Hi, Jennifer. Sounds like you are having a wonderful sabbatical. (Where?)
The cavities are totally created within Jmol. No additional program.
Cavity volume. This is a very challenging concept. I have not attempted to
do this in Jmol because I am told that you really have to do it right to
have it a meaningful quantity. Jmol's cavities should be considered strictly
qualitative. I'm pretty sure other software does this much better than Jmol
ever could.
So have you tried
set navigationMode ON
and then *navigating* through the cavities? That's fun.
Animations. 100 PDB files is not a problem. You can either load them as one
file -- this could be as simple as scripting a "MODEL nnn" line (where nnn
is an integer 1,2,3,....) in between whole PDB files (I think) or some sort
of Perl script to get the models into one file, with the header only for the
first file.
You might recall that Chime had the limitation that there had to be exactly
the same number of atoms and atom types in each section of the XYZ file.
This is not an issue for Jmol, but IF it is the case -- as it probably is
here, you can save gobs of memory by using the
load TRAJECTORY
command. This loads the file into separate frames, but if you "select all"
then you just see the number of atoms in one frame, and you can only display
the model sequentially, one frame at a time -- which sounds like what you
might want to do. But everything should work as expected -- "cartoons only"
produces a set of cartoons that automatically adjusts for one model to the
next during the animation.
This is the same mechanism used for the upcoming addition of molecular
dynamics trajectories, but in that case the file loading is a bit different.
Bob
On Mon, Sep 29, 2008 at 3:24 PM, Jennifer L. Muzyka <
[EMAIL PROTECTED]> wrote:
> I just showed some of the capabilities of Jmol in group meeting for the
> group where I'm doing my sabbatical. There was a lot of interest in the
> features of Jmol, so I have a couple of questions. The first one is whether
> it would be possible for Jmol to calculate and display volumes of the
> cavities inside of proteins? This question came up when I was showing the
> AChE tutorial built using JTAT, which shows the cavities in different forms
> of the enzyme. I'm guessing that the cavity surfaces were calculated in
> some other software and then passed on to Jmol like some of the other
> surfaces. If it's not already possible to do this, would it be difficult to
> implement?
>
> Question number 2. I've made several animations with small molecules by
> concatenating the xyz files. Is it possible to do the same thing with
> proteins and their pdb files? Or do the different pdb files need to be
> packaged into one file as separate models? Would it be possible to do an
> animation like this with 100 pdb files? I'm an organic chemist rather than
> a biochemist, so I must admit I'm uneducated about what's possible to
> accomplish with the larger files and with the different format.
> -Jennifer
>
>
>
>
> Jennifer Muzyka
> Professor of Chemistry
> On sabbatical at University of Kentucky College of Pharmacy
> Centre College
> Danville, KY 40422
>
> [EMAIL PROTECTED]
> http://web.centre.edu/muzyka
>
> -------------------------------------------------------------------------
> This SF.Net email is sponsored by the Moblin Your Move Developer's
> challenge
> Build the coolest Linux based applications with Moblin SDK & win great
> prizes
> Grand prize is a trip for two to an Open Source event anywhere in the world
> http://moblin-contest.org/redirect.php?banner_id=100&url=/
> _______________________________________________
> Jmol-users mailing list
> Jmol-users@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/jmol-users
>
--
Robert M. Hanson
Professor of Chemistry
St. Olaf College
1520 St. Olaf Ave.
Northfield, MN 55057
http://www.stolaf.edu/people/hansonr
phone: 507-786-3107
If nature does not answer first what we want,
it is better to take what answer we get.
-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
-------------------------------------------------------------------------
This SF.Net email is sponsored by the Moblin Your Move Developer's challenge
Build the coolest Linux based applications with Moblin SDK & win great prizes
Grand prize is a trip for two to an Open Source event anywhere in the world
http://moblin-contest.org/redirect.php?banner_id=100&url=/
_______________________________________________
Jmol-users mailing list
Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users
