Re: [PyMOL] Session scene compatibility with MacPymol?
For what it's worth, for teaching/training (and general research use), I've
always recommended using pml scripts instead of pse sessions. Turning on
logging can help with tracking what should end up going into the pml.
It's a little more work, and requires a little more forethought - but it's
also something that essentially never has issues with different PyMOL
versions. If anyone's curious, the only one I ran into was when PyMOL
changed how density maps were interpreted ("just load this block of density
over this region" to "treat this density as a seed for symmetry
expansions") around the 1.4 -> 1.5 transition.
Best,
Pete
On Fri, Sep 9, 2016 at 8:53 AM, Paul Paukstelis
wrote:
> Jared,
>
> Thanks for the input. I'll suggest it to my students. Unfortunately, many
> don't have Macs, and some are dependent on using our departmental computer
> labs (Windows) and are therefore stuck with the educational build.
>
> I wonder if there are plans to update the educational version to allow
> backward scene compatibility? Not having that is a real pain for incentive
> users wanting to use mol. vis. for instruction purposes (having to recreate
> all the scenes!)
>
> Also, it seems strange to have an option to export a pse to an older
> version, but not have it actually be compatible with that older version!
>
> --paul
>
> On 09/08/2016 03:10 PM, Sampson, Jared M. wrote:
>
> Hi Paul -
>
> I'm a little late on this thread, but thought I'd add my 2¢. Probably the
> easiest way get around this issue (as you realize) is probably to save a
> 1.7.4.5-compatible PSE file. But, for the adventurous, there is another
> way:
>
> With a small effort (and the willingness to use the command line), your
> students with Macs can replace the older Educational build of MacPyMOL with
> a current version of Open Source PyMOL for free using the command line
> package manager, Homebrew
> wrote:
>
> Are there known session issues with MacPymol? I've saved a session for
> my students to look at using my linux incentive linux build and tried
> various session compatibility settings (1.6, 1.74, 1.76) but in all
> cases the preset scenes I've saved in the session are not loaded when
> the session is opened in MacPymol (educational version 1.7.6 I believe).
>
> Thanks,
>
> --paul
>
>
> --
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Re: [PyMOL] no module named multiarray -- autodock plugin
Blake, From the stack trace you posted, it looks like the import that needs to be changed is in /usr/share/pyshared/numpy/core/__init__.py , not autodock.py . But before changing things there, it might be worth checking from the python interpreter (aka if import multiarray throws ImportError, does from numpy.core import multiarray?). Pete Blake Mertz wrote: Pete, Thanks for the quick reply. I'm not sure how to incorporate that into the autodock plugin, because it doesn't specifically call multiarray (at least I can't find an occurrence of it in autodock.py). The plugin initially calls numpy with from import numpy *, which should enable me to use multiarray, since it is part of numpy. I'm not well-versed in python, so I could be off, but after changing the line in autodock.py to your suggestion and re-installing the plugin, I get the same error message. Blake On Tue, Jan 28, 2014 at 4:02 PM, Pete Meyer pame...@mcw.edu wrote: Hi Blake, I haven't used the autodoc plugin, but from your stack trace (and a quick check of the numpy install on my system) you may be able to resolve this by changing the import multiarray statement to from numpy.core import multiarray. Hope this helps, Pete Blake Mertz wrote: Hello, I came across a short thread started by James Starlight last month (December) which was not resolved, and I have been having the same issue. I upgraded to v1.6 in December, and since then am unable to load the autodock plugin. When I go to import autodock.py, I get the following error: Unable to initialize plugin 'autodock_plugin' (pmg_tk.startup.autodock_plugin). parser: matching files: autodock.py autodock.pyc PyMOLimport autodock.py Traceback (most recent call last): File /usr/lib/python2.7/dist-packages/pymol/parser.py, line 260, in parse exec(layer.com2+\n,self.pymol_names,self.pymol_names) File string, line 1, in module File autodock.py, line 48, in module from numpy import * File /usr/share/pyshared/numpy/__init__.py, line 137, in module import add_newdocs File /usr/share/pyshared/numpy/add_newdocs.py, line 9, in module from numpy.lib import add_newdoc File /usr/share/pyshared/numpy/lib/__init__.py, line 4, in module from type_check import * File /usr/share/pyshared/numpy/lib/type_check.py, line 8, in module import numpy.core.numeric as _nx File /usr/share/pyshared/numpy/core/__init__.py, line 5, in module import multiarray ImportError: No module named multiarray After searching online, it sounds to me like this is a combination issue -- often with Debian users (which is what I am using) there are issues importing numpy. But when I execute python from the shell and import numpy, I get no errors: blake@NEI-GPU:/tmp$ python Python 2.7.6 (default, Jan 11 2014, 14:34:26) [GCC 4.8.2] on linux2 Type help, copyright, credits or license for more information. import numpy So I don't know if there is also an issue with pymol. I would greatly appreciate any help from the community, because Daniel Seeliger's plugin is orders of magnitude better than autodocktools, and I don't want to contemplate going back to the dark ages of analyzing my docking results Blake -- WatchGuard Dimension instantly turns raw network data into actionable security intelligence. It gives you real-time visual feedback on key security issues and trends. Skip the complicated setup - simply import a virtual appliance and go from zero to informed in seconds. http://pubads.g.doubleclick.net/gampad/clk?id=123612991; iu=/4140/ostg.clktrk ___ 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 -- WatchGuard Dimension instantly turns raw network data into actionable security intelligence. It gives you real-time visual feedback on key security issues and trends. Skip the complicated setup - simply import a virtual appliance and go from zero to informed in seconds. http://pubads.g.doubleclick.net/gampad/clk?id=123612991iu=/4140/ostg.clktrk ___ 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] no module named multiarray -- autodock plugin
