Re: [PyMOL] (no subject)
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Re: [PyMOL] PyMOL 1.6 final release
Hi all,
I am experiencing a problem with the X11 version of 1.6 (MAC user).
The new version is not auto loading the plugins in the repository directory,
which worked fine to me until yesterday, (pymol 1.5.3)
When opening HybridPymol no error messages are displayed, but if I manually
give the commands in the window:
import sys, os
sys.path.append(os.path.expanduser('/MYPATH/Pymol'))
import pymolplugins
Pymol give me this error message:
File /Applications/PyMOLX11Hybrid.app/pymol/modules/pymol/parser.py, line
260, in parse
exec(layer.com2+\n,self.pymol_names,self.pymol_names)
File string, line 1, in module
File /MYPATH/Pymol/pymolplugins/__init__.py, line 65, in module
x__initializePlugins = pmg_tk.PMGApp.initializePlugins
Any idea?
thank you
Gianluigi
Da: Thomas Holder thomas.hol...@schrodinger.com
A: pymol-users pymol-users@lists.sourceforge.net
Inviato: Mercoledì 12 Giugno 2013 8:42
Oggetto: [PyMOL] PyMOL 1.6 final release
Greetings,
We are happy to announce the final release of PyMOL v1.6.0.0. Official
PyMOL sponsors can download ready-to-use installers as usual from
http://pymol.org/dsc/ip . The open-source code has been pushed to
sourceforge svn (revision 4030) and a downloadable bz2 source file is
also available from http://sf.net/p/pymol/ .
This release completes the transition to GLSL based real-time rendering.
Apart from that, it includes many fixes and improvements.
Changes in both Incentive and Open-Source:
* Completed OpenGL engine update; improved graphics performance.
* High-speed fonts, indicators, and 2D drawables (menus)
* Support sweep_angle setting with Program Scene Loop Nutate/Rock
* Add bz2 support for reading PDB files
* Add support for width/height units in png command
* New command line argument -y: Exit on error
* Support object=aln argument with alignto command
* VMD plugins have been updated
* New commands: split_chains, mse2met
* Spectrum command enhanced to take color lists like spectrumany
* ANISOU records are now saved if present
* Fixed alignment objects from super do not contain N atoms
* Fixed writing PDB files
* END before ENDMDL (SF-3496006)
* always right justify resn (SF-3539436)
* Fixed crash when loading with connect_mode=2
* Fixed shortcut auto-completion with exact prefixes
* Feedback fixes
* Fixed leading whitespace parsing in LITERAL parsing mode
* Fixed reading last ANISOU record from PDB file
* Surface lighting was enhanced/smoothed
* Fixed Scripts ending on pymol.py
* Cealign alignment object: support for multiple alignments
Changes in Incentive only:
* Presets for coloring by representation
* Settings
* Most settings are now documented in the Settings Edit All GUI
* Tk Settings Edit All GUI refactored to allow window resizing
and mouse wheel scrolling
* Iterate and alter have improved performance
* Morphing updates
* A generate morph
* Multi-state morphs
* ramps in C (color) menu
* Arbitrary object-level and atom-level properties
* Mouse wheel scrolls object-menu-panel and other scrollable widgets
* Spectrum command enhanced to take the new properties as expression
* Better tracking of hydrogens when editing with the Builder
* Add bz2 support for reading PDB/MAE/MOE/... files
We encourage PyMOL sponsors to check out the internal documentation:
http://pymol.org/dsc/dokuwiki/doku.php?id=media:new16
http://pymol.org/dsc/dokuwiki/doku.php?id=properties
http://pymol.org/dsc/dokuwiki/doku.php?id=media:morphing_updates
We welcome any feedback and bug reports.
Cheers,
- The PyMOL Team at Schrödinger
--
Thomas Holder
PyMOL Developer
Schrödinger Contractor
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Re: [PyMOL] PyMOL 1.6 final release
I missed it! Sorry
cheers,
Gianluigi
Da: Thomas Holder thomas.hol...@schrodinger.com
A: Gianluigi Caltabiano chimic...@yahoo.it
Cc: pymol-users pymol-users@lists.sourceforge.net
Inviato: Giovedì 13 Giugno 2013 10:10
Oggetto: Re: [PyMOL] PyMOL 1.6 final release
Hi Gianluigi,
since 1.5.0.6 PyMOL has an integrated Plugin Manager which supersedes
and is incompatible with the script that you are using.
