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

[Georg Steinkellner]

Hi!

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)

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

There is currently no user guide for BNI-Tools but most of the BNI-Tools 
commands act on the (sele) selection. If you want to give BNI-Tools a 
try  download it from
http://sourceforge.net/projects/bni-tools/
and experiment with it. Its not a completely bug-free version, so any 
bug-reports and suggestions are welcome.

Regards,
Georg





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Re: [PyMOL] Summary of Extracting Amino Acid Sequence from PDB File, (Buz Barstow)

[Georg Steinkellner]

Hi!

You can also try bni-tools.

 http://sourceforge.net/projects/bni-tools/

It's a pymol plugin containing various little scripts i needed for 
myself which i summed up there.
Unfortunately i had no time to write a manual, and i don't know if it 
works with every pymol version.
(and it is not entirely bug-proofed)
Most of the commands work on the selection  (sele)  for  simplicity.
Just give it a try  and experiment with it.
Install the plugin and you will find it at Plugin--BNI Pymol Plugin v. XX
Select the amino acids you want to convert into sequence and click on 
get sequences and select the format.
It also should work on multiple selections and should split the output 
into objects and chains.
Copy the sequences from the output window and paste it wherever you want.

Cheers,
Georg

Georg Steinkellner
Research Centre Applied Biocatalysis
Enzyme Development and Analytics
c/o Karl-Franzens University of Graz
(ZMB) Centre of Molecular Biosciences


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