U_iso_or_equiv is being read now for the CIF format. This is working in
11.5.30
--
Robert M. Hanson
Professor of Chemistry
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr
If nature does not answer first what we want,
it is better to take what answer we get.
-- Josiah Wil
Bob Hanson said:
>>For such small structures, solid surfaces for Uij,
>>like your very attractive isosurfaces, should perhaps not take too long?
>>
> No, not long. It's done. I woke up this morning with the solution and
> worked on it after classes today.
I meant the time to draw the surfaces Bob
Alan Hewat wrote:
>Great work Bob. Difficult to keep up with you. But your server:
>http://www.chemapps.stolaf.edu/jmol/docs/examples-11/Jmol-11_5.jar
>(even when I remove the superfluous "www" :-) seems to have reverted to a
>version of 28 slightly earlier than the one I had earlier, and I couldn
Great work Bob. Difficult to keep up with you. But your server:
http://www.chemapps.stolaf.edu/jmol/docs/examples-11/Jmol-11_5.jar
(even when I remove the superfluous "www" :-) seems to have reverted to a
version of 28 slightly earlier than the one I had earlier, and I couldn't
find 29 with the fea
OK, Alan, that's great. I look forward to hearing about your user feedback.
Rendering. I think you are going to like this. It is NOT your typical
football rendering -- but I will argue that you can get that with other
programs, and maybe Jmol should do better.
Football dots. Pointilist football
OK, I have this working with ICSD, but how do I display the ellipsoid
surface plot? Examples are on:
http://icsd.ill.fr/icsd/index.php?action=Search&remarks=AHT
There are not many if you only have access to the demo database, and you
may have to switch off the polyhedra and bonds. To see very anis
On Thu, April 17, 2008 10:46 am, Bob Hanson wrote:
> Note that I am defining temperature as
>
> (U11 + U22 + U33)/3.0 * 100
>
> If this is not correct, please let me know. (I can't find where I read
> that, and I don't know if I remember it correctly.)
>
David Watkin prefers:
Uequiv = (U1*U2*U3)*
Note that for PDB files, ANISOU parameters cannot be processed without
also processing the CELL records.
To enable viewing anisotropic displacement parameters for PDB files in
Jmol 11.5.28, then, you must
load .pdb {1 1 1} # get full unit cell
or (this is new)
load .pdb {1 1 0} # d
Brian McMahon wrote:
>Dear Bob
>
>At first glance, tested against a number of Acta Cryst. C structures
>with relatively large or elongated ellipsoids, this is looking very
>nice indeed.
>
>So far the only issue I have come across is the logic of handling
>mixed isotropic/anisotropic refinements; i
Those examples look great Bob. This will be very instructive for inorganic
structures, and I have already put it into ICSD. But unfortunately the
version I found as listed below was 11.5.27 and not 11.5.28 so
"ellipsoids" is not yet recognised (caching problem?). A simple aniso ICSD
example among
Alan Hewat wrote:
>unfortunately the
>version I found as listed below was 11.5.27 and not 11.5.28
>
I just notice that and am uploading now.
>>http://chemapps.stolaf.edu/jmol/docs/examples-11/Jmol-11_5.zip
>>
>>Bob
>>
>>
>__
>Dr Alan Hewat, Neutron
Those examples look great Bob. This will be very instructive for inorganic
structures, and I have already put it into ICSD. But unfortunately the
version I found as listed below was 11.5.27 and not 11.5.28 so
"ellipsoids" is not yet recognised. A simple aniso ICSD example among
others is:
http://ic
Those examples look great Bob. This will be very instructive for inorganic
structures, and I have already put it into ICSD. But unfortunately the
version I found as listed below was 11.5.27 and not 11.5.28 so
"ellipsoids" is not recognised :-( A simple aniso example among others is:
http://icsd.ill
Those examples look great Bob. This will be very instructive for inorganic
structures, and I have already put it into ICSD. But unfortunately the
version I found as listed below was 11.5.27 and not 11.5.28 so
"ellipsoids" is not recognised :-( A simple aniso example among others is:
http://icsd.ill
Dear Bob
At first glance, tested against a number of Acta Cryst. C structures
with relatively large or elongated ellipsoids, this is looking very
nice indeed.
So far the only issue I have come across is the logic of handling
mixed isotropic/anisotropic refinements; in the CIF
http://scripts.