Go to Plugin Plugin Manager Settings and add /MYPATH/Pymol to
the plugin override search path.
Cheers,
Thomas
Gianluigi Caltabiano wrote, On 06/13/13 10:52:
Hi all,
I am experiencing a problem with the X11 version of 1.6 (MAC user).
The new version is not auto loading the plugins in the repository
directory, which worked fine to me until yesterday, (pymol 1.5.3)
When opening HybridPymol no error messages are displayed, but if I
manually give the commands in the window:
import sys, os
sys.path.append(os.path.expanduser('/MYPATH/Pymol'))
import pymolplugins
Pymol give me this error message:
File /Applications/PyMOLX11Hybrid.app/pymol/modules/pymol/parser.py,
line 260, in parse
exec(layer.com2+\n,self.pymol_names,self.pymol_names)
File string, line 1, in module
File /MYPATH/Pymol/pymolplugins/__init__.py, line 65, in module
x__initializePlugins = pmg_tk.PMGApp.initializePlugins
Any idea?
thank you
Gianluigi
--
Thomas Holder
PyMOL Developer
Schrödinger Contractor--
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Re: [PyMOL] Cartoon transparency
You need to create a new object of the part you want transparent and then set that cartoon as transparent (and hide the original cartoon for the selection). G. Da: James Starlight jmsstarli...@gmail.com A: pymol-users pymol-users@lists.sourceforge.net Inviato: Giovedì 6 Giugno 2013 12:36 Oggetto: [PyMOL] Cartoon transparency Dear PyMol users! I want to set transparency on the selected carton region of my protein ( I have closed GFP barell with the chromophore inside it so I'd like set transparency of some beta-shits to make chromophore easily visible ). In PyMol I've selected region corresponded to that Beta-sheets and than used set cartoon_transparency, 0.5, sele unfortunatelly there were no any changes after this :( How I could solve it ? Thanks for help, James -- How ServiceNow helps IT people transform IT departments: 1. A cloud service to automate IT design, transition and operations 2. Dashboards that offer high-level views of enterprise services 3. A single system of record for all IT processes http://p.sf.net/sfu/servicenow-d2d-j ___ 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-- How ServiceNow helps IT people transform IT departments: 1. A cloud service to automate IT design, transition and operations 2. Dashboards that offer high-level views of enterprise services 3. A single system of record for all IT processes http://p.sf.net/sfu/servicenow-d2d-j___ 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] Transparency of VASCo surfaces
Hi all, I often use VASCo surfaces and I am experiencing a strange behaviour on transparency settings as VASCo surfaces do not respond to: set transparency, value, object Not from the command line, not from the plugin itself. Pymol's surfaces get transparent but not the object corresponding to VASCo surface. I am not sure but I would say it worked to me before. I am on pymol 1.5.0.3 on a Macbook pro 2011 (Pymol Hybrid). Am I missing something? thanks and regards Gianluigi-- Precog is a next-generation analytics platform capable of advanced analytics on semi-structured data. The platform includes APIs for building apps and a phenomenal toolset for data science. Developers can use our toolset for easy data analysis visualization. Get a free account! http://www2.precog.com/precogplatform/slashdotnewsletter___ 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] PyMOL to 3D PDF
Hi Troels, yes I did try many save name.idtf, selection / object / all / * and no output in the command window did appear... thanks anyway, Gianluigi Da: Troels Emtekær Linnet tlin...@gmail.com A: Gianluigi Caltabiano chimic...@yahoo.it Cc: pymol-users@lists.sourceforge.net pymol-users@lists.sourceforge.net Inviato: Mercoledì 13 Marzo 2013 18:26 Oggetto: Re: [PyMOL] PyMOL to 3D PDF Hi Gianluigi. The line goes into LaTeX. I guess it tells something about the center of the molecule, or some light settings. Have you tried: save pymol.idtf, all (or some other selection) The line should come out in the command window, like the get_view command. Jmol automatically write this line in the .tex file it exports. Best Troels 2013/3/13, Gianluigi Caltabiano chimic...