[PyMOL] Segmentation Fault / Bus Error

Hey Folks - I am trying to assign colors via APBS plugin to a surface which fails with a Bus error on Mac and Segfault on Linux. Versions are 1.1r2pre on Linux and Mac, as well as the latest from svn- trunk on Mac as well... The command that actually fails is ramp_new, as I found out by

[PyMOL] select by absolute coordinate

I quickly checked the selection algebra and property selector wiki pages and couldn't find anything related to this. Is it possible e.g. to select all atoms with (absolute) z - coordinates greater than 5A? Best Martin

[PyMOL] running script on startup

Hey folks, I am trying to fire up a script with pymol -r doit.pml PyMOLrun doit.pml,main Traceback (most recent call last): File /sw/lib/pymol-py25/modules/pymol/parser.py, line 334, in parse parsing .run_file(exp_path(layer.args[0]),__main__.__dict__,__main__.__dict__) File

Re: [PyMOL] running script on startup

Am 20.02.2009 um 17:54 schrieb Pete Meyer: I am trying to fire up a script with pymol -r doit.pml pymol doit.pml should be sufficient (no need for -r). Oh ok, without -r it works :-) Best Martin

Re: [PyMOL] System freezes in cause of memory abuse

Am Sonntag, 12. Oktober 2008 schrieb Christian Seifert: Hi! I'm working with big structures and even bigger trajectories. When I try to load a trajectory, pymol takes the full 2GB RAM and freezes my PC (ubuntu 7.10/gnome/core 2 duo/2 GB RAM). The only way out is pulling the plug. :-( My

Re: [PyMOL] protein contact potential

Am Freitag, 5. September 2008 schrieb cortines: would anybody know by which calculations pymol generates the proteins' electrostatic maps? Is there a place where I can read about it? I tried the manual and the wikipymol and could not find it. To my knowledge, this can be (only?) done via the

[PyMOL] Cluster / Cave / Holobench version of PyMol

Hello all, has anybody of you knowledge of efforts to use PyMol on CAVE like setups for 3D visualization? We have a Holobench with a Headtracking System here and I wonder if anybody knows more than I do. The only thing I found is: http://www.gruchalla.org/papers/C4_111_Gruchalla.pdf where

[PyMOL] Keeping PDB ordering

Hi all, is there a simple way to prevent reordering of atoms and insertion of additional TER records by pymol? I have a protein embedded in a bilayer with tip4p water, where this occurs when I delete parts and export the rest of the System. Best wishes Martin

Re: [PyMOL] algorithm for alignment

Am Samstag, 26. Januar 2008 schrieb Lu Lin: Hi, Abhi, You mean save them separately? Is there some way to save them into one file? Thanks!! By default, the save command should save all (visible?) atoms. Should be in documentation of save. Any way you can also make a selection of your two

Re: [PyMOL] best linux distribution to run pymol

Am Freitag, 13. Juli 2007 schrieb Joris Beld: Gruezi Boris, I do not want to start a linux distribution war but we are curious under which distribution pymol is developed/tested and what people generally are using to run pymol (with 3D capability!)?? Thanks a lot for the info. Every recent

[PyMOL] spectral coloring

Hi there, i am trying to map b factors on a surface representation. I am using spectrum b,blue_white_red,mymol and the colors are fine. Is there a way to fine tune the color spectrum, such as with the Midpoint and Offset sliders in vmd? Best Martin

Re: [PyMOL] coloring based on sequence identity

Am Dienstag, 26. Juni 2007 schrieb Eva Vanamee: Hi, I'd like to color a molecule based on its sequence similarity to another molecule. Can this be done in Pymol? If you can quantify similarity in a number you can write it into the b-factors of the atoms and then color it by them. Best

[PyMOL] dimension lock feature

Hi there, just asking if anyone here would need it too? When using the drag tool to move/rotate tool, what about some buttons to constrain movement to specific dimensions. e.g. only rotate arond z-axis, move in x-y-plane and so on. Secondly, a rotation in fixed segments of x degrees, or

[PyMOL] mutagenesis script

Hi there, does anybody of you has an idea, if the mutagenesis stuff is available for use inside scripts too? I wanna load a pdb, mutate a resid and save the resulting pdb via commandline. The only thing I found was modifying atoms, when I searched via help and also checked the wiki, i hope