Hi Blake, I haven't used the autodoc plugin, but from your stack trace (and a quick check of the numpy install on my system) you may be able to resolve this by changing the import multiarray statement to from numpy.core import multiarray. Hope this helps, Pete Blake Mertz wrote: Hello, I came across a short thread started by James Starlight last month (December) which was not resolved, and I have been having the same issue. I upgraded to v1.6 in December, and since then am unable to load the autodock plugin. When I go to import autodock.py, I get the following error: Unable to initialize plugin 'autodock_plugin' (pmg_tk.startup.autodock_plugin). parser: matching files: autodock.py autodock.pyc PyMOLimport autodock.py Traceback (most recent call last): File /usr/lib/python2.7/dist-packages/pymol/parser.py, line 260, in parse exec(layer.com2+\n,self.pymol_names,self.pymol_names) File string, line 1, in module File autodock.py, line 48, in module from numpy import * File /usr/share/pyshared/numpy/__init__.py, line 137, in module import add_newdocs File /usr/share/pyshared/numpy/add_newdocs.py, line 9, in module from numpy.lib import add_newdoc File /usr/share/pyshared/numpy/lib/__init__.py, line 4, in module from type_check import * File /usr/share/pyshared/numpy/lib/type_check.py, line 8, in module import numpy.core.numeric as _nx File /usr/share/pyshared/numpy/core/__init__.py, line 5, in module import multiarray ImportError: No module named multiarray After searching online, it sounds to me like this is a combination issue -- often with Debian users (which is what I am using) there are issues importing numpy. But when I execute python from the shell and import numpy, I get no errors: blake@NEI-GPU:/tmp$ python Python 2.7.6 (default, Jan 11 2014, 14:34:26) [GCC 4.8.2] on linux2 Type help, copyright, credits or license for more information. import numpy So I don't know if there is also an issue with pymol. I would greatly appreciate any help from the community, because Daniel Seeliger's plugin is orders of magnitude better than autodocktools, and I don't want to contemplate going back to the dark ages of analyzing my docking results Blake -- WatchGuard Dimension instantly turns raw network data into actionable security intelligence. It gives you real-time visual feedback on key security issues and trends. Skip the complicated setup - simply import a virtual appliance and go from zero to informed in seconds. http://pubads.g.doubleclick.net/gampad/clk?id=123612991iu=/4140/ostg.clktrk ___ 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 -- WatchGuard Dimension instantly turns raw network data into actionable security intelligence. It gives you real-time visual feedback on key security issues and trends. Skip the complicated setup - simply import a virtual appliance and go from zero to informed in seconds. http://pubads.g.doubleclick.net/gampad/clk?id=123612991iu=/4140/ostg.clktrk ___ 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] loadDir script
Hi James, Assuming your going from the pymol wiki loadDir script; you'd need to change glob(c) loop (sort the list in your preferred order before the loop, rather than using the result list unmodified). If I'm understanding your problem correctly (numbered pdb files being loaded as 1.pdb, 100.pdb, 2.pdb ... instead of 1.pdb, 2.pdb, ... 100.pdb) it might be easier rename your pdb files so that the default string sorting from glob matches the numerical order you want. Using the same example, the filenames would change to 001.pdb, 002.pdb, ... 100.pdb. Pete James Starlight wrote: Dear PyMol users! I've forced with the problem of the loading of the my structural ensemble (pdb files of the protein listed as 1.pdb 2.pdb 3.pdb ..;. 100.pdb) into pymol via loadDir.pml script. In particular after loading of my ensemble in the right contex pymol's window I want to preserve structural order according to the pdb's names ( so that structures were listed in order from 1 to the 100.pdbs but not in the random (mixed) order). What additions to the loadDir script should I do to make such ordering ? James -- Own the Future-Intel(R) Level Up Game Demo Contest 2013 Rise to greatness in Intel's independent game demo contest. Compete for recognition, cash, and the chance to get your game on Steam. $5K grand prize plus 10 genre and skill prizes. Submit your demo by 6/6/13. http://altfarm.mediaplex.com/ad/ck/12124-176961-30367-2 ___ 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 -- Minimize network downtime and maximize team effectiveness. Reduce network management and security costs.Learn how to hire the most talented Cisco Certified professionals. Visit the Employer Resources Portal http://www.cisco.com/web/learning/employer_resources/index.html ___ 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] Newbie question: launch PyMOL from a link
I suspect this depends on the browser you're using. If you're serving the PDB files with an appropriate MIME-type, and the browser is configured to open files of those types with pymol, then things should work. That said, going through pymol through a web interface seems like it might be more complications than it's worth. Pete David García Aristegui wrote: Hello, i have a simple PHP web interface with PDB structures... Do you know if is possible to launch PyMOL (Linux) when we click in the link of a PDB structure, with this PDB loaded? I'm unable to find a recipe to do launch PyMOL this way. Thank you very much for your help, best regards. David. -- Everyone hates slow websites. So do we. Make your web apps faster with AppDynamics Download AppDynamics Lite for free today: http://p.sf.net/sfu/appdyn_d2d_mar ___ 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 -- Everyone hates slow websites. So do we. Make your web apps faster with AppDynamics Download AppDynamics Lite for free today: http://p.sf.net/sfu/appdyn_d2d_mar ___ 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] ccp4 map sigma setting
Unless the values have changed since I last checked the documentations, by default pymol contours maps at 1.0 sigma and coot defaults to 1.5 sigma (for non-difference maps). Pete Yarrow Madrona wrote: Hi, When I display ccp4 maps in pymol they look a bit larger than I am used to seeing in coot for a given sigma setting. Is it common for users to increase the sigma setting when displaying maps in pymol? -- Everyone hates slow websites. So do we. Make your web apps faster with AppDynamics Download AppDynamics Lite for free today: http://p.sf.net/sfu/appdyn_d2d_feb ___ 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] Problem Opening Session File
