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Dear Jane,
If you rename one of domains with a different chain ID (in the PDB) you can
submit the structure to PISA
(http://www.ebi.ac.uk/msd-srv/prot_int/pistart.html) and it will do the job.
Regards
Rafa
===
Rafael Fernández Leiro
Departamento de Biología
Dear All,
Apologies for a non-CCP4question. I have a structure of a dimeric molecule,
where the interfaces between monomers is held by a couple of tyrosine
residues (per monomer) juxtaposed with each other. The molecule exists as a
dimer in solution. Are there ways/programs to show that the
amit sharma wrote:
Apologies for a non-CCP4question.
Aggh! Stop! Stop it! Stop apologising for using CCP4BB in the way
it is supposed to be used!
And not only that, this is not a non-CCP4 question.
I have a structure of a dimeric molecule, where the interfaces between
monomers is
Dear colleagues,
I would like to draw your attention to an upcoming educational webinar
that will cover data processing with XDS. This webinar is the 2nd in the
previously posted webinar series to cover X-ray diffraction data
processing packages.
This week's webinar, presented by Kay
Dear Amit
As Paul suggests, you can get some idea if the interaction is consistent
with biologically relevant protein-protein interfaces through looking at the
the size of the interface and the nature of the contacts in the interface.
There is substantial literature on this topic, see
On Monday 22 February 2010 15:23:35 Ed Pozharski wrote:
I want to process bunch of frames with extremely short step - i.e. these
are 0.5degree oscillations but crystal only rotates by 1 degree over
1000 frames (I would have kept it at the same orientation if Rigaku
control software would allow
I want to process bunch of frames with extremely short step - i.e. these
are 0.5degree oscillations but crystal only rotates by 1 degree over
1000 frames (I would have kept it at the same orientation if Rigaku
control software would allow zero step). Denzo can process the frames
all right, but
Try grepping crystal your .x files (or whatever you called the
denzo output files). Also grep for start.
By default denzo updates start-phi to the end
of the previous oscillation. Since 0,5 degree is within radius of
convergence, it re-refines crystal rotx to be compatible with this
assumption
Edward A. Berry wrote:
Try grepping crystal your .x files (or whatever you called the
denzo output files). Also grep for start.
By default denzo updates start-phi to the end
of the previous oscillation. Since 0,5 degree is within radius of
convergence, it re-refines crystal rotx to be
Dear Amit,
You might want to take a look at NOXclass webserver:
http://noxclass.bioinf.mpi-inf.mpg.de/help.php
Relevant paper is available at:
http://www.biomedcentral.com/1471-2105/7/27
Goold Luck,
Partha Sampathkumar
NYSGXRC
On Mon, Feb 22, 2010 at 6:49 AM, amit sharma 3112a...@gmail.com
Hi all,
I am comparing 4 very similar (1.5A rmsd) large (750 residues) structures,
but struggling to find a way to generate a figure that conveys where they
are most alike and where they diverge.
Simply drawing a superimposed set of backbone traces results in what looks
like colored
Applications are invited for a postdoctoral position in Dr. Fang Li's
lab at the Department of Pharmacology, University of Minnesota Twin
Cities. Research involves biochemical and structural studies on
proteins that guide invasion and replication of important viral
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Strong background
One possible representation is the sausage produced by MOLMOL. It is
meant for NMR ensembles - the thickness of sausage is directly proportional
to local RMSD. Take a look at this image:
http://www.msg.ucsf.edu/local/programs/molmol/images/tutorial_ex3.gif
MOLMOL can be downloaded from
I am pretty sure you can do this using LSQMAN from Gerard (BluRay?) Kleywegt.
The pertinent commands are MCENTRAL to determine the 'most
representative structure' (i.e. the one to align upon and show in the
figure), MALIGN to do the alignment and then MPLOT to calculate a
'multi-RMSD' for each
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