[PyMOL] grid_mode?

Hi, I've just noticed the grid_mode command announcement in the wiki. I've checked the latest beta, but it seems to be 1.1 beta 3, which is the same I have installed (without the grid_mode command). This seems a great feature, so... how can I enable it? Thanks, Xavier Deupi Laboratory of

[PyMOL] (no subject)

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[PyMOL] Animations between two pdb files

Hi! I wish to show a smart animation between two pdb files, or between two loaded objects. Something like a transform_selection[1], but doing the transformation like a movie. I don't know if exists such a feature in Pymol, and obviously I can make some intermediate transformation matrix and apply

Re: [PyMOL] Animations between two pdb files

Toni, Let me know if you get a best solution for this problem. ggb Gregory G. Burrows, Ph.D. Research Associate Professor, Department of Neurology School of Medicine, Oregon Health Science University 3181 S.W. Sam Jackson Park Rd., UHS-46 Portland, Oregon 97239 (503) 494-4345 (office) //

Re: [PyMOL] Isotropic thermal ellipsoids

Carsten, Thank you for the suggestion. It has got me thinking... In the meantime, you can already use Python itself to store additional molecular properties which can be mapped to b, q, or vdw as needed using the alter command over various selection. However, I'm not sure that would enable

Re: [PyMOL] Color residues by b-factor

Tiago, It's a little hard to tell from the code, but it appears to be the first atom encountered in the traversal (the would usually be N). The byres option wasn't really intended for coloring by property, but rather, for coloring by sequence (e.g. in a rainbow). If were were to change the

Re: [PyMOL] grid_mode?

Xavier, grid_mode can currently only be found in the open-source code, but it will be present in the next beta build. This feature was added directly in response to recent requests from people wishing to visualize two or more structures in a juxtaposed fashion. Cheers, Warren -- DeLano

Re: [PyMOL] Selecting single type amino acids within X angstrom fromeach other

Dmitry, You need to iterate through the histidines to do this. This can be done in PyMOL as follows: # select C-alpha atoms in all HIS residues as our query set select c_alphas, his/ca # create a selection to hold the resulting atom set select result, none # iterate through each query atom