The handling of density maps changed with (I believe) version 1.5 - earlier versions would just load the map as given, later ones appear to try to do symmetry expansion (even if the map isn't covering the ASU). I've seen this result in a similar error message when loading session files (with electron density, created in 1.4) with 1.5. My solution has been to stick with 1.4. However, I don't generally use multi-state session files, so I don't know if the electron density problem is related to the multi-state problem or not. Pete Mike Feldkamp wrote: I created a session file with Pymol Version 1.5.0.4 that I am unable to open up on my laptop which is running 1.2r5pre. I am able to see the first state but all of the other remaining states are lost. I haven't had opening session files with saved states in the past so I do not suspect it is a issue of compatibility between versions. The one difference that I think is causing the problem is that the session contains an electron density map that does not appear to save along with the session. Below is the message that I receive from when I go to the state containing the density map. Has anyone else had this issue and been able to resolve it? If so how? This Executable Build integrates and extends Open-Source PyMOL 1.2r3pre.Warning: This session was created with a newer version of PyMOL (15.04).Warning: Some content may not load completely.ExectiveSetSession-Error: after names.ExectiveSetSession-Warning: restore may be incomplete.ObjectMeshUpdate-Error: map 'Density' has been deleted. Thanks,Michael -- Master SQL Server Development, Administration, T-SQL, SSAS, SSIS, SSRS and more. Get SQL Server skills now (including 2012) with LearnDevNow - 200+ hours of 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_122512 ___ 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 SQL Server Development, Administration, T-SQL, SSAS, SSIS, SSRS and more. Get SQL Server skills now (including 2012) with LearnDevNow - 200+ hours of 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_122512 ___ 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] Normalize ccp4 maps- problem
Hi Vasan, Changing the sampling of the map would require re-calculating it on a different (coarser or finer) grid. This would have only incidental effects on normalizing the map values. Hope this helps, Pete Srinivasan Rengachari wrote: Dear Pymol Users, I am a basic level user of the Pymol. I am trying to make a figure with my ligand showing electron density. In principle, the guide on the pymol wiki works and i get to show the map. But I wanted to lower the sampling of the mesh in the electron density and tried to unset normalizing ccp4 maps before loading the map and the pdb. After this, the isomesh map, mymap.map, 2.0, site, carve=1.6 updates the map but i dont see any electron density mesh on the screen. I request your help regarding this problem. The pymol version is 1.504. Many thanks in anticipation, Vasan -- Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ ___ 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 -- Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ ___ 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] Using cmd.png with ray=False still ray traces the image
It may be worth trying pymol 1.4 (instead of 1.5) - although this shouldn't make a difference, it might provide some more information (you also mentioned that you've got a large scene - depending on composition 1.4 may use less memory than 1.5). You may also want to try using a pml script vs python (start pymol with -q -c your_raytrace_script.pml arguments) and see if that helps, or at least breaks in different ways. Pete João Rodrigues wrote: Hi Jason, I've tried a lot of stuff, thus the renderer=2.. (i installed povray and tried to use it). With the default option the result is the same. cmd.png(default_name+'.png', width, height, dpi, ray=0) Doing what you wrote still causes the renderer to kick in.. I'm a bit out of ideas.. Cheers, João [...] Rodrigues http://nmr.chem.uu.nl/~joao No dia 17 de Abril de 2012 22:33, Jason Vertrees jason.vertr...@schrodinger.commailto:jason.vertr...@schrodinger.com escreveu: João, I'm not sure why this is giving you problems. Why do you have renderer=2? Why not the default? Are you counting primitives? If so, I suggest: cmd.set(ray_default_renderer, 2) # snapshot cmd.png(myFile, width=w, height=h, dpi=d, ray=0) # this will ray trace cmd.png(myFile, width=w, height=h, dpi=d, ray=1) Cheers, -- Jason On Tue, Apr 17, 2012 at 1:21 PM, João Rodrigues anar...@gmail.commailto:anar...@gmail.com wrote: Same result Jason, i also tried =false... No dia 17 de Abr de 2012 20:45, Jason Vertrees jason.vertr...@schrodinger.commailto:jason.vertr...@schrodinger.com escreveu: Hi João, What about cmd.png(default_name+'.png', dpi=300, ray=0) Cheers, -- Jason On Tue, Apr 17, 2012 at 11:18 AM, João Rodrigues anar...@gmail.commailto:anar...@gmail.com wrote: Hello all, I'm using Pymol v1.5 (from fink, so open source version) to trace large scene that I have. To that end, I'm avoiding having PyMOL open and I wrote a small python script to do the rendering for me. All goes well, except this last part (don't mind the obvious variable names): cmd.ray(width, height, renderer=2) cmd.png(default_name+'.png', dpi=300, ray=False) This actually renders my scene twice. I've tried cmd.do and it does the same.. am I missing something or is this not supposed to happen? Thanks and cheers, João [...] Rodrigues http://nmr.chem.uu.nl/~joao -- Better than sec? Nothing is better than sec when it comes to monitoring Big Data applications. Try Boundary one-second resolution app monitoring today. Free. http://p.sf.net/sfu/Boundary-dev2dev ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.netmailto: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 Schrödinger, LLC (e) jason.vertr...@schrodinger.commailto:jason.vertr...@schrodinger.com (o) +1 (603) 374-7120tel:%2B1%20%28603%29%20374-7120 -- Jason Vertrees, PhD PyMOL Product Manager Schrödinger, LLC (e) jason.vertr...@schrodinger.commailto:jason.vertr...@schrodinger.com (o) +1 (603) 374-7120tel:%2B1%20%28603%29%20374-7120 -- Better than sec? Nothing is better than sec when it comes to monitoring Big Data applications. Try Boundary one-second resolution app monitoring today. Free. http://p.sf.net/sfu/Boundary-dev2dev ___ 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] Question about ray tracing, set_view, surface smoothness
