From: Lecher, J. <j.l...@fz...> - 2011-11-10 10:13:59
|
I started this some time ago and also announced it on the mailing list. But it didn't caught much interest. https://github.com/jlec/Pymol-script-repo So if there is interest, please feel free to check in your scripts. Justin ----- Reply message ----- Von: "Thomas Holder" <sp...@us...> Datum: Do., Nov. 10, 2011 10:47 Betreff: [PyMOL] Put scripts in a svn folder An: "Troels Emtekær Linnet" <tl...@gm...> Cc: "pym...@li..." <pym...@li...> Hi Troels, your idea sounds good, indeed! We are working on a improved plugin system for PyMOL that supports fetching from repositories, versioning and metadata for plugins. It will handle "scripts" and "plugins" the same way. It will rather not include the subversion <> wiki interface as you suggested, but other functionality that will provide similar convenience. More news about that soon. Cheers, Thomas Troels Emtekær Linnet wrote, On 11/09/11 23:57: > Hi Pymolers. > > I sometimes find small errors in my scripts, which I then correct. > But then I get a little "sad", that now my "unfinished" script still > lives "out there". > > So I think, why is the pymolwiki scripts not under subversion control? > > Then authors could push corrections to their scripts to the subversion > directory, and users would get these corrections. > > I dont know if the pymol wiki could fetch and display the scripts from > the subversion folder. > > How does this idea sounds? > > Bes > Troels -- Thomas Holder MPI for Developmental Biology Spemannstr. 35 D-72076 Tübingen ------------------------------------------------------------------------------ RSA(R) Conference 2012 Save $700 by Nov 18 Register now http://p.sf.net/sfu/rsa-sfdev2dev1 _______________________________________________ PyMOL-users mailing list (PyM...@li...) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pym...@li... ------------------------------------------------------------------------------------------------ ------------------------------------------------------------------------------------------------ Forschungszentrum Juelich GmbH 52425 Juelich Sitz der Gesellschaft: Juelich Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498 Vorsitzender des Aufsichtsrats: MinDirig Dr. Karl Eugen Huthmacher Geschaeftsfuehrung: Prof. Dr. Achim Bachem (Vorsitzender), Karsten Beneke (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt, Prof. Dr. Sebastian M. Schmidt ------------------------------------------------------------------------------------------------ ------------------------------------------------------------------------------------------------ |
From: Jason V. <jas...@sc...> - 2011-11-10 16:30:12
|
Hi Justin, > I started this some time ago and also announced it on the mailing list. But > it didn't caught much interest. The idea didn't get much traction because it was ahead of its time. I think now is its time. The plugin manager that Thomas is creating will be able to aggregate scripts from various locations and install them on the fly without one needing to restart PyMOL. Do you mind working with Thomas to help integrate with the git-hub repo? Downloading scripts and running them creates a security hazard. So, we need to be careful about that. Some points to consider for the repository: * it should mirror or host the code from the PyMOLWiki, not fork it * be secure from misuse (can anyone commit or just you?) What do you think? Cheers, -- Jason -- Jason Vertrees, PhD PyMOL Product Manager Schrodinger, LLC (e) Jas...@sc... (o) +1 (603) 374-7120 |
From: Troels E. L. <tl...@gm...> - 2011-11-10 16:45:45
|
I personally think git hub is a good suggestion. And we need you wikiguys (Jason etc. ) to catch the idea and implement it. :-) Security is an issue, and I also believe that you need to control this. I don't know if github is able to make securities in groups of a owner of a script and some "super users". So only a few users can change the script. Would it possible to have the same user credentials to the github as the wiki? Host / mirror. As far as I know, one can find each file at a github webpage. So, maybe the pymolwiki could show that file in a window at the wiki? People with github experience should throw in some experience. :-) Best Troels Troels Emtekær Linnet Slotsvej 2 4300 Holbæk Mobil: +45 60210234 2011/11/10 Jason Vertrees <jas...@sc...> > Hi Justin, > > > I started this some time ago and also announced it on the mailing list. > But > > it didn't caught much interest. > > The idea didn't get much traction because it was ahead of its time. I > think now is its time. > > The plugin manager that Thomas is creating will be able to aggregate > scripts from various locations and install them on the fly without one > needing to restart PyMOL. Do you mind working with Thomas to help > integrate with the git-hub repo? > > Downloading scripts and running them creates a security hazard. So, we > need to be careful about that. > > Some points to consider for the repository: > * it should mirror or host the code from the PyMOLWiki, not fork it > * be secure from misuse (can anyone commit or just you?) > > What do you think? > > Cheers, > > -- Jason > > -- > Jason Vertrees, PhD > PyMOL Product Manager > Schrodinger, LLC > > (e) Jas...@sc... > (o) +1 (603) 374-7120 > > > ------------------------------------------------------------------------------ > RSA(R) Conference 2012 > Save $700 by Nov 18 > Register now > http://p.sf.net/sfu/rsa-sfdev2dev1 > _______________________________________________ > PyMOL-users mailing list (PyM...@li...) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > Archives: http://www.mail-archive.com/pym...@li... > |
