Re: [PyMOL] How to draw clashes in pymol

Hi Bondurant, I really like the merging of the graphic beauty of pymol with the detailed depictions of reduce and probe. I have a method that is a bit clunky for doing what you ask, but I don't know if it ever made it to the mainstream in MolProbity. The caveat of wanting to work with a ligand m

[PyMOL] Installation problem

Dear All: Help! Re-installing Pymol 1.7.0.5 after uninstalling failed with the following error: "Pymol 64 bit setup:Object already exists." When I pressed OK, the following message appeared: "Setup wizard ended prematurely because of an error. To install at a later time run setup wizard aga

[PyMOL] More efficient alternative to get_model() mentioned in chempy_model02.py

Hello, There's a file at examples/devel/chempy_model02.py that uses get_model() with the following comment at the bottom. # Summary: this is portable, safe, but inefficient. For real-time visualization # of coordinate changes, there is a way to do this by passing in an opaque # C data structure.

Re: [PyMOL] Other coloring strategies based on user-provided properties

Thank you Jared, Then probably I will just modify the PDB file directly. Best, Chen On Fri, Aug 29, 2014 at 12:56 PM, Sampson, Jared wrote: > Hi Chen - > > As you guessed, this is commonly done by modifying the B-factor column > directly. You can do this with data available to you in PyMOL

Re: [PyMOL] Other coloring strategies based on user-provided properties

Hi Chen - As you guessed, this is commonly done by modifying the B-factor column directly. You can do this with data available to you in PyMOL (e.g. distances, charges, and so forth) using alter and iterate and a fe

[PyMOL] Other coloring strategies based on user-provided properties

Dear all, I am thinking whether it is possible to color a molecule by a specific property residue-wise or atom-wise like generally be done on B-factor? This property could be provided as numbers in a column. An obvious way might just be to change the B-factor column to the user-provided column and

Re: [PyMOL] How to draw clashes in pymol

Why don't you to modify the show_bump.py file? You could try playing with the line cmd.show_as('cgo', name) and change cgo to, for exemple, dots and see what happens. Cheers On 8/29/14 4:30 PM, Bondurant wrote: > Hello community, > I would like to draw a figure similar to this one > http://www.ce

[PyMOL] How to draw clashes in pymol

Hello community, I would like to draw a figure similar to this one http://www.cell.com/cms/attachment/615980/4968633/gr1.jpg showing the clashes between a potential ligand and the protein. The only way i know how to do this in pymol is using the show_bumps plugin, but i don't really like the "red d