Re: [PyMOL] change the sphere size of a chosen atom ?

Ni Hao Feng, First of all, please do not include an complete daily digest in a question (or reply) on this or any user list. If required, cut out only that part which connects to your question or reply. Then, in addition to Bobs comments, you can also use the terminal or a script, using the

Re: [PyMOL] Pymol cone shape?

Hi William, Maybe the attached python script will be of some use. It contains a function (and some helper functions) to draw a CGO arrow in PyMOL. It contains code for drawing a cone for the head of the arrow. Hope it helps, Tsjerk On 1/10/07, William Scott wgsc...@chemistry.ucsc.edu wrote:

Re: [PyMOL] distance atom-protein surface

I needed to have a measurement of the actual physical long dimension of a protein model to compare with x-ray scattering data. I activated the surface mesh feature and at the extreme ends of the longest axis, right at the surface boundary, created a carbon atom at each position, then simply

[PyMOL] Sequence view size

Is their any way to get the size in pixels of the sequence view like their is of the internal gui, or the size in pixels of the space actually used for drawing? I know that glGetDouble(GL_VIEWPORT) but this doesn't take into account the internal gui or the sequence view. I can find a way to get

[PyMOL] CE Align v0,1

Howdy, I've just finished implementing the CE alignment algorithm in Python/C as a PyMol plugin. The CE algorithm, is a fast/accurate structure-based alignment program. (At this point, I have left out a few optimization steps; those will come later.) Before I release the code to the public,

Re: [PyMOL] Sequence view size

Aaron, Unfortunately, there is no good way to do this at present. A very ugly hack would be to save the current image and then measure its dimensions. Cheers, Warren -- DeLano Scientific LLC Subscriber Support Services mailto:del...@delsci.info Not yet a PyMOL Subscriber, but want to

[PyMOL] Merge PDB files

I was wondering if there was a simple way to merge pdb files generated by Pymol's 'generate symmetry mates' command? I have a dimer in the available pdb file and want to make the full hexamer that is formed via a trimer of dimers. Any suggestions would be most appreciated. Josh

Re: [PyMOL] Merge PDB files

Josh, The trick is that each otherwise identical structure in a PDB file must have its own segment identifier in order to avoid ambiguity. In recent version of PyMOL, there is a segi=1 option to symexp which will automatically assign such an identifier to each copy. load $TUT/1hpv.pdb symexp