@yahoo.it: Very interesting features! I have never tried and was trying to do it, following the tutorial in pymolwiki but at : * Save your molecule to an IDTF file in PyMOL: save pymol.idtf, * PyMOL will print a line that looks like: 3Daac=20.0, 3Droll=0, 3Dc2c=0 0 1, 3Droo=62.45, 3Dcoo=0 0 -62.45 I did not have any line like this, not in the window panel neither in the idtf file. Where should I take this line? I used Hybrid PyMOL 1.5.0.3 on an iMAC. Thanks, Gianluigi Da: Troels Emtekær Linnet tlin...@gmail.com A: Mike Marchywka marchy...@hotmail.com Cc: pymol-users@lists.sourceforge.net Inviato: Mercoledì 13 Marzo 2013 13:01 Oggetto: Re: [PyMOL] PyMOL to 3D PDF Hi Mike. Try the example pdfs at: http://pymolwiki.org/index.php/3d_pdf 1zqa PDF beamer 1zqa PDF Troels Emtekær Linnet Ved kløvermarken 9, 1.th 2300 København S Mobil: +45 60210234 2013/3/13 Mike Marchywka marchy...@hotmail.com From: blaine-moo...@ouhsc.edu To: tlin...@gmail.com Date: Wed, 13 Mar 2013 04:45:59 -0500 CC: pymol-users@lists.sourceforge.net Subject: Re: [PyMOL] PyMOL to 3D PDF PyMOL will also save surfaces in addition to cartoons to vwrl and idtf. Any representation composed of triangular surfaces should work. Thus, PuMOL fails to save labels to vmrl or idtf. This is another major advantage of JMOL over PyMOL at present. When you make 3D PDF how well do they display and manipulate? I thought this would be a nice feature for even 3D plots and IIRC tried it with an example from CRAN's R a while back , I can't remember how it came out in detail but seem to recall the pages took a while to load etc and at the time it was easier to load the data in an app rather than try to publish it that way. for many actual pubs, they provide links in supplementary information section and it may be just as easy to publish a viewer script along with static images for illustration. A plugin would be nice, I always liked CHIME and that worked well on Internet Explorer about 10 years ago. Blaine Mooers Assistant Professor Director Macromolecular Crystallography Lab Member Stephenson Cancer Center Department of Biochemistry and Molecular Biology University of Oklahoma Health Sciences Center S.L. Young Biomedical Research Center Rm. 466 Letter address: P.O. Box 26901, BRC 466 Oklahoma City, OK 73190 Shipping address: 975 NE 10th Street, BRC 466 Oklahoma City, OK 73104-5419 office: (405) 271-8300 lab: (405) 271-8313 fax: (405) 271-3910 e-mail: blaine-moo...@ouhsc.edu Faculty webpage: http://www.oumedicine.com/department-of-biochemistry-and-molecular-biology/faculty/blaine-mooers-ph-d- X-ray lab webpage: http://www.oumedicine.com/department-of-biochemistry-and-molecular-biology/department-facilities/macromolecular-crystallography-laboratory SAXS Links webpage: http://www.oumedicine.com/docs/default-source/ad-biochemistry-workfiles/small-angle-x-ray-scattering-links.html?sfvrsn=0 From: Troels Emtekær Linnet [tlin...@gmail.com] Sent: Wednesday, March 13, 2013 4:19 AM To: Mooers, Blaine H.M. (HSC) Cc: pymol-users@lists.sourceforge.net Subject: Re: [PyMOL] PyMOL to 3D PDF Yeah. That is a cool feature, and is kind of the future of publishing. :-) Or at least, a very powerful tool for teaching. But it is sad that it only have cartoon export. I wish that it could include other representations. For now I use Jmol, which can export the whole representation in the window. I can import small molecules through. Files-Get MOL- And then CAS number or smiles. For proteins I scoop into rcsb.orghttps://urldefense.proofpoint.com/v1/url?u=http://rcsb.orgk=7DHVT22D9IhC0F3WohFMBA%3D%3D%0Ar=ftLbjJYpc5s5JQz9Q6qd7uT7FxPLb4V0aIwH4RJhyZU%3D%0Am=9qhiQpTD7yw1v1CYn82swYWLHkc%2FkmViU2tMT7DUu9c%3D%0As=13813dfb4e17158190791d134f870a433ff7cc614007ae72c21c5a5810c10091, and find the protein in the Jmol online viewer. (Just changing to white back ground). Right click in Jmol window-Export file-Export IDTF 3D model. That saves a .idtf file
Re: [PyMOL] PyMOL to 3D PDF