Hi Gudrun, But the mesh is black afterwards and not anymore blue. You may want to check your light position, or try a slighter blue. Is there a chance to keep the color and have less dominant lines for the mesh? I'm not artistically skilled enough to know about less dominant lines, but the mesh_width setting can be used to make thinner (or thicker) lines. Is there a chance to view the object in question for example in the XY, YZ plane? Are there somewhere easy rotation matrix available? I tried to bring my object manually into the YZ plane view, for example, but it works only halfhearted. It would be nice to be able to tell pymol in a very easy way which view I would like to see the object. The turn/rotate commands can be used fairly easily for 90 degree turns; but I'm not sure if that's what you're asking about. Pete -- Try before you buy = See our experts in action! 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-dev2 ___ 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] v1.5.0.1: maps and sessions bug
Anyone thinking about upgrading to 1.5 should be aware that there's a bug in loading session (pse) files containing map objects. Loading pse files (I checked ones created with 1.2 or 1.4) deletes these objects and reports an error: ExectiveSetSession-Error: after names.\nExectiveSetSession-Warning: restore may be incomplete. The isomesh/isosurface objects created from the maps aren't deleted, but they're empty (aka not displaying when enabled). Reconstructing the same session from a script didn't show any problems. Pete -- Virtualization Cloud Management Using Capacity Planning Cloud computing makes use of virtualization - but cloud computing also focuses on allowing computing to be delivered as a service. http://www.accelacomm.com/jaw/sfnl/114/51521223/ ___ 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 memory, disk, and CPU usage
I've run into similar situations in the past, although in my case usually due to large maps (a 3.5 MB pdb file, or even a set of them, typically requires less memory than a ~50MB electron density map). In my experience, it's much better to load things from scripts (pml) rather than storing things in session files (pse). I may be remembering incorrectly, but from previous mailing list discussions I believe the higher memory usage for pse files was due to overhead for python de-pickling. You may also want to check your graphics drivers - a friend of mine was having some pymol performance problems that turned out to be driver related. Pete John Ladasky wrote: I'm currently using PyMol 1.4.1 on Ubuntu Linux 11.10. My hardware is fairly up-to-date, an AMD 6-core, 3.2 GHz CPU ,and 4 GB of DDR1200 RAM. My only old hardware is my NVidia 8800 GTS graphics card. I have started to assemble rather large visualizations. I am noticing CPU performance lags, and unexpectedly high memory usage. In my hands, PyMol is behaving like the infamous Flash Player browser plug-in -- hogging memory and CPU cycles (as well as disk space) for no obvious reason. Here's an example. I have superimposed 15 PDB files which are snapshots from GROMACS molecular dynamics simulations. These contain protein molecules in a water box. I admit, the PDB files are pretty large, around 3.5 MB each. Still, 15 x 3.5 MB = 52.5 MB. That should be manageable, I think. Ambitious, but still within reasonable limits. But what is the size of the PyMol session (.pse) file that I built from this stack of PDB files? 234 MB! Why did this bloat up to fully five times the size of the source data (which is already in plain text, and full of white space)? What's more, when I load this 234-MB file into PyMol, the Python interpreter which PyMol invokes grabs a full 1.0 GB of memory. The CPU usage of that Python interpreter (single-core, of course) immediately jumps to around 40% even when I'm not asking PyMol to do anything. After I've worked with PyMol a bit with this file loaded, CPU usage will jump to 100%, and it stays there. Once that happens, the cursor will lag, jitter or freeze, and I can end up selecting unintended menu items. Keep in mind, this is with a completely stationary image in the PyMol Viewer window. I'm looking to reduce all of this overhead. Excluding some water molecules from the source PDB files comes to mind. Perhaps I can find a way to clip my simulation box (I would like to retain the option to visualize any water molecules which actually contact the protein). However, I seem to have more fundamental problems than excess water molecules. Alternately, if there are settings in PyMol that I can adjust to get it to behave, that would be great. Thanks for any advice you may have! -- Virtualization Cloud Management Using Capacity Planning Cloud computing makes use of virtualization - but cloud computing also focuses on allowing computing to be delivered as a service. http://www.accelacomm.com/jaw/sfnl/114/51521223/ ___ 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 1.4 not running on Ubuntu Linux 11.10
Hi John, I don't think you need a re-install. My take on the problem is that using the repositories installs the pymol libraries to the system python (not sure offhand which that is for ubuntu 11.10). But pymol is apparently trying to start up with /usr/bin/env python, which is picking up the python you've got installed in /usr/local. Short version - try edit pymol (probably /usr/bin/pymol) to hard-code the system python. Pete John Ladasky wrote: Hi folks, I just upgraded my Ubuntu Linux installation to 11.10. Of course, this removes obsolete versions of applications. So I had to reinstall PyMol. The Ubuntu Linux 11.10 manifest states that PyMol 1.4.1 is the supported version, and a package file is available. So, I downloaded and (supposedly) installed PyMol 1.4.1 -- first through Ubuntu Software Center, and then through Synaptic Package Manager when Software Center failed (I didn't expect it to to make a difference, but I tried anyway). The way in which PyMol is failing is very simple. When I click on the PyMol icon to start the application, nothing happens. There were no error messages visible in the GUI during the installation, nor when attempting to start the application. So next I tried to run PyMol from a terminal prompt, and here I saw errors: 23:29:55 - pymol Traceback (most recent call last): File string, line 1, in module ImportError: No module named pymol /usr/local/bin/python2.7: No module named pymol This tells me that there's an executable file on my system path named pymol.py, which starts. Then pymol.py tries to import a module, also named pymol (why is the name pymol used twice?), which fails. I'm a bit baffled at this behavior, especially as it comes from a standard package file. Any help you might offer is appreciated. -- Ridiculously easy VDI. With Citrix VDI-in-a-Box, you don't need a complex infrastructure or vast IT resources to deliver seamless, secure access to virtual desktops. With this all-in-one solution, easily deploy virtual desktops for less than the cost of PCs and save 60% on VDI infrastructure costs. Try it free! http://p.sf.net/sfu/Citrix-VDIinabox ___ 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] Electron Density
