Hello-
I'm using a data statement to add a detached ethane to a model so that I can
edit the ethane and add the subsequent substructure to the original model.
This all works well within the context of the editors click callback
routines.
Subsequent clean-up or the new structure by minimize makes
On Wed, Feb 24, 2010 at 3:24 PM, Otis Rothenberger o...@chemagic.comwrote:
I included point and click atom and bond deletion into a Jmol molecular
editor. This works just fine, but there are some deletion followup issues:
1) minimize addHydrogens is not functional on a multivalent atom that
On Fri, Feb 26, 2010 at 1:05 PM, Robert Hanson hans...@stolaf.edu wrote:
Hmm, now looking at that -- Why two minimize commands?
instead, for example, why not:
calculate hydrogens
select *
minimize steps 100
That second select might be important, since there are new atoms there.
Bob
On Sat, Feb 20, 2010 at 12:53 PM, Eric Martz martze...@yahoo.com wrote:
Is it possible to animate non-consecutive frames? For example, in
http://proteopedia.org/wiki/index.php/Sandbox_5_Eric_Martz I would like to
animate just 2 frames, 1.1 and 1.10.
I didn't guess any syntax to display two
Bob-
Using your approach, picking deletes an H on propane. But minimize
addHydrogens does not add it back. I'm thinking maybe I have the wrong Jmol
version. I'm using 11.9.30_dev 2010-02-12 12:26. Is this the wong version?
The two minimization steps simply reflect the fact that I forgot
Ha! Yeah, I don't think Google was a consideration when this program was
named back in the 70's...
O was written and is still maintained by T. Alwyn Jones of Uppsala
University in Sweden. His central clearing house can be found at:
http://xray.bmc.uu.se/alwyn/
I have already written to him and
An idea just popped up for Eric:
As a roundabout solution:
Maybe you could load just the selected frames, in the desired order, using
load models
and then animate them?
So,
http://proteopedia.org/wiki/index.php/Sandbox_5_Eric_Martz I would like to
animate just 2 frames, 1.1 and 1.10.
load
Note that you have two options there with loading a specific model:
load models ({0:3 6 8 10}) filename.pdb
will load models 0, 1, 2, 3, 6, 8, and 10, where 0 is the first model.
These aren't model numbers as found on the PDB MODEL line. These are counted
from the beginning starting with 0.
Looks like it is here: http://www.uoxray.uoregon.edu/tnt/manual/node104.html
Alas, sadly, a binary file that does not identify itself. Too bad not
everyone thinks of adding a magic number at the beginning. Still, we might
be able to do something with this.
Bob
On Fri, Feb 26, 2010 at 1:55 PM,
Ah - Good find! And yes, that's the modern version of the format - the
DSN2 or Frodo-style map has been relegated to the dustbins of history.
There are no other useful map formats listed on that web site. My opinion
would be that the triad of CCP4/MRC, CNS/XPLOR and DSN6 (O-style) covers
99+%
Bob-
OK, I think I see something consistent in the delete problem now:
Delete followed by minimize addHydrogens works if the deleted hydrogen is
the only hydrogen on the multivalent atom. In every other case I look at, I
see it failing:
I'll use methanol to exemplify this, but I think it's
Jmol Users,
Here's something I've always wanted to do with Jmol -- use clipping planes
to show students the *fractions* of atoms in a unit cell (similar to
attached image of NaCl generated using POV-Ray). I know I can use slab HKL
and depth HKL, but those don't slice through the atoms like the
Oops, I missed that the original molecule is pretty easy to select after the
append of ethane. RotateSelected then gets the job done.
I'm still interested in finding out if a mouse click/drag rotation is
possible on selected atoms, however.
Otis
On Fri, Feb 26, 2010 at 1:54 PM, Otis
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