Very interesting features! I have never tried and was trying to do it, following the tutorial in pymolwiki but at : * Save your molecule to an IDTF file in PyMOL: save pymol.idtf, * PyMOL will print a line that looks like: 3Daac=20.0, 3Droll=0, 3Dc2c=0 0 1, 3Droo=62.45, 3Dcoo=0 0 -62.45 I did not have any line like this, not in the window panel neither in the idtf file. Where should I take this line? I used Hybrid PyMOL 1.5.0.3 on an iMAC. Thanks, Gianluigi Da: Troels Emtekær Linnet tlin...@gmail.com A: Mike Marchywka marchy...@hotmail.com Cc: pymol-users@lists.sourceforge.net Inviato: Mercoledì 13 Marzo 2013 13:01 Oggetto: Re: [PyMOL] PyMOL to 3D PDF Hi Mike. Try the example pdfs at: http://pymolwiki.org/index.php/3d_pdf 1zqa PDF beamer 1zqa PDF Troels Emtekær Linnet Ved kløvermarken 9, 1.th 2300 København S Mobil: +45 60210234 2013/3/13 Mike Marchywka marchy...@hotmail.com From: blaine-moo...@ouhsc.edu To: tlin...@gmail.com Date: Wed, 13 Mar 2013 04:45:59 -0500 CC: pymol-users@lists.sourceforge.net Subject: Re: [PyMOL] PyMOL to 3D PDF PyMOL will also save surfaces in addition to cartoons to vwrl and idtf. Any representation composed of triangular surfaces should work. Thus, PuMOL fails to save labels to vmrl or idtf. This is another major advantage of JMOL over PyMOL at present. When you make 3D PDF how well do they display and manipulate? I thought this would be a nice feature for even 3D plots and IIRC tried it with an example from CRAN's R a while back , I can't remember how it came out in detail but seem to recall the pages took a while to load etc and at the time it was easier to load the data in an app rather than try to publish it that way. for many actual pubs, they provide links in supplementary information section and it may be just as easy to publish a viewer script along with static images for illustration. A plugin would be nice, I always liked CHIME and that worked well on Internet Explorer about 10 years ago. Blaine Mooers Assistant Professor Director Macromolecular Crystallography Lab Member Stephenson Cancer Center Department of Biochemistry and Molecular Biology University of Oklahoma Health Sciences Center S.L. Young Biomedical Research Center Rm. 466 Letter address: P.O. Box 26901, BRC 466 Oklahoma City, OK 73190 Shipping address: 975 NE 10th Street, BRC 466 Oklahoma City, OK 73104-5419 office: (405) 271-8300 lab: (405) 271-8313 fax: (405) 271-3910 e-mail: blaine-moo...@ouhsc.edu Faculty webpage: http://www.oumedicine.com/department-of-biochemistry-and-molecular-biology/faculty/blaine-mooers-ph-d- X-ray lab webpage: http://www.oumedicine.com/department-of-biochemistry-and-molecular-biology/department-facilities/macromolecular-crystallography-laboratory SAXS Links webpage: http://www.oumedicine.com/docs/default-source/ad-biochemistry-workfiles/small-angle-x-ray-scattering-links.html?sfvrsn=0 From: Troels Emtekær Linnet [tlin...@gmail.com] Sent: Wednesday, March 13, 2013 4:19 AM To: Mooers, Blaine H.M. (HSC) Cc: pymol-users@lists.sourceforge.net Subject: Re: [PyMOL] PyMOL to 3D PDF Yeah. That is a cool feature, and is kind of the future of publishing. :-) Or at least, a very powerful tool for teaching. But it is sad that it only have cartoon export. I wish that it could include other representations. For now I use Jmol, which can export the whole representation in the window. I can import small molecules through. Files-Get MOL- And then CAS number or smiles. For proteins I scoop into rcsb.orghttps://urldefense.proofpoint.com/v1/url?u=http://rcsb.orgk=7DHVT22D9IhC0F3WohFMBA%3D%3D%0Ar=ftLbjJYpc5s5JQz9Q6qd7uT7FxPLb4V0aIwH4RJhyZU%3D%0Am=9qhiQpTD7yw1v1CYn82swYWLHkc%2FkmViU2tMT7DUu9c%3D%0As=13813dfb4e17158190791d134f870a433ff7cc614007ae72c21c5a5810c10091, and find the protein in the Jmol online viewer. (Just changing to white back ground). Right click in Jmol window-Export file-Export IDTF 3D model. That saves a .idtf file, and a .tex file ready for LaTeX. Rename the .idtf file, so it only ends on .idtf and not: filename.xyz.idtf Simpy converting the .idtf to .u3d