On Oct 1, 2009, at 7:51 PM, Charlie Bond wrote:
A note of caution: if a program doesn't show something as a beta
strand that must mean that that part of the molecule doesn't have
the attributes for strand. Rather than cosmetically fix it by
changing it in pymol, it might be a good idea to lo
Dear Raja,
A note of caution: if a program doesn't show something as a beta strand
that must mean that that part of the molecule doesn't have the
attributes for strand. Rather than cosmetically fix it by changing it in
pymol, it might be a good idea to look closely at the structure/density
an
Raja
Here is a snippet from one of my PML scripts.
# beta sheets: alter A/447-451/, ss='S' ; rebuild
alter A/447:451/ and "MyModel", ss='S'
rebuild
Hope this helps,
Mark
On Thu, 2009-10-01 at 16:11 -0500, Raja Dey wrote:
>
> Dear Friends,
> Sorry for the off topic question
On Thu, Oct 1, 2009 at 2:11 PM, Raja Dey wrote:
> Dear Friends,
> Sorry for the off topic question. How I can force PYMOL
> to display a portion of the molecule as beta sheet? PYMOL is displaying this
> part as a loop by default, but I like to see this as beta sheet. Is there
>
Dear Friends,
Sorry for the off topic question. How I can force PYMOL to
display a portion of the molecule as beta sheet? PYMOL is displaying this part
as a loop by default, but I like to see this as beta sheet. Is there any way?
Thanking you in advance...
Raja
Yahoo!
Does anyone know how to convert data in Saint format into a format that
is recognized by Scala?
Best regards
Sylvia Fanucchi Ph.D
Protein Structure-Function Research Unit
East Campus, Gate House Room 416
School of Molecular and Cell Biology
University of the Witwatersrand
Johannesburg 205
MACROMOLECULAR CRYSTALLOGRAPHY BEAMLINE X06DA AT SLS
Deadline: Thursday, October 15, 2009
Periods:
January 1, 2010 - April 30, 2010 ( Normal / Test proposals)
January 1, 2010 - December 31, 2011 ( Long-term proposals)
Beamline features: (http://sls.web.psi.ch/view.php/beamlines/px3/index.ht
Whilst Eleanor is reformatting ACORN2 you might like to try the new
beta-test autotracing version of SHELXE which is also very good at
expanding from a small but accurate fragment given relatively high
resolution data, with or without experimental phase information.
At the moment you have to sen
Dear all,
Another job advertisement :-)
We have an opening at the ESRF Macromolecular crystallography group (
http://www.esrf.fr/UsersAndScience/Experiments/MX) for a Post-Doc to study
proteins sensitive to X-ray damage or Reactive Oxygen Species using X-ray
crystallography and complementary spec
Dear all,
Another job advertisement :-)
We have an opening at the ESRF Macromolecular crystallography group (
http://www.esrf.fr/UsersAndScience/Experiments/MX) for a Post-Doc to study
proteins sensitive to X-ray damage or Reactive Oxygen Species using X-ray
crystallography and complementary spec
Then I suspect the sequence is overriding the model.
My preferred approach.
Get a sequence alignment from somewhere and use CHAINSAW to edit the
model you want to use. That is documented! And it will edit both
monomers in turn I believe..
Then you will have a dimer with the appropriate seque
Mea culpa
I am (slowly) getting it from Michael Woolfson form to a CCP4 compatible
version.
If you like I can send you the old version but you will have to reformat
mtz etc.
Thank you for the reminder -0 I wll move the job to a higher personal
priority!
Eleanor Dodson
José Manuel Otero C
How can that be! Are you also providing a sequence?
Eleanor
Tommi Kajander wrote:
Hi,
I have been using a dimer as a search model in MOLREP (there will be
several in AU),
for some reason the program tends to break the dimer into monomers
wihtout asking me..
how is this determined in the prog
It is hard to believe that REFMAC is being driven by rotamer
conformations - REFMAC weighting scheme gives a low priority to fitting
a preferred rotamer - quite rightly since the SD on rotamer angles is
high. The ideal is only "ideal" for a residue in a near vacuum - the
interactions with othe
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