isomesh [mesh name], [map name], 6.0 Manas Sule wrote: Is there some way to show electron density at 6 sigma and above in pymol especially for metal ions like in Coot? Manas -- 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 (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 organize those .py
Another approach would be appending to sys.path, and loading the scripts with import instead of run. Arne Dieckmann wrote: That is a hot tip. However, can I also specify some path that would tell pymol the location of my scripts? I have a number of scripts that I need to call while already in Pymol and I do not want to type in the complete path every time. Also, copying these scripts to the current working directory is not a really good solution. Cheers, Arne On Sep 19, 2011, at 12:48 AM, Thomas Holder wrote: Hi Lina, you can put a .pymolrc file in your home directory, it's a script that PyMOL will read on each startup. You can have it either in PyMOL syntax or as a python script, depending on the file extension. /home/lina/.pymolrc (in PyMOL syntax) /home/lina/.pymolrc.py (in python syntax) http://www.pymolwiki.org/index.php/Pymolrc Then create a directory -- lets say /home/lina/.pymol -- and put the PyMOLWiki scripts there. And in your .pymolrc you put lines like these (PyMOL syntax): run /home/lina/.pymol/Grepsel.py run /home/lina/.pymol/Polarpairs.py run /home/lina/.pymol/Propka.py ... and so on Cheers, Thomas lina wrote, On 09/19/11 07:10: Hi, Just a quick Q: How can I better organize those *.py I mainly obtained from pymol wiki, not those can be installed by the plugins, pymol run in different directory each time. Thanks, -- Best Regards, lina -- Thomas Holder MPI for Developmental Biology Spemannstr. 35 D-72076 Tübingen -- BlackBerryreg; DevCon Americas, Oct. 18-20, San Francisco, CA Learn about the latest advances in developing for the BlackBerryreg; mobile platform with sessions, labs more. See new tools and technologies. Register for BlackBerryreg; DevCon today! http://p.sf.net/sfu/rim-devcon-copy1 ___ 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 -- 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. Business sense. IT sense. Common sense. http://p.sf.net/sfu/splunk-d2dcopy1 ___ 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 -- 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. Business sense. IT sense. Common sense. http://p.sf.net/sfu/splunk-d2dcopy1 ___ 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] saving maps for a presentation
I don't know if there's a way to do this from within pymol, but it's fairly straightforward to do using mapman (from ccp4) - or your favorite map utility. Pete Tatyana Sysoeva wrote: Dear Pymol experts! I am going to make a presentation with running Pymol during it. I would like to show small details (ligand densities) of several ED maps in this presentation. I will have to keep several Pymol instances running due to setup of the presentation to avoid loading big files on the fly. I am worrying that if I open and carve all maps within one of the Pymol instances it will be very resource consuming. That is why I am wondering if there is a way to save the carved ED around the ligands as a volume object and use this for the life presentation instead of the maps? I found a short article named volume and mentioning of the map_new but I could not fine a fuller description of these commands. The main problem is that I am using stereo projection and do not want to render pictures and movies, therefore all view will show up in 3D. I am using Win7 system with the Pymol v1.3. If there is any additional information or details are needed - I am more than happy to provide them! Thank you very much in advance! Cheers, Tanya -- Special Offer -- Download ArcSight Logger for FREE! Finally, a world-class log management solution at an even better price-free! And you'll get a free Love Thy Logs t-shirt when you download Logger. Secure your free ArcSight Logger TODAY! http://p.sf.net/sfu/arcsisghtdev2dev ___ 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] Fetching scripts
Hi, From a security perspective, it seems like the ideas on the wiki page are all related to securing the remote source. It might be worth considering what could be done to minimize how much pymol has to trust the remote source or the network. A few ideas: - Sandboxing would be ideal, but I don't know if there's infrastructure in python to support it. It might be easier to filter fetched scripts to only allow a restricted subset of python functions (the ast library looks like it might make this a bit easier). If a script can't access the network or hard disk, then it doesn't need to be trusted as much. - The wiki doesn't appear to support SSL. So that means trusting the network to get to the wiki correctly, in addition to the wiki itself. I don't have any good ideas for how to work around this one. Pete Michael Lerner wrote: Hi all, I'm considering building in a mechanism for automatically fetching scripts from the PyMOL Wiki. The goal is to allow users to say fetch findSurfaceResidues, type=script findSurfaceResidues doShow=True, cutoff=0.5 The convenience benefits are obvious, especially for new users, and I think that lowering the barrier to script usage will greatly increase both the number of people who use various scripts and the incentive to place scripts on the wiki (especially if the fetch mechanism makes it easy for script authors to provide a citation/DOI/etc.). I've put up a tentative page about this on the wiki (http://pymolwiki.org/index.php/Fetching_scripts), and I'd love comments either via the list, private email or on the wiki, especially about - whether you think it's a good idea - security and validation - options you'd like - implementation issues The plan is to write this as a userland script first. If issues relating to security and validation can be resolved, we'll see if the official builds want to include it. Cheers, -Michael -- 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) -- WhatsUp Gold - Download Free Network Management Software The most intuitive, comprehensive, and cost-effective network management toolset available today. Delivers lowest initial acquisition cost and overall TCO of any competing solution. http://p.sf.net/sfu/whatsupgold-sd ___ 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 segmentation fault
Does anyone have any thoughts?