as instructed in, http://www.pymolwiki.org/index.php/3d_pdfhttps://urldefense.proofpoint.com/v1/url?u=http://www.pymolwiki.org/index.php/3d_pdfk=7DHVT22D9IhC0F3WohFMBA%3D%3D%0Ar=ftLbjJYpc5s5JQz9Q6qd7uT7FxPLb4V0aIwH4RJhyZU%3D%0Am=9qhiQpTD7yw1v1CYn82swYWLHkc%2FkmViU2tMT7DUu9c%3D%0As=25a32bf64cd6f0227c7a8a73361f42721f9a6a377010deef4b50acdb49f29ccd) and you are ready to go from the given .tex file. (Removing the last looong comment section.) With a little practice, it only takes 3 min, to have 3d implementation of your molecule in teaching material / beamer presentation. I wish that could be implemented in PyMOL, and I have been looking for a wish list, but I don't know where
Re: [PyMOL] Memory not released after load and delete of structure
The suspension of undo doesn't have any effect on my accumulation of GB when working with Hybrid PyMol... Gianluigi Da: Thomas Holder thomas.hol...@schrodinger.com A: pymol-users@lists.sourceforge.net Inviato: Venerdì 21 Dicembre 2012 17:31 Oggetto: Re: [PyMOL] Memory not released after load and delete of structure Hi Gianluigi and Martin, thanks for reporting, this is a serious issue and we are looking into it. As far as we can reproduce, it's related to the undo feature. Adding this to your scripts should help: cmd.set(suspend_undo, 1) Cheers, Thomas On Dec 21, 2012, at 9:53 AM, Gianluigi Caltabiano chimic...@yahoo.it wrote: I have the same problem since pymol 1.5, mainly with the hybrid (I can reach 10GB of ram memory with relatively small sessions). I'm on MAC OS 10.7.5 and pymol version 1.5.0.3. I had to renounce working with Hybrid unless I really need some plug-in. Gianluigi Da: Jason Vertrees jason.vertr...@schrodinger.com A: Martin Hediger ma@bluewin.ch Cc: pymol-users@lists.sourceforge.net pymol-users@lists.sourceforge.net Inviato: Giovedì 20 Dicembre 2012 17:05 Oggetto: Re: [PyMOL] Memory not released after load and delete of structure Martin, That sounds like a memory leak in v1.3. Can you try a newer version of PyMOL and let us know if it still happens? We've fixed lots of bugs since v1.3. Also, is your script simply iterating over structures and deleting them when done? You sure you're not missing a cleanup step somewhere? (Any chance we can see the script or a stub of it?) Cheers, -- Jason On Fri, Dec 21, 2012 at 3:17 AM, Martin Hediger ma@bluewin.ch wrote: Hi Jason, I'm using PyMOL 1.3. Best regards Martin On 20.12.12 15:53, Jason Vertrees wrote: Hi Martin, Which version of PyMOL are you using? Cheers, -- Jason On Fri, Dec 21, 2012 at 1:37 AM, Martin Hediger ma@bluewin.ch wrote: Dear PyMOL users In a directory are PDB files of combined size equal to around 3MB. When I load all files into PyMOL, I observe that the required RAM of PyMOL (MacOS X 10.6) increases by roughly this amount. When I delete all objects, the RAM requirement remains the same and when I then reload all structures, the RAM requirement increases even further. I'm currently using PyMOL to batch process a number of files where a structure is loaded, modified and then deleted again from the objects list. This then results in RAM requirements of over 1GB and together with other applications, I run out of memory. Is there a way I can prevent PyMOL from behaving this way? Best regards and thanks for any help Martin -- Jason Vertrees, PhD Director of Core Modeling Product Management Schrödinger, Inc. (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- Thomas Holder PyMOL Developer Schrödinger Contractor -- LogMeIn Rescue: Anywhere, Anytime Remote support for IT. Free Trial Remotely access PCs and mobile devices and provide instant support Improve your efficiency, and focus on delivering more value-add services Discover what IT Professionals Know. Rescue delivers http://p.sf.net/sfu/logmein_12329d2d ___ 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-- Master Visual Studio, SharePoint, SQL, ASP.NET, C# 2012, HTML5, CSS, MVC, Windows 8 Apps, JavaScript and much more. Keep your skills current with LearnDevNow - 3,200 step-by-step video tutorials by Microsoft MVPs and experts. SALE $99.99 this month only -- learn more at: http://p.sf.net/sfu/learnmore_122412___ 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] Memory not released after load and delete of structure
