[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 doin

[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

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

[PyMOL] running script on startup

Hey folks, I am trying to fire up a script with pymol -r doit.pml PyMOL>run 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 "/sw/l

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. :-( >

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 th

[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 Cave

[PyMOL] Script: Loading gromacs ndx files into pymol

Hi all, here's a small script that allows loading of a gromacs index file into pymol. The corresponding molecule has to be loaded with preserved atom order. I have also a question/feature request concerning the "load" operation: Is it possible to register e.g. this script, to handle loading of

[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 m

[PyMOL] Communication with external program

Hi all, Is it possible to communicate with a "fully running pymol" (means started with gui and TK menu) over a network socket or other means? Or has anyone already written a plugin for this purpose? Basically, it should just take every command, execute it as if it has been typed directly on th

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 rece

Re: [PyMOL] spectral coloring

Am Mittwoch, 27. Juni 2007 schrieb Robert Campbell: Hey Robert, > You are welcome to modify it to add new features, of course. You can > find it at: > >http://pldserver1.biochem.queensu.ca/~rlc/work/pymol/color_b.py I found it this morning via google and the pictures are now really great. If

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. Bes

[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

[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 movemen

Re: [PyMOL] mutagenesis script

Hi Andreas and others, i wasn't aware about pymol's log functionality. Great and that makes script building pretty easy but just doing the stuff in the gui first. Thx for your suggestion, i think this feature should get more attention :-) Best Martin

[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 fi

[PyMOL] delete states

Hi there, is there an command i overlooked to delete states? I am loading trajectories in a structure and it would be great if one could delete the frames or frame ranges. Cheers Martin

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 centroi

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 docume

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. Che

[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 > gradua

[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 dxmap;de

[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)

Re: [PyMOL] electrostatic potential structure

Am Mittwoch, 29. November 2006 15:31 schrieb shivesh kumar: > Dear all, > How can I get the electrostatic potential structure of my protein > molecule.Thanx in advance. S what do you mean by "electrostatic potential structure"? The potential can be calculated with apbs (by hand or via plugin).

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

Am Dienstag, 21. November 2006 15:58 schrieb Christian Seifert: > $PYTHONPATH is not set on my machine. > > > > You wrote: > > Re: segmentation fault after switching mainwindow between > visualisation and commandline > From: Martin - 2006-11-13 05:15 > >... i had a similar Prob

[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 6600/PC

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 16:48 schrieb Ezequiel Panepucci: > It is *not* the GPL. It is the Python license > > http://sourceforge.net/projects/pymol/ > see also: http://www.python.org/doc/Copyright.html ah ok, then forget about what I was telling you ;-) ... i just read somewhere that the

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

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. l

[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 triangle

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". PyMOL>load /home/martin/workspace/testdat

[PyMOL] Support for gromacs trajectories and cube files

Hi everybody, Does somebody of you know if gromacs trajectories (xtc or trr) are supported by some plugin? Same thing with volumetric data in cube files? I am using gromacs trajectories from python already by using the gromacs c-libraries via ctypes. This is not truely platform independant or at

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 "nv