Hi Sara,
I don't think this is directly possible, since the centers of the aromatic
rings are not declared per se. But I see another way to obtain the result
you want, maybe this can be written as a small Python script (sorry I never
wrote any Python scripts, so I can't translate my idea!!).
The i
On Tue, 2005-05-24 at 11:34 +0200, Grégori Gerebtzoff wrote:
> 3) define two interlaced loops and calculate the distance between all 6
> carbons of Phe1 with all 6 carbons of Phe2, either with cmd.dist or with
> simple mathematical functions; sum these distances
>
> 4) divide the result by 36, and
A more informative distance to measure between two aromatic (or planar) groups
would be the plane-to-plane separation. I don't know how to code that, but if
anyone out there has done, maybe it would make a handy addition to the set of
tools.
Pierre Rizkallah
***
Warren, et al,
I discovered a funny bug in 0.98.
If one turn off round helices
and turn on cartoon highlight color:
like;
set cartoon_round_helices, off
set cartoon_highlight_color,grey50
the highlight color and helix colors are mixed up!!
Björn
***
Hi List,
After a quick search of the list archives and the wiki, I couldn't find
information about calculating the radius of gyration. Is this possible
in pymol? And if it is, can you select specific residues and calculate
the radius of gyration of your selection?
Thanks in advance,
Sara
This would be a nice option to have incorporated into pymol, and is a
relatively short amount of code. In the meantime, I have a fortran program
that will read a pdb file and calculate these values. Feel free to contact
me off-list if you need it.
Cheers,
Steve
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