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#36 Color ORCA-cube MEP surfaces
I have now used JMOL 14.6.4_2016.11.05 on linux 64bit to map mep cube onto eldens, cube being created from ORCA-NAMD QM-MM calculations (QM part). As far as I can see, the cube fornat is GAUSSIAN.
--$ load qmmm_0.input.eldens.cube
Cube data generated by ORCA - Total electron density
whereby structure 15%vanderwaals
--From Menu Display ... Atom ...None, whereby structure as sticks
--$ isosurface "qmmm_0.input.eldens.cube" map "qmmm_0.input_mep.cube"
reading isosurface data from /home/francesco/tmp/qmmm_0.input.eldens.cube
reading isosurface data from /home/francesco/tmp/qmmm_0.input_mep.cube
isosurface1 created with cutoff=0.02 min=0.0 max=16.1043;
isosurface count:1
isosurface full data range -1.0112914 to 0.05302538 with color scheme
spanning -1.0112914 to 0.05302538
1 id:isosurface1; model:1.1; vertices:5044; polygons:10096; visible:true;
dataRange:[-1.0112914, 0.05302538, -1.0112914, 0.05302538];
title:isosurface "qmmm_0.input.eldens.cube" map "qmmm_0.input_mep.cube";
--$ isosurface translucent
1 id:isosurface1; model:1.1; vertices:5044; polygons:10096; visible:true;
dataRange:[-1.0112914, 0.05302538, -1.0112914, 0.05302538];
title:isosurface "qmmm_0.input.eldens.cube" map "qmmm_0.input_mep.cube";
Colors appear as yellow_pale-red for high potential and pale blue for low potential (attached screenshot). I would like to have a definite red for the highest potential and definite blue for the lowest potential. Possibly I also would like to reverse the colors, with blue for high potential. I tried with { colorscheme "rwb" color absolute -0.15 0.15 map ..} and a variety of other ranges without success.
Beg pardon for this low-level ticket. I have just now discovered that JMOL can do a lot through a very complex language, particularly for surfaces. I had used JMOL for merely checking bond orders.
thanks for advice
I have now noticed with water eldens/mep cube files found on the web, and
presumably generated with GAUSSIAN, that - by working with JMOL exactly as
I described previously for my system - colors appear just as I would like
with my system, i.e., blue for high and red for low potential, see
attachment.
Therefore, my question is, has anyone ever tried JMOL with cube files from
ORCA? The layout looks like - at my eyes - as GAUSSIAN cube format but the
results are as I described.
thanks for taking t his into consideration.
On Thu, May 28, 2020 at 5:45 PM Francesco Pietra chiendarret@users.sourceforge.net wrote:
Related
Patches: #36
If you can put these in a dropbox for hansonr@stolaf.edu, I can take a
look. Should be just a setting in the isosurface command that we are
missing.
On Fri, May 29, 2020 at 4:35 AM Francesco Pietra chiendarret@users.sourceforge.net wrote:
--
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 Willard Gibbs, Lecture XXX, Monday, February 5, 1900
Related
Patches: #36
one thing you can do is to use less translucency. It will brighten the
image.
On Fri, May 29, 2020 at 6:14 AM Robert Hanson hansonr@stolaf.edu wrote:
--
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 Willard Gibbs, Lecture XXX, Monday, February 5, 1900
Related
Patches: #36
Hi Rob dropbox today does not work for me. Please find the files attached
francesco
On Fri, May 29, 2020 at 1:35 PM Bob Hanson hansonr@users.sourceforge.net
wrote:
Related
Patches: #36
Using reverse range and demonstrating the use of write jvxl to hugely reduce the size of the files, in case you need to transmit these:
zap
isosurface c:/temp/qmmm_0.input.eldens.cube color range 0.0 -0.4 map c:/temp/qmmm_0.input_mep.cube
center $isosurface1
write "qmmm_test.png"
write "qmmm_test.jvxl"
refresh
isosurface file "qmmm_test.jvxl"
write "qmmm_test_jvxl.png"
05/29/2020 10:02 AM 918,112 qmmm_0.input.eldens.cube
05/29/2020 10:03 AM 7,268,521 qmmm_0.input_mep.cube
05/29/2020 10:17 AM 20,485 qmmm_test.jvxl
05/29/2020 10:17 AM 431,381 qmmm_test.png
05/29/2020 10:17 AM 431,822 qmmm_test_jvxl.png
Bob thanks a lot. Intuitively I had used reverse range, however with wrong
figures. I have tried other viewers for my cube files, the result from
JMOL, once transparency is activated and the molecular skeletons aid
understanding the surfaces, is by far the best. The various pi-pi and
halo-pi stacking can be investigated now in more depth than from numerical
table.
For any (hopefully) future publication, I have now tried rendering a stereo
image (cross eye or wall) so that one can see behind. Is anything simple
for that? From the user blog it appears to be a very laborious task with
JMOL.
francesco
On Fri, May 29, 2020 at 5:22 PM Bob Hanson hansonr@users.sourceforge.net
wrote:
Related
Patches: #36
For any (hopefully) future publication, I have now tried rendering a
stereo
image (cross eye or wall) so that one can see behind. Is anything
simplefor that? From the user blog it appears to be a very laborious task
withJMOL.
Well, first off, I would hope that we are done with stereo images! (People
such as myself in the 5% of the population with strabismus can make nothing
of them. But, if you must, the Jmol application popup menu had a
Stereographic submenu (Style|Stereographic) that allows you to create such
images with substantial flexibility. See also the STEREO command.
https://chemapps.stolaf.edu/jmol/docs/index.htm?command=stereo&ver=14.31
[image: image.png]