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
>
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> 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
> ******************************************
------------------------------------------------------------------------------
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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
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