Two things to try that may or may not help:
1. Check if the problem persists when running pymol in single-threaded
mode (cmd.set('max_threads',1)). libpthread in the trace might
indicate that one of the libraries is having issues with multiple threads.
2. On Kubuntu 8.04.3 LTS x64, I can't reproduce the problem with 1.2
from svn trunk. This is using Tcl/Tk 8.4 (with pymol using it's own
source build of python 2.4.2, which may or may not be relevant); so
installing Tcl/Tk 8.4 instead of 8.5 (source or binary) might help
resolve the problem, or at least eliminate one possible source.
Pete
Here is the backtrace portion from catchsegv:
Backtrace:
/usr/lib/libtcl8.5.so.0[0x7f63977b3eb0]
/usr/lib/libtcl8.5.so.0(Tcl_CreateHashEntry+0x59)[0x7f6397761839]
/usr/lib/libtcl8.4.so.0(Tcl_FindNamespaceVar+0xff)[0x7f6391d8352f]
/usr/lib/libtcl8.4.so.0(TclLookupSimpleVar+0xfb)[0x7f6391d9bf0b]
/usr/lib/libtcl8.4.so.0(TclLookupVar+0xab)[0x7f6391d9b70b]
/usr/lib/libtcl8.4.so.0(Tcl_SetVar2Ex+0x59)[0x7f6391d9c8e9]
/usr/lib/libtcl8.4.so.0(Tcl_SetVar2+0x4f)[0x7f6391d9c80f]
/usr/lib/libBLT.2.4.so.8.4(Blt_Init+0x169)[0x7f6392311859]
/usr/lib/libtcl8.5.so.0[0x7f639777dee6]
/usr/lib/libtcl8.5.so.0[0x7f63977102f1]
/usr/lib/libtcl8.5.so.0[0x7f63977543b8]
/usr/lib/libtcl8.5.so.0(TclObjInterpProcCore+0x110)[0x7f6397796ed0]
/usr/lib/libtcl8.5.so.0[0x7f63977102f1]
/usr/lib/libtcl8.5.so.0[0x7f6397710a5f]
/usr/lib/libtcl8.5.so.0[0x7f63977926d1]
/usr/lib/libtcl8.5.so.0(Tcl_PkgRequireProc+0x9)[0x7f6397792209]
/usr/lib/libtcl8.5.so.0[0x7f6397793192]
/usr/lib/libtcl8.5.so.0[0x7f63977102f1]
/usr/lib/libtcl8.5.so.0(Tcl_EvalObjv+0x43)[0x7f6397710413]
/usr/lib/python2.6/lib-dynload/_tkinter.so[0x7f6398063a32]
/usr/bin/python(PyEval_EvalFrameEx+0x52fd)[0x4a290d]
/usr/bin/python(PyEval_EvalFrameEx+0x5837)[0x4a2e47]
/usr/bin/python(PyEval_EvalFrameEx+0x5837)[0x4a2e47]
/usr/bin/python(PyEval_EvalFrameEx+0x5837)[0x4a2e47]
/usr/bin/python(PyEval_EvalFrameEx+0x5837)[0x4a2e47]
/usr/bin/python(PyEval_EvalCodeEx+0x860)[0x4a40e0]
/usr/bin/python(PyEval_EvalFrameEx+0x4e4f)[0x4a245f]
/usr/bin/python(PyEval_EvalCodeEx+0x860)[0x4a40e0]
/usr/bin/python(PyEval_EvalFrameEx+0x4e4f)[0x4a245f]
/usr/bin/python(PyEval_EvalCodeEx+0x860)[0x4a40e0]
/usr/bin/python[0x52bdf0]
/usr/bin/python(PyObject_Call+0x47)[0x41d6e7]
/usr/bin/python[0x4254ff]
/usr/bin/python(PyObject_Call+0x47)[0x41d6e7]
/usr/bin/python(PyEval_CallObjectWithKeywords+0x43)[0x49c623]
/usr/bin/python[0x49c06f]
/usr/bin/python(PyEval_EvalFrameEx+0x52fd)[0x4a290d]
/usr/bin/python(PyEval_EvalCodeEx+0x860)[0x4a40e0]
/usr/bin/python[0x52bdf0]
/usr/bin/python(PyObject_Call+0x47)[0x41d6e7]
/usr/bin/python[0x4254ff]
/usr/bin/python(PyObject_Call+0x47)[0x41d6e7]
/usr/bin/python(PyEval_CallObjectWithKeywords+0x43)[0x49c623]
/usr/lib/python2.6/lib-dynload/_tkinter.so[0x7f6398061376]
/usr/lib/libtcl8.5.so.0(TclInvokeStringCommand+0x7f)[0x7f639770e80f]
/usr/lib/libtcl8.5.so.0[0x7f63977102f1]
/usr/lib/libtcl8.5.so.0[0x7f63977543b8]
/usr/lib/libtcl8.5.so.0[0x7f63977527b9]
/usr/lib/libtcl8.5.so.0(TclEvalObjEx+0x196)[0x7f6397711706]
/usr/lib/libtk8.5.so.0[0x7f6397a556f6]
/usr/lib/libtcl8.5.so.0[0x7f63977102f1]
/usr/lib/libtcl8.5.so.0(Tcl_EvalObjv+0x43)[0x7f6397710413]
/usr/lib/libtcl8.5.so.0(TclEvalObjEx+0x300)[0x7f6397711870]
/usr/lib/libtcl8.5.so.0[0x7f639779668f]
/usr/lib/libtcl8.5.so.0[0x7f63977102f1]
/usr/lib/libtcl8.5.so.0[0x7f63977543b8]
/usr/lib/libtcl8.5.so.0(TclObjInterpProcCore+0x110)[0x7f6397796ed0]
/usr/lib/libtcl8.5.so.0[0x7f63977102f1]
/usr/lib/libtcl8.5.so.0[0x7f6397710a5f]
/usr/lib/libtk8.5.so.0(Tk_BindEvent+0x890)[0x7f6397a29c90]
/usr/lib/libtk8.5.so.0(TkBindEventProc+0x185)[0x7f6397a2fa35]
