[PyMOL] Pymol and Gromacs XTC

Dear all, I think there is no easy way of reading Gromacs xtc trajectories into PyMOL, At least in the version compiled for Debian, which I don't think includes the vmd plugins. I should have probably asked about this before, but now I just coded a little script that loads xtc in pymol. It has

[PyMOL] movie from chempy objets

Greetings I need to create pseudo-atoms with Van der Waals radius defined by me, I know how to do it using chempy, and loading the chempy objets into pymol, but i need to create several chempy objets and show them in pymol as frames of a movie. (i.e getting a movie of an objetc which VdW radius ch

[PyMOL] Problem loading chempy objects to pymol

load the models with the right values of VdW radius (even if i can't use b-factors) I would really appreciate it. Thanks in advance, and sorry about my english (not a native speaker) Raúl Mera-Adasme __ Correo Yahoo! Espacio para todos tus mens

Re: [PyMOL] Problem loading chempy objects to pymol

Hello Robert, Thanks you a lot, it worked perfectly. As soon as I get an account in the PyMOL Wiki, i will complete the info about the load_model command. Thanks again and regards Raúl __ Correo Yahoo! Espacio para todos tus mensajes, antivirus y a

[PyMOL] Message: 2

Hi all, my system is a newly installed debian-3.1 linux. 'pymol' seems to be part of the installed package. But when I try to open pymol, I get the following error: $ pymol Traceback (most recent call last): File "/usr

[PyMOL] chempy documentation

Hello all. I'm planning to write a couple of Pymol plugins, and I would like to know if there is some documentation for the chempy library, and if so, how can I get it Thanks in advance Raul __ Correo Yahoo! Espacio para todos tus mensajes, antivi

Re: [PyMOL] chempy documentation

My preference would be for something implemented in Python/C. The project could start with a clean, extensible (it should be easy to add new molecules) and modular Python library and then start replacing some functions with C equivalents. I would like a library that doesn't use inheritance, or use

Re: [PyMOL] PyMOL-users Digest, Vol 6, Issue 22

Hi Florian I have also been unable to use pdb2pqr within the plugin (I had similar problems althought I was only using standard residues), but what I did is to use pqr2pdb as stand-alone program and then feed the plugin with the previously generated pqr files. Hope it helps Raul > Message: 2

[PyMOL] A little plugin

Dear pymolers, I just coded a quick and dirty (and also pretty slow), but functional (It have worked for me, at least) pymol plugin that takes a trajectory loaded in pymol and set the b-factor so the trajectory can be colored by frame (first frame blue, second frame green, etc, and last frame red)

[PyMOL] New plugin and Doubt with APBS Tools

Dear all, Two things. First, I just written a small plugin that uses the program "reduce" to add hydrogens to a molecule or to a trajectory loaded in Pymol.(since each frame of the trajectory is hydrogenated by reduce, I think that protonation states could vary between frames) This allow us to hav

[PyMOL] Mapping potentials in PyMOL

Hello All. Having a electrostatic potentials map loaded in PyMOL (an apbs map), does somebody know if there is a way to get the potential associated with a given point in space (i.e. to give a set of 3 spatial coordinates and get the value for the potential at that point)? Thanks in advance, Rau

Re: [PyMOL] Mapping potentials in PyMOL

Hello again I coded a python class to read the apbs output (dx format), so if someone has a similar problem, please email me and I will be happy to send it. Think I will s get a website to upload it anyway Cheers, Raul >Hello All. >Having a electrostatic potentials map loaded in PyMOL >(an

[PyMOL] RMSD and color between two very similar structures.

Hi, I think Leo's is the right way. In a little variant, you could change the b-factor value directly from pymol, instead of manipulating PDB. It should not be difficult prepare an script that ask for two selections (already superimposed and with the same number of residues) get the RMSDs and as

Re: [PyMOL] RMSD and color between two very similar structures

Hi all, I coded a little plugin that performs what Horacio asked for: It takes 2 selections with the same number of residues calculates RMSD for the backbone atoms and assigns each backbone atom's b-factor the corresponding RMSD. (assigns 0.0 to non-backbone atoms) (It only work for aminoacidic

[PyMOL] Website with PyMOL plugins

Hello all, Due to the (unexpected) popularity of my plugin to color 2 backbones according to their RMSD (color_rmsd.py), I managed to have a working website of my lab from which you can download that plugins and other scripts I have coded. The site is: http://mrcc.ciq.uchile.cl/ and has a "soft

[PyMOL] Guessing bonds for a chempy model.

Hi all, I want to load a chempy model into PyMOL. Unfortunately, the model has all the coordinate information, but not bonds defined. I know PyMOL can guess the bonds from the distances, but it does not do it if I just use cmd.load_model, and I could not find a way of doing it. Does anyone know h

[PyMOL] 2 new plugins, and a bit more :-)

Dear all, I develop goChem, an open source library for computational chemistry written in the Go language. I have incorporated a couple of Python functions that allow easily writing PyMOL plugins with goChem, using JSON and pipes for data transfer. As a proof of concept, I wrote two (also open so

[PyMOL] loading a cube file from the API

Hi all, I am trying to code a little script that needs to load Guassian cube files (to later create some isusurfaces). The cube format is supported, and one can easily use the TK interface (file->open) to load the file into PyMOL. I have been looking for the command to do it automatically in a scr

Re: [PyMOL] loading a cube file from the API

en" from the gui. Thanks! Raul On Mon, Feb 17, 2014 at 11:41 PM, Thomas Holder wrote: > Hi Raul, > > there should be no difference between loading from the GUI or using the > "load" (not "Load") command. > > The cube file needs to have a ".cube&q