Aidan, don't apologize. I'm grateful to you for testing this with me. Fixing
features is not a pain; if it were, I'd quit!
Aidan Heerdegen wrote:
look now, Aidan. I've wanted to be able to do this myself for some
time. Still not PERFECT, because current measures are not selectively
addressable, but an advancement, I think. Certainly it should do what
you want it to do.
Yes ... and no! Sorry to be a pain, but I am trying to load my
disordered structures into jmol 10.x.* and then use the new symmetry
features to fill out the unit cell and neighbouring cells.
the PDB reader has not been set up to read symmetry. It can read the unit cell,
certainly, but not the symmetry. It should not be difficult to do this, BUT we
are going to have to add a "set" flag for it, because we can't change the
default behavior of the PDB reader. The combination of unit cells and symmetry
automatically put in place a couple of settings that are more crystallographic
-- unit cell axes instead of cartesians, perspective off (because in that
context it looks ridiculous). That was just a design decision I made -- we might
want to discuss this idea of "context" that we really have three general
contexts for Jmol -- biomolecular, small molecule, and crystallographic.
In any case, PDB files in general cross the contexts, because some people use
them for small molecules, some biomolecules, and here you are using them in a
semi-crystallographic sense because you want that symmetry.
I'll admit, I was (sort of) dreading the thought of someone asking for lattice
considerations with an enzyme. I hate to think what would happen when you load
load enzyme.pdb {2 2 2}
Holy cow! But, if you are patient, and your machine has the memory, it might
work.....
OK, there's an option, in fact: What if adding that lattice information is the
flag that you want symmetry? It can be as simple as
load enzyme.pdb {1 1 1}
for a single unit cell. But then OBVIOUSLY you want the symmetry stuff. That's
probably what you have been trying anyway.
OK, so I am not familiar with how PDB files record symmetry information. Best
send me a link to one that does. (Please do not attach the file.)
When I try to load a pdb file (which has the correct conect records so I
don't have spurious bonds) jmol does not seem to recognise their is
symmetry information in the file (there is, trust me), so I cannot do
the symmetry expansions. If I use shelx (.res) or CIF files the
symmetry information is recognised, but there is no bonding information,
so I get spurious bonds and the automagic "molecule" identification does
not work!
No bonding information -- right, that's because we can't clone the bonding
information in the context of symmetry. At least, I haven't figured out how to
do that. Clone atoms, yes, bonding.... maybe?
Should PDB symmetry information be respected? Or is this unimplemented
as of now?
show me the file....
Thanks again for your help,
Cheerio
Aidan
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Robert M. Hanson, [EMAIL PROTECTED], 507-646-3107
Professor of Chemistry, St. Olaf College
1520 St. Olaf Ave., Northfield, MN 55057
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http://www.stolaf.edu/people/hansonr
"Imagination is more important than knowledge." - Albert Einstein
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