/usr/lib/libtk8.5.so.0(Tk_HandleEvent+0x6c0)[0x7f6397a374c0]
/usr/lib/libtk8.5.so.0[0x7f6397a37b48]
/usr/lib/libtcl8.5.so.0(Tcl_ServiceEvent+0x7f)[0x7f639778764f]
/usr/lib/libtcl8.5.so.0(Tcl_DoOneEvent+0x8f)[0x7f63977878ff]
/usr/lib/python2.6/lib-dynload/_tkinter.so[0x7f639805f201]
/usr/bin/python(PyEval_EvalFrameEx+0x52fd)[0x4a290d]
/usr/bin/python(PyEval_EvalCodeEx+0x860)[0x4a40e0]
/usr/bin/python(PyEval_EvalFrameEx+0x4e4f)[0x4a245f]
/usr/bin/python(PyEval_EvalCodeEx+0x860)[0x4a40e0]
/usr/bin/python(PyEval_EvalFrameEx+0x4e4f)[0x4a245f]
/usr/bin/python(PyEval_EvalCodeEx+0x860)[0x4a40e0]
/usr/bin/python[0x52beed]
/usr/bin/python(PyObject_Call+0x47)[0x41d6e7]
/usr/bin/python(PyEval_EvalFrameEx+0x3921)[0x4a0f31]
/usr/bin/python(PyEval_EvalFrameEx+0x5837)[0x4a2e47]
/usr/bin/python(PyEval_EvalFrameEx+0x5837)[0x4a2e47]
/usr/bin/python(PyEval_EvalCodeEx+0x860)[0x4a40e0]
/usr/bin/python[0x52bdf0]
/usr/bin/python(PyObject_Call+0x47)[0x41d6e7]
/usr/bin/python[0x4254ff]
/usr/bin/python(PyObject_Call+0x47)[0x41d6e7]
/usr/bin/python(PyEval_CallObjectWithKeywords+0x43)[0x49c623]
/usr/bin/python[0x4d0c4d]
/lib/libpthread.so.0[0x7f639cf69a04]
/lib/libc.so.6(clone+0x6d)[0x7f639c4317bd]
Thanks,
Ian
Re: [PyMOL] Light Command Details needed
Hi Sean, I ended up using light, [1,5,-100]. I know these are X,Y,Z coordinates, but relative to what origin and in what units? After wasting way too much time, I concluded that the values might be Angstroms relative to the eyes of the current view. In examples I found online, the numbers are small, so this doesn't make much sense. These values are the x,y,z components of the light vector. The units are irrelevant ( [1,1,-1] == [2,2,-2], at least to my eyes judging the output images). I don't believe there's a defined origin, either (it's not a point light source). Pete -- Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day trial. Simplify your report design, integration and deployment - and focus on what you do best, core application coding. Discover what's new with Crystal Reports now. http://p.sf.net/sfu/bobj-july ___ 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] compilation problem with the latest pymol
Looks like you need to install the appropriate python-dev package (or otherwise point setup.py to the appropriate include directory if you build python from source). Vivek Ranjan wrote: I downloaded the latest pymol by using the following command: svn co https://pymol.svn.sourceforge.net/svnroot/pymol/trunk/pymol pymol Then, while running the command python setup.py install, I encountered the following: In file included from layer5/main.h:35, from layer0/Block.c:20: layer0/os_python.h:28:19: error: Python.h: No such file or directory In file included from layer0/Block.c:20: layer5/main.h:45: error: expected ‘)’ before ‘*’ token layer5/main.h:46: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘*’ token error: command 'gcc' failed with exit status 1 Any help ?? Thanks, Vivek -- Crystal Reports - New Free Runtime and 30 Day Trial Check out the new simplified licensing option that enables unlimited royalty-free distribution of the report engine for externally facing server and web deployment. http://p.sf.net/sfu/businessobjects ___ 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 -- Crystal Reports - New Free Runtime and 30 Day Trial Check out the new simplified licensing option that enables unlimited royalty-free distribution of the report engine for externally facing server and web deployment. http://p.sf.net/sfu/businessobjects ___ 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] get color function?
