Date: Mon, 30 Mar 2009 12:01:10 -0500
To: Forum for the Proteopedia User Community
proteopedialist-for-us...@bioinformatics.org
From: Eric Martz ema...@microbio.umass.edu
Today I am able to get older snapshot versions of PDB files. They
have changed the compression from unix .Z to gzip
Eric, Jmol does not use atom serial numbers in state scripts. It uses atom
indexes, but maybe that's what you were referring to. I could see how that
would cause a problem if the file is being extracted from the PDB on the
fly, and the underlying PDB file has changed atom order.
The only viable
So, Eric -- you solved your own problem, right? You just need to upload
older versions of those files that match the state script you are using.
Yes?
Bob
--
Robert M. Hanson
Professor of Chemistry
St. Olaf College
1520 St. Olaf Ave.
Northfield, MN 55057
http://www.stolaf.edu/people/hansonr
11.6.18 and 11.7.28
The command
hover myText
applies to all atoms, not to the currently selected set. I was of course
expecting the latter. The documentation says nothing but that's the
behaviour for all commands.
How can one set custom hovers?
You have to set a hoverCallback.
set hovercallback jmolscript:set hoverlabel @{\this is atom \ +
_atomHovered}
for example, displays this is atom 3 when it is over that atom.
You can also put anything in a Jmol script function and use that to define
hoverlabel. The function is run after
Dear Bob,
How difficult would it be to change the state script generator in Jmol to
avoid using atom serial numbers?
I'm sure none of us ever envisioned the current state of affairs. We have
who knows how many state scripts saved in Proteopedia, and now an unknown
number of March-17-remediated
Dear Eric,
Your email mentioned atom serial numbers but Bob said in a previous
email Eric,
Jmol does not use atom serial numbers in state scripts. It uses atom
indexes, but maybe that's what you were referring to.
However, Bob, if atom indexes are the same as atom serial numbers, then I
too would
Have the atom names stayed unique through the various remediation cycles
of the PDB? If so use the CIF files with the names rather than the .pdb
format files.
Rich
--
___
On Mon, Mar 30, 2009 at 4:16 PM, Eric Martz ema...@microbio.umass.eduwrote:
Dear Bob,
How difficult would it be to change the state script generator in Jmol to
avoid using atom serial numbers?
impossible. It has to use atom index numbers (what you are calling serial
numbers). That I know.
Let's clear up the atom serial number business.
PDB file contain atom serial numbers. These are in the ATOM and HETATM
records. Behind the scenes, in the Jmol code, we call these atom serial
numbers as opposed to atom index numbers, which start at 0 and go
consecutively through ALL models loaded.
Bob,
Thank you for the clarification. Everything makes sense.
Eran
On Tue, Mar 31, 2009 at 1:39 AM, Robert Hanson hans...@stolaf.edu wrote:
Let's clear up the atom serial number business.
PDB file contain atom serial numbers. These are in the ATOM and HETATM
records. Behind the scenes, in
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