I have the same problem since pymol 1.5, mainly with the hybrid (I can reach 10GB of ram memory with relatively small sessions). I'm on MAC OS 10.7.5 and pymol version 1.5.0.3. I had to renounce working with Hybrid unless I really need some plug-in. Gianluigi Da: Jason Vertrees jason.vertr...@schrodinger.com A: Martin Hediger ma@bluewin.ch Cc: pymol-users@lists.sourceforge.net pymol-users@lists.sourceforge.net Inviato: Giovedì 20 Dicembre 2012 17:05 Oggetto: Re: [PyMOL] Memory not released after load and delete of structure Martin, That sounds like a memory leak in v1.3. Can you try a newer version of PyMOL and let us know if it still happens? We've fixed lots of bugs since v1.3. Also, is your script simply iterating over structures and deleting them when done? You sure you're not missing a cleanup step somewhere? (Any chance we can see the script or a stub of it?) Cheers, -- Jason On Fri, Dec 21, 2012 at 3:17 AM, Martin Hediger ma@bluewin.ch wrote: Hi Jason, I'm using PyMOL 1.3. Best regards Martin On 20.12.12 15:53, Jason Vertrees wrote: Hi Martin, Which version of PyMOL are you using? Cheers, -- Jason On Fri, Dec 21, 2012 at 1:37 AM, Martin Hediger ma@bluewin.ch wrote: Dear PyMOL users In a directory are PDB files of combined size equal to around 3MB. When I load all files into PyMOL, I observe that the required RAM of PyMOL (MacOS X 10.6) increases by roughly this amount. When I delete all objects, the RAM requirement remains the same and when I then reload all structures, the RAM requirement increases even further. I'm currently using PyMOL to batch process a number of files where a structure is loaded, modified and then deleted again from the objects list. This then results in RAM requirements of over 1GB and together with other applications, I run out of memory. Is there a way I can prevent PyMOL from behaving this way? Best regards and thanks for any help Martin -- LogMeIn Rescue: Anywhere, Anytime Remote support for IT. Free Trial Remotely access PCs and mobile devices and provide instant support Improve your efficiency, and focus on delivering more value-add services Discover what IT Professionals Know. Rescue delivers http://p.sf.net/sfu/logmein_12329d2d ___ 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 Product Management Schrödinger, Inc. (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- LogMeIn Rescue: Anywhere, Anytime Remote support for IT. Free Trial Remotely access PCs and mobile devices and provide instant support Improve your efficiency, and focus on delivering more value-add services Discover what IT Professionals Know. Rescue delivers http://p.sf.net/sfu/logmein_12329d2d ___ 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-- LogMeIn Rescue: Anywhere, Anytime Remote support for IT. Free Trial Remotely access PCs and mobile devices and provide instant support Improve your efficiency, and focus on delivering more value-add services Discover what IT Professionals Know. Rescue delivers http://p.sf.net/sfu/logmein_12329d2d___ 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] Info graphical cards
Dear PyMOLers, I am going to buy a new PC and want to make sure no issues come with the graphical card and PyMOL. The PC will run on Ubuntu 11.10 on a Intel Core i5 2400 vPro. The card will be NVIDIAGeForceGTX 560 Ti Does anybody had any issues with this card? cheers Gianluigi-- Keep Your Developer Skills Current with LearnDevNow! The most comprehensive online learning library for Microsoft developers is just $99.99! Visual Studio, SharePoint, SQL - plus HTML5, CSS3, MVC3, Metro Style Apps, more. Free future releases when you subscribe now! http://p.sf.net/sfu/learndevnow-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] APBS-electrostatics