The way I use (which I'm sure could be improved), is to get the color index with iterate sele, print color, followed by print cmd.get_color_index( idx ). This gives you the rgb tuple for the color on 0-1 scale. I'd be curious to know if there's a way to avoid the iterate step, or get the color name (instead of index or rgb values), but haven't had the time to dig into it. Pete Matthew O'Meara wrote: Hi Is there a way I can get the color of a given atom? eg if I do cmd.color( color, sele ) is there a function like gotten_color = cmd.get_color_of_selection( sele ) so that something like assert( gotten_color == color ) or atleast a function to get the color a given atom? Many thanks, Matt -- OpenSolaris 2009.06 is a cutting edge operating system for enterprises looking to deploy the next generation of Solaris that includes the latest innovations from Sun and the OpenSource community. Download a copy and enjoy capabilities such as Networking, Storage and Virtualization. Go to: http://p.sf.net/sfu/opensolaris-get ___ 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 -- OpenSolaris 2009.06 is a cutting edge operating system for enterprises looking to deploy the next generation of Solaris that includes the latest innovations from Sun and the OpenSource community. Download a copy and enjoy capabilities such as Networking, Storage and Virtualization. Go to: http://p.sf.net/sfu/opensolaris-get ___ 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] advice for the novice movie maker
I wouldn't claim it's necessarily the best way, but if I've had decent luck with scripting the transitions (either pymol or python) to generate a set of images. From there, it's fairly easy to encode a movie with ffmpeg or mencoder. But it probably depends on the type of movie you're trying to make. Pete Thomas S. Leyh, Ph. D. wrote: Hello everyone, I'm trying to assess the best way to begin making molecular movies with Pymol. It seems eMovie is higly rated. I understand it is a Pymol plug-in, however I gave this a run on my PC (Vista) only to discover, ultimately through Warren, that that approach won't work, a Mac is required. (This came a surprise since, in in their TRENDS article, the eMovie author's claim that it runs under windows.) I have access to an iMac (duo 2 core, OS 10.5), and I wonder whether this is the preferred path. Further, there is the issue of which Pymol version to downloaded. Finally, is a Pymol build with rigimole required - this is a special (expert) build that requires unix-like, command-line fluency. Thanks a bunch, Tom Leyh -- This SF.net email is sponsored by: High Quality Requirements in a Collaborative Environment. Download a free trial of Rational Requirements Composer Now! http://p.sf.net/sfu/www-ibm-com ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
Re: [PyMOL] map for one molecule
Is it possible to load a map to only cover the molecule and not the complete asymmetric unit? Or is this only possible at the time of creating the map? Yes and no. For displaying a map, if you give a carve option to isomesh or isosurface, it'll only display around a molecule (or other selection). But when you load the map, it's still over the same range (so the display may change to accommodate that). Thanks in advanced, Ariel
Re: [PyMOL] Procedure for adding packages to pymol site-packages?
how would I go about adding a package to the $PYMOL_PATH/ext/.../site-packages w/o screwing up the install? For most packages the mechanism is python setup.py install. Would this work to run this from within pymol? With my usual way of installing pymol is to build most of the dependencies from source, including python. This copy of python gets sym-linked to pymol.python for building pymol (aka pymol.python setup.py build , etc in the pymol source directory) and is only used for running pymol. If you've installed things this way, then pymol.python setup.py install for your package should work, assuming your environmental python environmental variables are kept straight. But this is something I haven't needed to test, so if Warren says it's not possible he's probably found a problem with this approach I missed. Pete
Re: [PyMOL] .phs file open in PyMol
Hi, I have experimental phases/map_coeff's in a .phs file. Can anyone tell me how to most easily get them read read into PyMol to display electron density? I assume I need to convert the file somehow first, I usually use mapman for this utility but don't see an option for .phs files. First, you need to calculate a map. This is a calculation rather than a format conversion (which is why mapman doesn't have an option for this format). Assuming that .phs is a phases formatted file, you can use fsfour to calculate a map (although you'll probably have to convert that phases formatted map to ccp4 or xplor map format). You could also use the CNS or CCP4 packages, although in either case you'll have to convert the reflection file. Pete
Re: [PyMOL] running script on startup
I am trying to fire up a script with pymol -r doit.pml pymol doit.pml should be sufficient (no need for -r). File doit.pml, line 2 select resname SOL Unless the syntax has changed, try 'select resname, SOL'. Does this script work when run from an already started pymol? Pete
Re: [PyMOL] PyMOL crashes under Vista Home Premium Ubuntu 8.04 LTS
with maximum quality. Size of the relevant PyMOL v1.1 file is 100 MB (or 31 MB after reducing objects I do not need for the figure production). If lack of memory is the problem, try loading your scene manually or through a script instead of using a session file. For reasons I don't recall at the moment, pymol uses more memory with a pse file than with the same objects loaded through a script (you could check the list archives for more details if you're curious). PyMOL simply crashes under Windows Vista Home Premium as well as under Ubuntu Linux v8.04 LTS without error report. My dual OS system is a Not sure about windows, but with linux you should get some level of messages by launching from a command prompt instead of an icon. If you're running out of memory, you'll get a core dump message (at least, that the usual symptom on my systems. both OS are 32 bit and therefore to my (limited) knowledge cannot handle more than 2 GB in a single task, RAM limitation might still be an issue You might want to have top running in a different terminal so watch how much memory pymol is trying to use (or is able to use before crashing).
[PyMOL] scripting apbs visualization?
Hi, Does anybody have suggestions for the simplest way to script loading an apbs grid and displaying the molecular surface colored by charge (possibly changing the low/high values as well)? I can do this interactively, but have come up blank trying to script this. Thanks, Pete
