ArcSight Logger for FREE (a $49 USD value)! > Finally, a world-class log management solution at an even better price-free! > Download using promo code Free_Logger_4_Dev2Dev. Offer expires > February 28th, so secure your free ArcSight Logger TODAY! > http://p.sf.net/sfu/arcsight-sfd2d > _______________________________________________ > 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 ------------------------------------------------------------------------------ Special Offer-- Download ArcSight Logger for FREE (a $49 USD value)! Finally, a world-class log management solution at an even better price-free! Download using promo code Free_Logger_4_Dev2Dev. Offer expires February 28th, so secure your free ArcSight Logger TODAY! http://p.sf.net/sfu/arcsight-sfd2d _______________________________________________ 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
