Hello everybody,
I have a protien structure file in pdb format which contains the
conservation values in the b-factor column. I would like to project these
values on to the individual residues using some color scheme in jmol and
display the structure.
Can anybody suggest an efficient way of doing
That's ridiculous.
Sorry, but to try to go retro on this is just too strange. Stay with 3D.
Enjoy the modern world of color (or grey scales) and interactivity. The Jmol
documentation gives plenty of help with getting the anisotropic ellipsoids
rendered various ways. We have the cutouts and lines
example please. I was working there recently.
On Sat, Mar 6, 2010 at 9:27 PM, Dean Johnston djohnsto...@gmail.com wrote:
Possible bug with newer version of Jmol (11.9.32).
I'm finding that the arcs that I'm drawing (with the FIXED option) are
popping on and off during animations. This
I'll post one as soon as I can - my current observations are on a complex
page - I'll try and nail it down to the simplest possible case.
Dean
On Mon, Mar 8, 2010 at 8:59 AM, Robert Hanson hans...@stolaf.edu wrote:
example please. I was working there recently.
On Sat, Mar 6, 2010 at 9:27 PM,
Dear Robert,
I really enjoy Jmol and am currently using it on a website I help create for
the kink-turn RNA motif
(http://www.dundee.ac.uk/biocentre/nasg/kturn/kturns_all.php).
Do you plan to develop a way to align model 1 onto model 2 in Jmol script?
Pairfit in PyMol does it, so there may be
I kinda agree with Bob. I certainly wouldn't want Jmol to be able to
produce something of the quality of the image in that first link Egon
quoted :-) But, if Jmol is to be a tool to produce hard-copy images for
publications then an argument could be made for a really good-looking ORTEP
style image
Labeling -- my experience is that label positioning for final copy is a real
pain, and no smart program is going to do it well. Most publishers will
prefer to put their own labels in anyway no matter what you do.
Nonetheless, the following is SUPPOSED to work well:
set picking labels
and then
This could be dead easy...Let's say I: load xxx.cif {5 5 5}and now want to select the 3x3x3 cells btwn {2 2 2} and {4 4 4}is there a clean way of doing so?--Phil
--
Download Intel#174; Parallel Studio Eval
Try the new
A suggestion:
If that is all you have, I would suggest pre-aligning. It's easy enough with
those other programs --- just get the offsets necessary and then apply them
in Jmol using
translate {some atom list} {x.xxx y.yyy z.zzz}
if you don't want to create all new model files.
On Mon, Mar 8,
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