Re: [PyMOL] Label by selection identifier
Hi Jordan, As a workaround you can label just the CA's (so this doesn't answer your question exactly, but might be usefull): label foo and n. CA, "foo" Hope this helps, Folmer 2013/5/21 Jordan Willis > Hello, > > This should be straightforward, > > Is it possible to label selections by their name? > > If I have a selection named "foo" and I say label foo, "foo", it of course > labels all the atoms. Is it possible to get one label for the entire > selection without using pseudoatoms? > > Jordan > > > > > > > > -- > Try New Relic Now & We'll Send You this Cool Shirt > New Relic is the only SaaS-based application performance monitoring service > that delivers powerful full stack analytics. Optimize and monitor your > browser, app, & servers with just a few lines of code. Try New Relic > and get this awesome Nerd Life shirt! http://p.sf.net/sfu/newrelic_d2d_may > ___ > 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 > -- Folmer Fredslund -- Try New Relic Now & We'll Send You this Cool Shirt New Relic is the only SaaS-based application performance monitoring service that delivers powerful full stack analytics. Optimize and monitor your browser, app, & servers with just a few lines of code. Try New Relic and get this awesome Nerd Life shirt! http://p.sf.net/sfu/newrelic_d2d_may___ 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] Label by selection identifier
Yes thank you! I meant to post that as my solution considering it works pretty good. It preserves depth and position. Jordan On May 21, 2013, at 3:45 AM, Folmer Fredslund wrote: > Hi Jordan, > > As a workaround you can label just the CA's (so this doesn't answer your > question exactly, but might be usefull): > > label foo and n. CA, "foo" > > Hope this helps, > Folmer > > > 2013/5/21 Jordan Willis > Hello, > > This should be straightforward, > > Is it possible to label selections by their name? > > If I have a selection named "foo" and I say label foo, "foo", it of course > labels all the atoms. Is it possible to get one label for the entire > selection without using pseudoatoms? > > Jordan > > > > > > > -- > Try New Relic Now & We'll Send You this Cool Shirt > New Relic is the only SaaS-based application performance monitoring service > that delivers powerful full stack analytics. Optimize and monitor your > browser, app, & servers with just a few lines of code. Try New Relic > and get this awesome Nerd Life shirt! http://p.sf.net/sfu/newrelic_d2d_may > ___ > 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 > > > > -- > Folmer Fredslund -- Try New Relic Now & We'll Send You this Cool Shirt New Relic is the only SaaS-based application performance monitoring service that delivers powerful full stack analytics. Optimize and monitor your browser, app, & servers with just a few lines of code. Try New Relic and get this awesome Nerd Life shirt! http://p.sf.net/sfu/newrelic_d2d_may___ 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] Label by selection identifier
Hi Jordan, use the "first" operator: PyMOL> label first foo, "foo" or for the first CA atom in foo: PyMOL> label first (foo and guide), "foo" Cheers, Thomas Jordan Willis wrote, On 05/21/13 11:07: > Yes thank you! > > I meant to post that as my solution considering it works pretty good. > It preserves depth and position. > > Jordan > > On May 21, 2013, at 3:45 AM, Folmer Fredslund wrote: > >> Hi Jordan, >> >> As a workaround you can label just the CA's (so this doesn't answer >> your question exactly, but might be usefull): >> >> label foo and n. CA, "foo" >> >> Hope this helps, >> Folmer >> >> 2013/5/21 Jordan Willis >> >> Hello, >> >> This should be straightforward, >> >> Is it possible to label selections by their name? >> >> If I have a selection named "foo" and I say label foo, "foo", it >> of course labels all the atoms. Is it possible to get one label >> for the entire selection without using pseudoatoms? >> >> Jordan -- Thomas Holder PyMOL Developer Schrödinger Contractor -- Try New Relic Now & We'll Send You this Cool Shirt New Relic is the only SaaS-based application performance monitoring service that delivers powerful full stack analytics. Optimize and monitor your browser, app, & servers with just a few lines of code. Try New Relic and get this awesome Nerd Life shirt! http://p.sf.net/sfu/newrelic_d2d_may ___ 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] Discrepancy between select within and distance?
Great, that seems to have fixed the problem.
Thanks for your help,
Dan
From: jason.vertr...@schrodinger.com
Date: Mon, 20 May 2013 10:25:14 -0500
Subject: Re: [PyMOL] Discrepancy between select within and distance?
To: psdny...@outlook.com
CC: pymol-users@lists.sourceforge.net
Hi,
Folmer is correct on both accounts.
First, "select" was selecting across various states into one multistate
selection. Then, the distance command was operating on the first state, which
is its default behavior. So, replace
select asdf, 1MM2CA w. 5 of 2kgi///22/CA
with
select asdf, 1MM2CA w. 5 of 2kgi///22/CA, state=1
or whichever state you want and try again. (Or use Folmer's suggestion of
splitting out the states.)
Second, please don't hind behind a pseudonym. We don't bite.
Cheers,
-- Jason
On Sun, May 19, 2013 at 4:55 PM, asdf asdf wrote:
Hello,
I'm measuring the distance between certain residues in an alignment and I've
noticed a discrepancy in the selections returned by the "select within command"
and the actual distances measured to the atoms returned by the selection. I
was wondering if maybe somebody knew where I was going wrong.
When I run the following commands
> fetch 1MM2
> fetch 2kgi
> align 2kgi, 1MM2
> select asdf, 1MM2CA w. 5 of 2kgi///22/CA
> iterate asdf, print(resi + " " + resn + " " + name + " " +
> str(cmd.distance("tmp", "2kgi///22/CA", "1MM2///" + resi + "/CA")))
I get this output:
24 CYS CA 5.15101623535
25 ASP CA 3.34501266479
26 THR CA 6.03605747223
47 GLU CA 3.80576062202
48 TRP CA 3.85521435738
49 LEU CA 4.28281402588
I'm just a little confused about why atoms that are further than 5 angstroms
away from the atom I specified in the select command are returned. Is there
some difference in the way "select within" and "cmd.distance", or have a
confused some of the commands?
Any suggestions are appreciated
--
AlienVault Unified Security Management (USM) platform delivers complete
security visibility with the essential security capabilities. Easily and
efficiently configure, manage, and operate all of your security controls
from a single console and one unified framework. Download a free trial.
http://p.sf.net/sfu/alienvault_d2d
___
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
Director of Core Modeling Products
Schrödinger, Inc.
(e) jason.vertr...@schrodinger.com
(o) +1 (603) 374-7120
--
Try New Relic Now & We'll Send You this Cool Shirt
New Relic is the only SaaS-based application performance monitoring service
that delivers powerful full stack analytics. Optimize and monitor your
browser, app, & servers with just a few lines of code. Try New Relic
and get this awesome Nerd Life shirt! http://p.sf.net/sfu/newrelic_d2d_may___
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