From: Justin L. <j.l...@fz...> - 2011-11-10 20:22:58
Attachments:
smime.p7s
|
Hi, That days I simply copied the scripts from the wiki into the repo. After that many scripts got updated in the wiki, so we need to synchronize it again. I am sorry but I lost the interest because I wanted it to be community based not as my own project. Currently the repo is set to be open for any commit. Of course this has know security implications but doesn't need selected commiters. If we would select one or some trusted commiter we could do it on github in a nice way. The main repo could be closed to commit access for the trusted ones. If someone wants to add/modify something the main repo can be forked, modified and request pull (http://help.github.com/fork-a-repo/). justin On 11/10/11 5:45 PM, Troels Emtekær Linnet wrote: > I personally think git hub is a good suggestion. > > And we need you wikiguys (Jason etc. ) to catch the idea and implement > it. :-) > > Security is an issue, and I also believe that you need to control this. > I don't know if github is able to make securities in groups of a owner > of a script and some "super users". > So only a few users can change the script. > Would it possible to have the same user credentials to the github as the > wiki? > > Host / mirror. > As far as I know, one can find each file at a github webpage. > So, maybe the pymolwiki could show that file in a window at the wiki? > > People with github experience should throw in some experience. :-) > > Best > Troels > > > > > Troels Emtekær Linnet > Slotsvej 2 > 4300 Holbæk > Mobil: +45 60210234 > > > > 2011/11/10 Jason Vertrees <jas...@sc... > <mailto:jas...@sc...>> > > Hi Justin, > > > I started this some time ago and also announced it on the mailing > list. But > > it didn't caught much interest. > > The idea didn't get much traction because it was ahead of its time. I > think now is its time. > > The plugin manager that Thomas is creating will be able to aggregate > scripts from various locations and install them on the fly without one > needing to restart PyMOL. Do you mind working with Thomas to help > integrate with the git-hub repo? > > Downloading scripts and running them creates a security hazard. So, we > need to be careful about that. > > Some points to consider for the repository: > * it should mirror or host the code from the PyMOLWiki, not fork it > * be secure from misuse (can anyone commit or just you?) > > What do you think? > > Cheers, > > -- Jason > > -- > Jason Vertrees, PhD > PyMOL Product Manager > Schrodinger, LLC > > (e) Jas...@sc... > <mailto:Jas...@sc...> > (o) +1 (603) 374-7120 <tel:%2B1%20%28603%29%20374-7120> > > ------------------------------------------------------------------------------ > RSA(R) Conference 2012 > Save $700 by Nov 18 > Register now > http://p.sf.net/sfu/rsa-sfdev2dev1 > _______________________________________________ > PyMOL-users mailing list (PyM...@li... > <mailto:PyM...@li...>) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > Archives: http://www.mail-archive.com/pym...@li... > > -- Justin Lecher Institute of Complex Systems ICS-6 Structural Biochemistry Research Centre Juelich 52425 Juelich, Germany phone: +49 2461 61 2117 |
From: Martin H. <ma...@bl...> - 2011-11-11 13:46:22
|
Dear List. When aligning two structures using the PyMOL align command, one gets a final RMS value indicating some kind of "convergence" i would say. Can I somehow access the function for calculating this value directly from the pymol prompt without aligning? Thanks for hints Martin |
From: Thomas H. <sp...@us...> - 2011-11-11 14:00:00
|
Hi Martin, is it the transform=0 argument what you are looking for? http://pymolwiki.org/index.php/Align#PYMOL_API x = cmd.align('foo', 'bar', transform=0) print 'RMSD:', x[0] About the "some kind of refinement": There are arguments "cutoff" and "cycles" that control this behaviour. Cheers, Thomas On 11/11/2011 02:46 PM, Martin Hediger wrote: > Dear List. > When aligning two structures using the PyMOL align command, one gets a > final RMS value indicating some kind of "convergence" i would say. Can I > somehow access the function for calculating this value directly from the > pymol prompt without aligning? > > Thanks for hints > Martin -- Thomas Holder MPI for Developmental Biology |
