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Re: [PyMOL] Independent Zooming in Grid Mode
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From: Schubert, C. [PRDUS] <CSC...@it...> - 2011-01-28 12:38:23
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Sean,
Just a thought, but the translate command looks like as if it should be possible to selectively modify the viewmatrix on a per object basis:
"translate" translates the atomic coordinates of atoms in a
selection. Alternatively, is modifies the matrix associated with
a particular object or object-state.
May be if you create two objects of interest, split states by object and then play around with the translate command you could achieve that effect.
> -----Original Message-----
> From: Jason Vertrees [mailto:jas...@sc...]
> Sent: Thursday, January 27, 2011 11:03 PM
> To: Sean Law
> Cc: pym...@li...
> Subject: Re: [PyMOL] Independent Zooming in Grid Mode
>
> 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 <mag...@ho...> 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: pym...@li...
> >> Subject: PyMOL-users Digest, Vol 56, Issue 9
> >> To: pym...@li...
> >> Date: Mon, 24 Jan 2011 22:11:17 +0000
> >>
> >> Send PyMOL-users mailing list submissions to
> >> pym...@li...
> >>
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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_inf
> o[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/pymol-
> us...@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_inf
> o[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_inf
> o[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
> >>
> >> ------------------------------
> >>
> >> _______________________________________________
> >> PyMOL-users mailing list
> >> PyM...@li...
> >> 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 (PyM...@li...)
> > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> > Archives: http://www.mail-archive.com/pymol-
> us...@li...
> >
>
>
>
> --
> Jason Vertrees, PhD
> PyMOL Product Manager
> Schrodinger, LLC
>
> (e) Jas...@sc...
> (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 (PyM...@li...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pym...@li...
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