[PyMOL] How to generate a DNA structure with given sequence?

I want to know how to generate a DNA structure with a given sequence. I heard that Pymol can do that but I couldn't find such command. Can you tell me how to do this? Sincerely, Hyun-Chul Kim Biomatics Lab. Department of Biosystems Korea Advanced Institute of Science and Technology Yusung-Gu, Ta

[PyMOL] Reading external grid files

Hi to all, I'm new to pymol, and maybe the question is very basic, but I hope to have your help. I would like to read grids files generated by in house program, how can I do this within pymol? Thank you very much in advance, Antonio -- Antonio Morreale Unidad de Bioinformática Centro de Biolog

[PyMOL] Translating and rotating

Is it possible somehow to translate and rotate selections using the mouse? The "translate" and "rotate" commands are a bit cumbersome to do visual alignments. Konrad. -- - Konrad Hinsen Laboratoire Léon Brillouin, CEA Saclay, 9

[PyMOL] Adding Hydrogens to GFP Chromophore

Hi all, I'm trying to use PyMol to add hydrogen atoms to this small fragment of a PDB file, the chromophore from the GFP structure 1EMA; REMARK S65T Chromophore from Ormo's coordintes (1EMB). HETATM 466 N1 CRO66 24.077 27.513 36.610 1.00 11.86 N HETATM 467 CA1 CRO

RE: [PyMOL] Adding Hydrogens to GFP Chromophore

Buz, You must fix the bond valences manually... Mouse menu -> 3 button editing mode Ctrl-right click on bond Ctrl-W to cycle valence (repeat as necessary to get correct valences) Then optinally remove hydrogens when done (use the action [A] menu on the object -> remove hydrogens) Cheers, Warr

RE: [PyMOL] Translating and rotating

Konrad, Yes, but it is currently awkward because you need to protect the other atoms in the object from moving first (action menu -> movement -> protect on the inverse selection), then you can drag the object moving just the atoms in the original selection. Cheers, Warren -- Warren L. DeLano,

[PyMOL] import pymol

Hi, In the interactive window, I get the following error while trying to either 'import pymol' or 'from pymol import cmd'. PythonWin 2.2.2 (#37, Oct 14 2002, 17:02:34) [MSC 32 bit (Intel)] on win32. Portions Copyright 1994-2001 Mark Hammond (mhamm...@skippinet.com.au) - see 'Help/About PythonWin'

[PyMOL] How do you reset to default bonds/connectivity for all states in an object?

Dear Pymol users, I am trying to use Pymol to make PNG frames in order to merge them into a movie. I am interested in small molecule vibrational animation. I have a series of PDB files containing the coordinates for the molecular motion for each of the frames of the movie. I am using a '*.pm

RE: [PyMOL] How do you reset to default bonds/connectivity for all states in an object?

Paul, Set the "discrete=1" option to the load command when loading multiple small molecules from a PDB. Otherwise, PyMOL will attempt to match them up atom for atom based on name, applying connectivity from the first state. Cheers, Warren PS. Humorous aside: Wow: "factory settings" -- I like