Alright. Time to test. See
http://chemapps.stolaf.edu/jmol/docs/examples-11/new.htm
http://chemapps.stolaf.edu/jmol/docs/examples-11/ellipsoids.jpg
http://chemapps.stolaf.edu/jmol/docs/examples-11/Jmol-11_5.zip
Bob
Bob Hanson wrote:
>Alan, Thomas, Brian, Rich, others,
>
>OK, progress. I have
Alan, Thomas, Brian, Rich, others,
OK, progress. I have just uploaded code introducing the ELLIPSOID
command. All it does at this point is draw the axes. But that's enough
to convince me I do have the Uij --> ellipsoid axes conversion correct,
and that is no small achievement! The ellipsoid axe
OK, maybe an axial ratio test switch in Jmol would be useful, but as
standard I would prefer to see the assigned atom colours used for the
ellipsoids. After all, you can actually see elongated ellipsoids even
without colouring them differently. And elongated ellipsoids are the most
interesting sinc
Bob
Just to keep up the flow of ideas on this, the IUCr checkCIF
issues "ALERTS" of various levels of severity in diagnosing
unrealistic ellipsoids according to the recipe below:
PLAT_211 Test for NPD ADP's in main residue(s)
This test reports on non-positive definite (i.e. complex and un
Yes, Bob - I believe that is correct!
-Tom
On Tue, Apr 15, 2008 at 1:47 PM, Bob Hanson <[EMAIL PROTECTED]> wrote:
> Thank you, Thomas. That's very interesting information. I hope that Jmol
> can be at the forefront of visualizing whatever is needed in that area.
>
> Am I correct that the PDB ANIS
Dear Bob
I agree entirely with Alan that the "football" style of ellipsoids
will be extremely valuable, especially if it can be realised in
short order. More ornamental ellipsoids at some stage in the future
will still be appreciated, and offer yet more added value.
If you want to test your effor
Thank you, Thomas. That's very interesting information. I hope that Jmol
can be at the forefront of visualizing whatever is needed in that area.
Am I correct that the PDB ANISOU records are coefficients for the equation
U11 x^2 + U22 y^2 + U33 z^2 + U12 xy + U13 xz + U23 yz - c = 0
where x,
Bob, if you can render the Uij ellipsoids without drawing the axes for
now, that would already be very interesting. Anisotropic thermal
ellipsoids are useful because they indicate disorder of some kind, either
static or dynamic (or else a problem with the refinement :-) Of particular
interest is an
Alan and Brian,
At least for starters, here's what I have done:
1) programmed the CIF reader to read Uij data from CIF and mmCIF files
2) added an ISOSURFACE option to display Cartesian Uij' data:
isosurface ellipsoid {[U11'],[U22'],[U33'],[U12'],[U13'],[U23']}
3) read Jeffery, Methods in X-R
I too am very supportive of adding this functionality! For macromolecules
however, I would like to comment though that the number of
"ultra-high-resolution" (sub 1.0-1.4Angstrom) structures is continuing to
increase rapidly. This is due to both better crystals and much more
powerful synchrotron X
I strongly support Brian's request for drawing anisotropic temperature
ellipsoids, and agree with Rich that the full ellipsoid surface should be
drawn, with an option for showing axial lengths. Actually, near the end of
last year we discussed standards for output of anisotropic temperature
factors
Dear Bob
> Brian, which of these appeal to you?
>
> http://skuld.bmsc.washington.edu/raster3d/html/rastep_options.gif
>
> Can we use PDB format?
>
> http://nist.rcsb.org/robohelp/files_formats/structures/pdb/coordinate_file_description/anisou.htm
>
> I see 1AL4 has these codes, so I could star
Brian, which of these appeal to you?
http://skuld.bmsc.washington.edu/raster3d/html/rastep_options.gif
Can we use PDB format?
http://nist.rcsb.org/robohelp/files_formats/structures/pdb/coordinate_file_description/anisou.htm
I see 1AL4 has these codes, so I could start with that.
What I need is
so, who can help me determine how to interpret file data in this regard?
What sample files do we have?
Bob
[EMAIL PROTECTED] wrote:
>On Mon, April 14, 2008 9:28 am, Bob Hanson wrote:
>
>
>>Brian, I would love to get this into Jmol. I think we can do a fabulous
>>job of it, but I need to unde
On Mon, April 14, 2008 9:28 am, Bob Hanson wrote:
> Brian, I would love to get this into Jmol. I think we can do a fabulous
> job of it, but I need to understand how thermal ellipsoids are
> designated in common file formats and how one would suggest depicting
> them (with the quarter-segment left
Brian, I would love to get this into Jmol. I think we can do a fabulous
job of it, but I need to understand how thermal ellipsoids are
designated in common file formats and how one would suggest depicting
them (with the quarter-segment left out?). I did look into this a while
back, but the desi
Probably a frequently-asked question, for which I apologise, but
I was wondering whether it is possible in Jmol to implement
"thermal ellipsoid plots" in the manner of the crystallographic
program ORTEP (i.e. atoms are represented by ellipsoids whose axes
are proportional in length to the relevant
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