Re: [PyMOL] PyMOL compilation from source

Am Samstag, 28. April 2007 schrieb Michael Kluge: Would that be feasable? Oh sorry, i overlooked the ia64 in your gcc line. I have no idea how much IA64 SuSE, differs from the others. OpenSuSE is only provided for i586 and x86_64, not Itanium. But if you want, you can either use my spec

Re: [PyMOL] center of mass and distances

Am Freitag, 2. März 2007 schrieb Filippo Marchioni: Hi all! Two questions: Does anyone know how to read the coordinates (x,y,z) of a selected atom in a protein? Or even better Does anyone know how to visualize the center of mass of the protein, reset the axis (x,y,z) using the centroid as

Re: [PyMOL] Visualizing Molecular Orbitals in PyMol

Am Donnerstag, 15. Februar 2007 schrieb BuzB: I think a way to do this would be to generate a map, like an electron density map, and then generate a mesh from this, contoured at a given value. A good point to start is maybe to look at Learner's APBS plugin. Also there should be some

Re: [PyMOL] image metadata plugin

Am Dienstag, 13. Februar 2007 schrieb DeLano Scientific: We have much work to do to make annotations more general and more accessible... Personally, i just store the session with the scene to reget an impression what I did, but you're right this does not explain what you actually see. Cheers

[PyMOL] OT: platform discussion

Am Samstag, 20. Januar 2007 00:55 schrieb DeLano Scientific: Hi all, Of course not: cost is a pragmatic consideration, but cost should not solely be defined in terms of purchase price. You must also include costs in terms of your time and frustration. (However, having once been a graduate

[PyMOL] surface coloring fails with gradient loaded

Hi there, i am trying to render fieldlines and sf potential together in a movie. The movie setup is like this: import os set gradient_spacing=5 load ProtOut.pdb,prot load trajshort.xtc,prot mset 1 -7 show surface set surface_solvent=1 for a in range(1,7): cmd.mdo(a,delete flines;delete

[PyMOL] seperate clipping planes for each object

Hi all, is it possible to change clipping planes for each object? Could't find anything related about it. Cheers Martin -- HTML erhöht den Informationsgehalt eines Postings *immer* um ein paar unvorteilhafte Informationen über den Verfasser. (Thore Tams, de.soc.netzkultur, 17.5.1999)

[PyMOL] weird crashes inside /home/$USER

Hi everybody, i install pymol via svn ebuild (attached). It crashes with a segfault but only if i am inside my home directory. If i am outside, everything works fine. Any ideas what this could be related to? OpenGL graphics engine: GL_VENDOR: NVIDIA Corporation GL_RENDERER: GeForce

Re: [PyMOL] segmentation fault after switching mainwindow between visualisation and commandline

... i had a similar Problem this morning. What is your PYTHONPATH? For me, unsetting it solved the problems. Cheers Martin

Re: [PyMOL] pymol licensing questions

Am Donnerstag, 9. November 2006 13:13 schrieb bgbg bg: After searching the pymol site for two hours I'm still very confused about the license issue. I understand that using (and from recently - downloading) the binary PyMol package requires subscription. Now what about the source code? May I

[PyMOL] cones in pymol?

Hello everybody, i found some cone related stuff in pyopengl (in contrib dir of pymol). Is it usable from pymol in some way? It would be great to visualize vector-fields with 3d-Arrows but you need a cone and a cylinder to construct them. Probably the performance when setting up through

Re: [PyMOL] cones in pymol?

Am Mittwoch, 1. November 2006 21:37 schrieben Sie: Hi Zheng, In my PyMOL scripts for our ANM online server, http://ignmtest.ccbb.pitt.edu/cgi-bin/anm/anm1.cgi we are using CGO in PyMOL to show the vector field. I enclose an example in the attachment. You can run the *.py file in PyMOL.

Re: [PyMOL] Support for gromacs trajectories and cube files

...got the svn code compiled with -D VMD... If i load a PDB, then load a topology and then try to load a trajectory via load loading the trajectory fails, complaining like this: CmdLoad: /home/martin/workspace/testdata/ProtOut.pdb loaded as ProtOut. PyMOLload

Re: [PyMOL] PyMOL and Suse10.0

Am Dienstag, 24. Oktober 2006 14:13 schrieb Neil Ranson: So in summary, there is no inherent problem with PyMOL, Suse 10.0 x86_64, nvidia cards and even recent beta drivers to the best of my knowledge. Hi Neil, what's exactly the output of pymol when it's crashing. Are you using the nvidia