Hello:
I am an avid user of Jmol. It is now installed at NERSC (www.nersc.gov) by
my request so that I could track simulations in real time. My students use
it all the time.
My question is probably based on my missing something fundamental about the
Jmol software strategy, but I would like to pose it.
My work entails using the CHARMM simulation software where one of the ways
to select a portion of the protein molecule entails using the "segid"
command: e.g. select segid PROA .and. .not. resname TIP3). There is a
similar issue with Amber software tools as well.
In addition, VMD, PyMol, and PDB format all allow selection on the segid
keyword.
For example, in my model protein, there are 6 segments proa ... prof. If I
want to use Jmol to descibe the proa segment, I have to edit the entire pdb
file, determine the atom numbering for proa, and then use the Jmol "atomno"
command. There's gotta be an easier way.
As I said earlier, I am a Jmol user, and I am not comparing Jmol to this or
that software, but it seems that Jmol would adopt canonical selection rules
that coincide with the PDB formatting style.
HELP! Thanks for your consideration about this.
Kind regards,
Angelo
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