Re: [PyMOL] Discrepancy between select within and distance?
Hi,
I thinks this is the expected behaviour
2013/5/19 asdf asdf
> 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
>
You do not specify what state (http://pymolwiki.org/index.php/State) you
want to look at, so the selection takes in any atoms that are within the
given distance. In your example the 7th model in 1MM2 is within 5 Å from
the 7th state of 2kgi, so that gets added to the selection.
> > iterate asdf, print(resi + " " + resn + " " + name + " " +
> str(cmd.distance("tmp", "2kgi///22/CA", "1MM2///" + resi + "/CA")))
>
>
If I understand correctly, here you just get the distances between the
selected atoms, which then gives the output you get.
> 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
>
>
It should work as expected if you split the model into states with
split_states (http://pymolwiki.org/index.php/Split_States) and then make
the selection on just one of those models.
Best regards,
Folmer Fredslund
PS: It's nice to put in you own name
>
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--
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Re: [PyMOL] Discrepancy between select within and distance?
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
>
>
> --
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> 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.
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Director of Core Modeling Products
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(e) jason.vertr...@schrodinger.com
(o) +1 (603) 374-7120
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Re: [PyMOL] internal surface
Hi Yarrow, See demo #2 on the PyMOLWiki gallery page ( http://pymolwiki.org/index.php/Gallery). Cheers, -- Jason On Fri, May 10, 2013 at 5:42 PM, Yarrow Madrona wrote: > Hello pymol Gurus, > > I previously made a figure where the protien is cut in half and you can > see the ligand binding cavity. However, I have forgot how to reproduce it. > > My problem is that I want to show a slab of the internal surface not just > the interior part of the external surface. Can anyone help me with this? > > -Yarrow > > > -- > Yarrow Madrona > > Graduate Student > Molecular Biology and Biochemistry Dept. > University of California, Irvine > Natural Sciences I, Rm 2403 > Irvine, CA 92697 > > > > > > -- > Learn Graph Databases - Download FREE O'Reilly Book > "Graph Databases" is the definitive new guide to graph databases and > their applications. This 200-page book is written by three acclaimed > leaders in the field. The early access version is available now. > Download your free book today! http://p.sf.net/sfu/neotech_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 > -- Jason Vertrees, PhD Director of Core Modeling Products Schrödinger, Inc. (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- 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
[PyMOL] how to show ligand surface
I have a question I've never been able to figure out. If I have a pdb file with a ligand bound in a protein I can show the protein as a mesh or surface but I can't ever show the surface of the ligand. Any advice? What am I missing? Thank you very much. Yours &c. John -- 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
Re: [PyMOL] how to show ligand surface
Try to extract the ligand from the protein, so you get two separate objects. Best Troels Emtekær Linnet 2013/5/20 John Quinn > I have a question I've never been able to figure out. If I have a pdb file > with a ligand bound in a protein I can show the protein as a mesh or > surface but I can't ever show the surface of the ligand. Any advice? What > am I missing? > > Thank you very much. > > Yours &c. > > John > > > > > > -- > 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 > -- 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
Re: [PyMOL] how to show ligand surface
Hi Troels, I've tried that in the past (and just tried again to make sure) but it doesn't work for me. By the way, I'm running the latest open source version of PyMol installed via fink on a Mac Yours &c. John Quinn 133 Jay St. Albany, NY 12210 (518) 312-7033 jqu...@uchicago.edu On May 20, 2013, at 4:03 PM, Troels Emtekær Linnet wrote: > Troels -- 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
Re: [PyMOL] how to show ligand surface
Hi, Extracting/copying the ligand is one way ( http://www.pymolwiki.org/index.php/Surface#Creating_a_Closed_Surface). You can also set surface mode (http://pymolwiki.org/index.php/Surface_mode) or flag a selection (http://www.pymolwiki.org/index.php/Flag). Cheers, -- Jason On Mon, May 20, 2013 at 3:03 PM, Troels Emtekær Linnet wrote: > Try to extract the ligand from the protein, so you get two separate > objects. > > Best > > Troels Emtekær Linnet > > > 2013/5/20 John Quinn > >> I have a question I've never been able to figure out. If I have a pdb >> file with a ligand bound in a protein I can show the protein as a mesh or >> surface but I can't ever show the surface of the ligand. Any advice? What >> am I missing? >> >> Thank you very much. >> >> Yours &c. >> >> John >> >> >> >> >> >> -- >> 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 >> > > > > -- > 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 -- 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
Re: [PyMOL] how to show ligand surface
John, fetch 1rx1, async=0 set surface_mode, 3 as surface, org Cheers, -- Jason On Mon, May 20, 2013 at 3:21 PM, John Quinn wrote: > Hi Troels, > > I've tried that in the past (and just tried again to make sure) but it > doesn't work for me. > > By the way, I'm running the latest open source version of PyMol installed > via fink on a Mac > > Yours &c. > > John Quinn > 133 Jay St. > Albany, NY 12210 > (518) 312-7033 > jqu...@uchicago.edu > > > > On May 20, 2013, at 4:03 PM, Troels Emtekær Linnet > wrote: > > Troels > > > > > -- > 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 -- 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
Re: [PyMOL] how to show ligand surface
Thank you. That was perfect. I see that Mesh_mode works the same way. Yours &c. John Quinn 133 Jay St. Albany, NY 12210 (518) 312-7033 jqu...@uchicago.edu On May 20, 2013, at 4:21 PM, Jason Vertrees wrote: > Hi, > > Extracting/copying the ligand is one way > (http://www.pymolwiki.org/index.php/Surface#Creating_a_Closed_Surface). You > can also set surface mode (http://pymolwiki.org/index.php/Surface_mode) or > flag a selection (http://www.pymolwiki.org/index.php/Flag). > > Cheers, > > -- Jason > > > On Mon, May 20, 2013 at 3:03 PM, Troels Emtekær Linnet > wrote: > Try to extract the ligand from the protein, so you get two separate objects. > > Best > > Troels Emtekær Linnet > > > 2013/5/20 John Quinn > I have a question I've never been able to figure out. If I have a pdb file > with a ligand bound in a protein I can show the protein as a mesh or surface > but I can't ever show the surface of the ligand. Any advice? What am I > missing? > > Thank you very much. > > Yours &c. > > John > > > > > -- > 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 > > > -- > 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 -- 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
[PyMOL] Label by selection identifier
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
