Re: [PyMOL] Write map from list of coordinates.

hold for Your solution Thomas? Loading directly from Python is the way to go in the future. In the meantime I solved my problem by writing a small script that dumps the data in dx file format, which can subsequently be loaded into PyMOL. #!/usr/bin/python # Esben Jannik Bjerrum 2014 #Write DX

[PyMOL] Write map from list of coordinates.

file format and subsequently load it, or can it be loaded directly into a map object via some fancy python code? Best Regards Esben Jannik Bjerrum -- WatchGuard Dimension instantly turns raw network data into actio

Re: [PyMOL] Problems with H_add when theres alternate conformations present

Thanks, valence guess was the key :-) This makes sense, valence/bond assignment is run once the PDB is loaded, but unfortunately fails with the alternate conformations. Removing the alternate conformation doesnt update the bond information, making the save/reload of the structure or valence gue

Re: [PyMOL] Problems with H_add when theres alternate conformations present

lete 1zw9 load temp.pdb, 1zw9 h_add 1zw9 zoom resi 12 Is there a command to get PyMOL to reparse the structure after removing the alternate conformations? Best Regards Esben Jannik Bjerrum ____ From: Jason Vertrees To: Esben Jannik Bjerrum Cc: "pymo

[PyMOL] Problems with H_add when theres alternate conformations present

alternate conformations inside PyMOL before adding hydrogens, but that doesnt fix the problem. I can fix the problem by removing the alternate conformations from the PDB file before I load it into pymol, but I would rather fix it inside pymol in my scripts. Best Regards Esben Jann

[PyMOL] The CRT is dead, long live the ?

Hi Everyone I know it might be a bit off-topic, but 3D stereo is an issue which I think many pymol-users care about. We need to equip some workstations with stereo capable CRT monitors. We have long used quadro cards on linux with emitters and stereo glasses, using CRT's capable of 130-1

[PyMOL] Benchmark Script for Pymol

Hi We're about to buy some new workstations for the students, and IT have asked about what graphics performance we need. It's of course possible to get glxgears to print FPS, with the -iacknowledgethatthistoolisnotabenchmark switch, but we're more interested in how pymol behaves:-) Do anyone h

Re: [PyMOL] Visualizing Molecular Orbitals in PyMol (BuzB)

Are you using PyMOL on a linux platform? The brick object needs numpy compiled into the binary, which it isnt in linux version, but mac and windows versions. If thats the case, I can email details when I get my notes from work. Esben _

Re: [PyMOL] pymol slow on linux PC (Beld, Joris)

I just looked at some old notes: If you try LIBGL_DEBUG=verbose pymol in a terminal, you might get additional information whats wrong. Esben Do you Yahoo!? Everyone is raving about the all-new Yahoo! Mail be

Re: [PyMOL] pymol slow on linux PC (Beld, Joris)

Hi How did you install the Nvidia-drivers? I Once had a similar problem because I had used both the linux distribution package and installed manually with nvidias driver. The old libraries were not properly removed by nvidias installer, giving rise to the partial working OpenGL. Cheers, Es

Re: [PyMOL] CE-align

Hi Pymol Users I wanted to try the new CEalign command and got the following error: run qkabsch.py Traceback (most recent call last): File "/usr/lib/python2.4/site-packages/pymol/parser.py", line 285, in parse parsing.run_file(exp_path(args[nest][0]),pymol_names,pymol_names) File "/usr/li

[PyMOL] Copy a selection for a new molecule?

Hi All in one of my scripts I have a problem with getting a selection for a new molecule which is created from a copy of another which also have a selection. In the first one a selection is made of the user, but after creating a new molecule from the whole of the old, I cannot use the old se

Re: [PyMOL] cones in pymol?

Hi Martin. Ive also experimented with primitive shapes and cones. Its not possible to get a rounded surface on the cone, as you cannot properly define the normals of the surface without the quad based openGL primitives, which is not supported by the inbuild raytracer. If you look in the Pymo

[PyMOL] Quadro4 + newest nvidia drivers => broken stereo

Hi All A quick fix to the problem with the newest nVIDIA linux drivers and broken stereo is to install the nvidia-glx-legacy package if it is available for your distribution. In Ubuntu this contains the 7184 driver which was the last to support TNT, TNT2, TNT Ultra, GeForce, and GeForce2 ch

Re: [PyMOL] Pymol Diagnosis (JOSHUA FRIEDMAN)

You probably have a problem with OpenGL libraries, Im surprised that pymol starts at all. Do other OpenGL programs run (try glxgears). Is mesa installed or do you have OpenGL drivers installed? What Ati card do you have? Have you installed the fglxr driver? What linux distribution are you using?

Re: [PyMOL] stereo on X.org

Hi All The Xorg >< Stereo problem might also be related to the driver versions of NVIDIA with new distributions. FX cards seem to be fine with 8xxx series of driver, while stereo might not work with quadro 4 cards (980XGL and similar). Theres a thread at nvnews with some info and a patch to make

[PyMOL] density_sliders.py not working on packaged installation.

Hi After compiling pymol from source myself, the density_sliders.py script of Gareth Stockwell stopped showing the interface, though the density_sliders command still does accept command line options. The only error-message is cmd-Error: unrecognized name. PyMOL>density_sliders cmd-Error: unr

[PyMOL] Difference in isosurface and isomesh representations with indexed brick object.

Hi Im using Pymol as a 3d plotter of some "volume density data". However, theres a difference in surface or mesh representations near zero. The following script illustrate(doesnt work without recompile of NumPy support into pymol on linux, but works on both mac and windows directly) from chempy.

[PyMOL] load_brick problem fixed.

The brick01.py script and also load_brick seem to want Numpy support compiled into pymol. (Which is isnt on the linux versions, but is on mac/windows). Thanks to Warren for troubleshooting. Heres what I did to make it work on Ubuntu 606. I already had python-numeric installed. sudo apt-get build

[PyMOL] load_brick broken?

Hi I dont know if my other post was sent to the mailinglist, but I want to load some volume density data from a python array I generate. I found the brick01.py example which seem to do exactly as I need, however it doesnt show any isosurfaces. I run brick01.py and it makes a brick object and so

[PyMOL] How to load volume density from python array?

Hi I have some data in the form of a python array which I would like to load as a volume density map in Pymol. Can this be done with the read_xplorstr, or is there another way? Can anyone shed any light on how I format the xplorstr? load_brick or load_map could be alternatives, but how do they wo

Re: [PyMOL] debian: error in opening pymol

This is probably more of a installation/debian problem than a pymol problem. I would say that somehow the freeglut3 package is not installed on your system. apt-get install freeglut3 should solve it. However the Pymol package depends on freeglut3 so there might be more wrong with your system. tr

[PyMOL] Any information on matrices from alignment of states?

figure out what. Best Regards Esben Jannik Bjerrum __ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com