Re: [PyMOL] Feature Requests/Ideas (Sean Law)

[Jason V. <jas...@sc...>]

Georg,

Thanks for the reply.  My comments are below.


> 1) Ever since I have used the ray function in PyMOL i ran into problems
> creating the right resolution/size of the ray trace images for
> posters/papers. I know its just a matter of x/y pixel settings, but
> every time i had to look it up again. However i wrote a little script
> embedded in the BNI-Tools plugin, where one easily can set the size and
> resolution of the ray trace image. Of course it would be nice to have
> VG, but maybe it is a "meantime solution".
> Load the BNI-Tools install it as plug-in and get to Plugin-->BNI PyMOLl
> Tools -->Create --> ray -->set  and input the width-size in millimetre
> (mm) and the resolution (in dpi) you want to have. (or you can select a
> pre-set)

So you'd like to see something like:

ray 10cm, 20cm, dpi=300?
ray 2.5in, 5in, dpi=300?


> 3) I have no solution for MD trajectories but BNI-Tools can also be used
> to import multiple pdb files (like snapshots)  into the same object
> using different states. (The object is named like the first read in)
> Maybe it is useful to you.
> BNI PyMOLl Tools --> Load Files --> Multiple Files into states

This is easily achieved using a mixture of Python and the PyMOL API.
Let's assume you have a 100 files in a directory, all trajectory
snapshots.  To load all 100 objects into one PyMOL object, just do:

import glob
for x in glob.glob("yourDirectoryName/*.pdb"): cmd.load(x, "myMultiStateObject")

PyMOL know that if you load more than one structure into the same
object name, to make it a multistate object.

-- Jason

-- 
Jason Vertrees, PhD
PyMOL Product Manager
Schrodinger, LLC

(e) Jas...@sc...
(o) +1 (603) 374-7120