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Jed Goldstone, PhD
Research Specialist
Woods Hole Oceanographic Instit
Vincent,
You could use data2bfactor.py and then "spectrum b" to color residues in
cartoon settings.
https://pymolwiki.org/index.php/Color
(data2bfactor from Robert Campbell's script repository:
http://pldserver1.biochem.queensu.ca/~rlc/work/pymol/
Jed
On 1/4/2017 11:05 AM, vincent Chaptal
Vaheh,
You can modify the b-factor column, and color by b-factor. I have used
various value-to-bfactor scripts, with different measures of alignment
similarity.
The one problem I've had is extending the Ca color to the rest of the
residue in stick mode.
Jed
On Oct 28, 2015 3:34 PM, "Oganesyan,
body, registered in
Scotland, with registration number SC005336.
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Jed Goldstone, PhD
Research Specialist
Woods Hole Oceanographic Institution
Redfield 3-52 MS#32
Woods Hole, MA 02543
http://www.whoi.edu/hpb/Site.do?id=481
Phone: 508-289-4823
up in the first state (and
the cartoon representation is a subset of what it should be (other
representations are fine).
I'm using incentive v1.6.0.0 on Windows 7.
Jed
--
Jed Goldstone, PhD
Research Specialist
Woods Hole Oceanographic Institution
Redfield 3-52 MS#32
end
Cheers,
-- Jason
On Thu, Jan 16, 2014 at 9:28 AM, Jed Goldstone jgoldst...@whoi.edu
mailto:jgoldst...@whoi.edu wrote:
I know this seems silly, but I can't figure out how to combine
multiple
separate objects into one multistate object. I have a set of Modeler
models loaded
-users@lists.sourceforge.net
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Jed Goldstone, PhD
Research Specialist
Woods Hole Oceanographic Institution
Redfield 3-52 MS#32
Woods Hole, MA 02543
http://www.whoi.edu/hpb/Site.do?id=481
Phone: 508-289-4823
))
File C:\Program
Files\PyMOL\PyMOL/modules\pmg_tk\startup\Caver3_0_1.py, line 638, in
loadFileContent
handler = open(file)
type 'exceptions.IOError': [Errno 2] No such file or directory:
'C:/Users/Jed/modeling/caver/caver_output/2/warnings.txt'
--
Jed
James-
I think you need to seriously consider using software that's actually
designed to compute and refine protein models, such as Modeller. There
are forcefield and structural constraints that PyMol is just not
designed to do, and your results may not have the scientific validity
you
/
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Jed Goldstone, PhD
You might want to try using Modeller instead.
http://www.salilab.org/modeller/wiki/Mutate%20model
It does higher level modelling.
Jed
Martin Hediger wrote:
Dear List
I'm trying to automate the following sequence of steps in a PyMOL python
script:
1. Start the mutagenesis wizard
2. Mutate a
\startup\CASTpyMOL_v2.pyc
Error: unable to initialize plugin 'CASTpyMOL_v2'.
Does anyone have any idea how to fix this issue?
Thanks, Tomas
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Jed Goldstone, PhD
Research Specialist
Woods Hole Oceanographic Institution
Redfield 3-52 MS#32
Woods Hole, MA 02543
unfamiliar with this, and do not know how to implement it
(my desktop runs PyMol 1.2r1 on Windows XP). Would this be an
appropriate solution? Would it work to call remote plugins?
Jed
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Jed Goldstone, PhD
Research Specialist
Woods Hole Oceanographic Institution
Woods
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Jed Goldstone
Research Specialist
Woods Hole Oceanographic Institution
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http://www.whoi.edu/hpb/Site.do?id=481
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Woods Hole Oceanographic Institution
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Jed Goldstone
.
Apologies to the list,
Jed
Robert Campbell wrote:
Hi Jed,
On Mon, 22 Mar 2010 10:23:34 -0400 Jed Goldstone jgoldst...@whoi.edu wrote:
Of course, you could just use the .pdb file as a text file:
grep CA .pdb | cut -f 2,4,7,8,9
will get you the amino acid number, the amino acid
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Jed Goldstone
Research Specialist
Woods Hole Oceanographic Institution
Redfield 3-52 MS#32
Woods Hole, MA 02543
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Error: unable to initialize plugin 'autodock'.
Any help would be greatly appreciated.
Jed
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Jed Goldstone
Research Specialist
Woods Hole Oceanographic Institution
Redfield 3-52 MS #32
?
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Jed Goldstone
Visting Investigator
Woods Hole Oceanographic Institution
Redfield 3-52 MS #32
Woods Hole, MA 02543
http://www.mit.edu/people/jedgold/home.html
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