From: Martin H. <ma...@bl...> - 2011-11-30 10:05:37
|
How does PyMOL calculate the RMSD between two structures where the number of atoms is different? Martin Am 11.11.11 14:59, schrieb Thomas Holder: > Hi Martin, > > is it the transform=0 argument what you are looking for? > > http://pymolwiki.org/index.php/Align#PYMOL_API > > x = cmd.align('foo', 'bar', transform=0) > print 'RMSD:', x[0] > > About the "some kind of refinement": There are arguments "cutoff" and > "cycles" that control this behaviour. > > Cheers, > Thomas > > On 11/11/2011 02:46 PM, Martin Hediger wrote: >> Dear List. >> When aligning two structures using the PyMOL align command, one gets a >> final RMS value indicating some kind of "convergence" i would say. Can I >> somehow access the function for calculating this value directly from the >> pymol prompt without aligning? >> >> Thanks for hints >> Martin > |
From: Tsjerk W. <ts...@gm...> - 2011-11-30 10:19:09
|
Hi Martin, It does an alignment, finding matching pairs of atoms, removing outliers and calculating the RMSD over the remaining matches. Cheers, Tsjerk On Wed, Nov 30, 2011 at 11:05 AM, Martin Hediger <ma...@bl...> wrote: > How does PyMOL calculate the RMSD between two structures where the > number of atoms is different? > Martin > > > > > > > Am 11.11.11 14:59, schrieb Thomas Holder: >> Hi Martin, >> >> is it the transform=0 argument what you are looking for? >> >> http://pymolwiki.org/index.php/Align#PYMOL_API >> >> x = cmd.align('foo', 'bar', transform=0) >> print 'RMSD:', x[0] >> >> About the "some kind of refinement": There are arguments "cutoff" and >> "cycles" that control this behaviour. >> >> Cheers, >> Thomas >> >> On 11/11/2011 02:46 PM, Martin Hediger wrote: >>> Dear List. >>> When aligning two structures using the PyMOL align command, one gets a >>> final RMS value indicating some kind of "convergence" i would say. Can I >>> somehow access the function for calculating this value directly from the >>> pymol prompt without aligning? >>> >>> Thanks for hints >>> Martin >> > > > ------------------------------------------------------------------------------ > All the data continuously generated in your IT infrastructure > contains a definitive record of customers, application performance, > security threats, fraudulent activity, and more. Splunk takes this > data and makes sense of it. IT sense. And common sense. > http://p.sf.net/sfu/splunk-novd2d > _______________________________________________ > 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 |
From: Thomas H. <sp...@us...> - 2011-11-30 10:33:03
|
One should emphasize that this alignment is a *sequence* alignment in case of the "align" command. Cheers, Thomas On 11/30/2011 11:19 AM, Tsjerk Wassenaar wrote: > Hi Martin, > > It does an alignment, finding matching pairs of atoms, removing > outliers and calculating the RMSD over the remaining matches. > > Cheers, > > Tsjerk > > On Wed, Nov 30, 2011 at 11:05 AM, Martin Hediger<ma...@bl...> wrote: >> How does PyMOL calculate the RMSD between two structures where the >> number of atoms is different? >> Martin -- Thomas Holder MPI for Developmental Biology Spemannstr. 35 D-72076 Tübingen |
From: Martin H. <ma...@bl...> - 2011-11-29 09:06:23
|
Is the RMS the same as RMSD? PyMOL writes "RMS" when using align. Martin Am 11.11.11 14:59, schrieb Thomas Holder: > Hi Martin, > > is it the transform=0 argument what you are looking for? > > http://pymolwiki.org/index.php/Align#PYMOL_API > > x = cmd.align('foo', 'bar', transform=0) > print 'RMSD:', x[0] > > About the "some kind of refinement": There are arguments "cutoff" and > "cycles" that control this behaviour. > > Cheers, > Thomas > > On 11/11/2011 02:46 PM, Martin Hediger wrote: >> Dear List. >> When aligning two structures using the PyMOL align command, one gets a >> final RMS value indicating some kind of "convergence" i would say. Can I >> somehow access the function for calculating this value directly from the >> pymol prompt without aligning? >> >> Thanks for hints >> Martin > |
From: Tsjerk W. <ts...@gm...> - 2011-11-29 09:25:32
|
Hi Martin, It should be RMSD indeed. Mind that the final RMSD from align is obtained after optimizing the fit by leaving out outliers. Cheers, Tsjerk On Nov 29, 2011 10:07 AM, "Martin Hediger" <ma...@bl...> wrote: Is the RMS the same as RMSD? PyMOL writes "RMS" when using align. Martin Am 11.11.11 14:59, schrieb Thomas Holder: > Hi Martin, > > is it the transform=0 argument what you are looking for? > > http://pymolwiki.org/i... ------------------------------------------------------------------------------ All the data continuously generated in your IT infrastructure contains a definitive record of customers, application performance, security threats, fraudulent activity, and more. Splunk takes this data and makes sense of it. IT sense. And common sense. http://p.sf.net/sfu/splunk-novd2d _______________________________________________ PyMOL-users mailing list (PyM...@li...urcefo... |