[PyMOL] Wiki down?
I am just getting a blank page when I try to access the Pymol Wiki. Do other people see the same problem? Carsten -- 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
Re: [PyMOL] Wiki down?
On Thu, Jan 27, 2011 at 9:54 AM, Schubert, Carsten [PRDUS] cschu...@its.jnj.com wrote: I am just getting a blank page when I try to access the Pymol Wiki. Do other people see the same problem? Working fine for me (using Safari on a Mac). -Nat -- 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
Re: [PyMOL] Wiki down?
OK, works here again as well. Main Page was somehow screwy or I had a dirty cache in my browser From: Nat Echols [mailto:nathaniel.ech...@gmail.com] Sent: Thursday, January 27, 2011 1:09 PM To: pymol-users@lists.sourceforge.net Subject: Re: [PyMOL] Wiki down? On Thu, Jan 27, 2011 at 9:54 AM, Schubert, Carsten [PRDUS] cschu...@its.jnj.com wrote: I am just getting a blank page when I try to access the Pymol Wiki. Do other people see the same problem? Working fine for me (using Safari on a Mac). -Nat -- 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
[PyMOL] can't save pdb from within pymol
Hi, I've apparently managed to create a pse of a protein that loads fine but won't save the pdb coordinates (I get a file with END in it, and nothing else). Any ideas how to get the coordinates out? pymol 1.1b3 linux, windows (same pse has same result under both OS's) Thanks, Dave - David A. Horita, Ph.D. Department of Biochemistry Wake Forest University School of Medicine Winston-Salem, NC 27157-1016 Tel: 336 713-4194 Fax: 336 716-7671 email: dhor...@wfubmc.edumailto:dhor...@wfubmc.edu web: http://www1.wfubmc.edu/biochem/faculty/Horita.htmhttp://www1.wfubmc.edu/biochem/faculty/Horita.htm/ -- 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
Re: [PyMOL] Wiki down?
There's been a flood of spam to the wiki recently. Most of it has been obvious spammy pages, but someone also deleted the main page. Cute. On Thu, Jan 27, 2011 at 12:54 PM, Schubert, Carsten [PRDUS] cschu...@its.jnj.com wrote: I am just getting a blank page when I try to access the Pymol Wiki. Do other people see the same problem? Carsten -- 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 -- Michael Lerner, Ph.D. IRTA Postdoctoral Fellow Laboratory of Computational Biology NIH/NHLBI 5635 Fishers Lane, Room T909, MSC 9314 Rockville, MD 20852 (UPS/FedEx/Reality) Bethesda MD 20892-9314 (USPS) -- 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
Re: [PyMOL] Wiki down?
Hi all, I'm traveling now, so I'm a little slow on responding. But, as Michael has said, someone (or group) has been targeting the PyMOLWiki with massive amounts of spam. I rolled back a change today (restoring the main page content). If you see nonsense on the PyMOLWiki, please feel free to clear it and msg me or Michael (or any other admin) and we can delete the user and his/her changes. The PyMOLWiki gets 4000+ views a day and has been visited over 5 million times. If we had 2 users and 30 hits, we'd make a bad target for spam as no one would see it. Cheers, -- Jason On Thu, Jan 27, 2011 at 2:26 PM, Michael Lerner mgler...@gmail.com wrote: There's been a flood of spam to the wiki recently. Most of it has been obvious spammy pages, but someone also deleted the main page. Cute. On Thu, Jan 27, 2011 at 12:54 PM, Schubert, Carsten [PRDUS] cschu...@its.jnj.com wrote: I am just getting a blank page when I try to access the Pymol Wiki. Do other people see the same problem? Carsten -- 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 -- Michael Lerner, Ph.D. IRTA Postdoctoral Fellow Laboratory of Computational Biology NIH/NHLBI 5635 Fishers Lane, Room T909, MSC 9314 Rockville, MD 20852 (UPS/FedEx/Reality) Bethesda MD 20892-9314 (USPS) -- 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
Re: [PyMOL] can't save pdb from within pymol
Hi David, Can you please send me the PSE? If not, do you have multiple states? Are you using the save command or the GUI? Cheers, -- Jason On Thu, Jan 27, 2011 at 1:50 PM, David A. Horita dhor...@wfubmc.edu wrote: Hi, I've apparently managed to create a pse of a protein that loads fine but won't save the pdb coordinates (I get a file with END in it, and nothing else). Any ideas how to get the coordinates out? pymol 1.1b3 linux, windows (same pse has same result under both OS's) Thanks, Dave - David A. Horita, Ph.D. Department of Biochemistry Wake Forest University School of Medicine Winston-Salem, NC 27157-1016 Tel: 336 713-4194 Fax: 336 716-7671 email: dhor...@wfubmc.edu web: http://www1.wfubmc.edu/biochem/faculty/Horita.htm -- 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
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 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 +
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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
--
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Finally, a world-class log management solution at an even better
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Download using promo code Free_Logger_4_Dev2Dev. Offer expires
February 28th, so secure your free ArcSight Logger TODAY!
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--
Tsjerk A. Wassenaar, Ph.D.
post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and
