[PyMOL] Independent Zooming in Grid Mode

[Sean L. <mag...@ho...>]

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: pym...@li...
> Subject: PyMOL-users Digest, Vol 56, Issue 9
> To: pym...@li...
> 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...@li...)
> 
> 
> ----------------------------------------------------------------------
> 
> Message: 1
> Date: Sun, 23 Jan 2011 10:48:20 +0100
> From: Tsjerk Wassenaar <ts...@gm...>
> Subject: Re: [PyMOL] Faster way to find polymer chains?
> To: Seth Harris <se...@gm...>
> Cc: pym...@li...
> Message-ID:
> 	<AANLkTi=JdC...@ma...>
> 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 <ts...@gm...> 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 <se...@gm...> 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 (PyM...@li...)
> >> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> >> Archives: http://www.mail-archive.com/pym...@li...
> >>
> >
> >
> >
> > --
> > 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 <sp...@us...>
> Subject: Re: [PyMOL] Faster way to find polymer chains?
> To: Seth Harris <se...@gm...>
> Cc: pym...@li...
> Message-ID: <4D3...@us...>
> 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" <wan...@gm...>
> Subject: [PyMOL] unable to open the file
> To: "pymol-users" <pym...@li...>
> Message-ID: <201...@gm...>
> 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 <cg...@uc...>
> Subject: Re: [PyMOL] unable to open the file
> To: pym...@li...
> Message-ID: <4D3...@uc...>
> 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 <se...@gm...>
> Subject: Re: [PyMOL] Faster way to find polymer chains?
> To: Thomas Holder <sp...@us...>
> Cc: pym...@li...
> Message-ID:
> 	<AANLkTi=9d7...@ma...>
> 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 <
> sp...@us...> 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...@li..." <rv...@li...>
> Subject: [PyMOL] dialogs in pyMOL
> To: pym...@li...
> 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
> 
> ------------------------------
> 
> _______________________________________________
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> End of PyMOL-users Digest, Vol 56, Issue 9
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