Hi everybody, I am trying to use the electrostatic wizard to read some .dx file I made. It always worked..since I up-graded to pymol 1.0. Now it doesn't work ( I have already checked the modification in __init__.py file, it's fine). The message it give to me is: Traceback (most recent call last): File C:\Archivos de programa\DeLano Scientific\PyMOL/modules\pymol\parser.py, line 251, in parse self.result=apply(layer.kw[0],layer.args,layer.kw_args) File C:\Archivos de programa\DeLano Scientific\PyMOL/modules\pymol\wizarding.py, line 86, in wizard r = _wizard(name,arg,kwd,0) File C:\Archivos de programa\DeLano Scientific\PyMOL/modules\pymol\wizarding.py, line 45, in _wizard wiz = apply(getattr(mod_obj,oname),arg,kwd) TypeError: __init__() got an unexpected keyword argument '_self' Thank you for your help Gianluigi Caltabiano - - L'email della prossima generazione? Puoi averla con la nuova Yahoo! Mail
Re: [PyMOL] APBS surface
YesI have already done as wrote My question iswhat if I up load ligand surface with receptor structure? Will it, as I think, shows me the potential of ligand on the receptor surface (giving me as sort of negative of ligand surface on receptor's)??? Thank for your answer, Gianluigi Caltabiano Lab of Computational Medicine, BioStatistic Dept. UAB, Universitat Autonoma de Barcelona Spain - Messaggio originale - Da: Mike Summers summ...@hhmi.umbc.edu A: Gianluigi Caltabiano chimic...@yahoo.it Inviato: Martedì 27 marzo 2007, 20:14:37 Oggetto: Re: [PyMOL] APBS surface You need to create individual proteins and then create maps for the individual protein; e.g, create A,(structure and residues_of_A_only) Mike On Tue, Mar 27, 2007 at 01:35:56PM +, Gianluigi Caltabiano wrote: Hi everyone, I am working with a protein-protein complex and I have calculated for each protein, let's say A and B, apbs electrostatic surfaces. Everything works fine. My question is: I have uploaded the structure of protein A and the surface of protein B. What it shows to me is a blank surface for most of the protein A but the part where protein B interact whit it. I think, but I would have confimations, that I am, in some way, projecting potential values of protein's surface B on the surface of protein A, like having a negative of the B interactions. It seems it works like this since I know both rotein's interacting residues and now I am facing interacting patch of residues from protein B on their counnter part on protein A. Am I wrong? Thank for your answer, in advance, Gianluigi Caltabiano Lab of Computational Medicine, BioStatistic Dept. UAB, Universitat Autonoma de Barcelona Spain ___ L'email della prossima generazione? Puoi averla con la nuova Yahoo! Mail: http://it.docs.yahoo.com/nowyoucan.html - Take Surveys. Earn Cash. Influence the Future of IT Join SourceForge.net's Techsay panel and you'll get the chance to share your opinions on IT business topics through brief surveys-and earn cash http://www.techsay.com/default.php?page=join.phpp=sourceforgeCID=DEVDEV ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users -- * Michael F. Summers Department of Chemistry and Biochemistry and Howard Hughes Medical Institute University of Maryland Baltimore County 1000 Hilltop Circle Baltimore, MD 21250 Phone: (410)-455-2527 FAX: (410)-455-1174 Email: summ...@hhmi.umbc.edu Web: www.hhmi.umbc.edu ___ L'email della prossima generazione? Puoi averla con la nuova Yahoo! Mail: http://it.docs.yahoo.com/nowyoucan.html
Re: [PyMOL] APBS surface
OK...it's as I thought. That is uploading the wrong structure it shows me the map from the ligand but on receptors VdW surface. Thanks all, Gianluigi Caltabiano Lab of Computational Medicine, BioStatistic Dept. UAB, Universitat Autonoma de Barcelona Spain - Messaggio originale - Da: Michael Lerner mgler...@gmail.com A: Gianluigi Caltabiano chimic...@yahoo.it Cc: pymol-users@lists.sourceforge.net Inviato: Lunedì 2 aprile 2007, 15:40:24 Oggetto: Re: [PyMOL] APBS surface PyMOL doesn't know where the electrostatic potential map comes from. If you load up a map and a structure, it will show the potential from that map on that structure. On 4/2/07, Gianluigi Caltabiano chimic...@yahoo.it wrote: YesI have already done as wrote My question iswhat if I up load ligand surface with receptor structure? Will it, as I think, shows me the potential of ligand on the receptor surface (giving me as sort of negative of ligand surface on receptor's)??? Thank for your answer, Gianluigi Caltabiano Lab of Computational Medicine, BioStatistic Dept. UAB, Universitat Autonoma de Barcelona Spain - Messaggio originale - Da: Mike Summers summ...@hhmi.umbc.edu A: Gianluigi Caltabiano chimic...@yahoo.it Inviato: Martedì 27 marzo 2007, 20:14:37 Oggetto: Re: [PyMOL] APBS surface You need to create individual proteins and then create maps for the individual protein; e.g, create A,(structure and residues_of_A_only) Mike On Tue, Mar 27, 2007 at 01:35:56PM +, Gianluigi Caltabiano wrote: Hi everyone, I am working with a protein-protein complex and I have calculated for each protein, let's say A and B, apbs electrostatic surfaces. Everything works fine. My question is: I have uploaded the structure of protein A and the surface of protein B. What it shows to me is a blank surface for most of the protein A but the part where protein B interact whit it. I think, but I would have confimations, that I am, in some way, projecting potential values of protein's surface B on the surface of protein A, like having a negative of the B interactions. It seems it works like this since I know both rotein's interacting residues and now I am facing interacting patch of residues from protein B on their counnter part on protein A. Am I wrong? Thank for your answer, in advance, Gianluigi Caltabiano Lab of Computational Medicine, BioStatistic Dept. UAB, Universitat Autonoma de Barcelona Spain ___ L'email della prossima generazione? Puoi averla con la nuova Yahoo! Mail: http://it.docs.yahoo.com/nowyoucan.html - Take Surveys. Earn Cash. Influence the Future of IT Join SourceForge.net's Techsay panel and you'll get the chance to share your opinions on IT business topics through brief surveys-and earn cash http://www.techsay.com/default.php?page=join.phpp=sourceforgeCID=DEVDEV ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users -- * Michael F. Summers Department of Chemistry and Biochemistry and Howard Hughes Medical Institute University of Maryland Baltimore County 1000 Hilltop Circle Baltimore, MD 21250 Phone: (410)-455-2527 FAX: (410)-455-1174 Email: summ...@hhmi.umbc.edu Web: www.hhmi.umbc.edu L'email della prossima generazione? Puoi averla con la nuova Yahoo! Mail - Take Surveys. Earn Cash. Influence the Future of IT Join SourceForge.net's Techsay panel and you'll get the chance to share your opinions on IT business topics through brief surveys-and earn cash http://www.techsay.com/default.php?page=join.phpp=sourceforgeCID=DEVDEV ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users -- Biophysics Graduate Student Carlson Lab, University of Michigan http://www.umich.edu/~mlerner http://lernerclan.net ___ L'email della prossima generazione? Puoi averla con la nuova Yahoo! Mail: http://it.docs.yahoo.com/nowyoucan.html
[PyMOL] APBS surface
Hi everyone, I am working with a protein-protein complex and I have calculated for each protein, let's say A and B, apbs electrostatic surfaces. Everything works fine. My question is: I have uploaded the structure of protein A and the surface of protein B. What it shows to me is a blank surface for most of the protein A but the part where protein B interact whit it. I think, but I would have confimations, that I am, in some way, projecting potential values of protein's surface B on the surface of protein A, like having a negative of the B interactions. It seems it works like this since I know both rotein's interacting residues and now I am facing interacting patch of residues from protein B on their counnter part on protein A. Am I wrong? Thank for your answer, in advance, Gianluigi Caltabiano Lab of Computational Medicine, BioStatistic Dept. UAB, Universitat Autonoma de Barcelona Spain ___ L'email della prossima generazione? Puoi averla con la nuova Yahoo! Mail: http://it.docs.yahoo.com/nowyoucan.html
