Hi,
Thanks for those who replied to this thread.
I have been trying all the means that people suggested: search protein
alone, DNA alone. However, both not working out.
One thing Ray Brown suggested "MR works if the molecules have identical
sequences". So I just played around with the following wa
That looks very hopeful. Do you know how the two molecules are related to
each other? Do they form a dimer or have some interesting relationship?
I would keep on improving the model - possibly use COOT to average the
density and build into that for a start. I presume there are still side
chains to
Hi
In iMosflm, check the bottom line of the display in the "Cell
Refinement" task at the end of refinement (there are three lines
there - initial cell (i.e. before refinement), final cell (after
refinement has finished) and "std dev" (the standard deviation
determined from the refinement)
On Jul 22, 2011, at 4:24 AM, Xiaoguang Xue wrote:
> I noticed that the Fink repository will not run on the Lion system
All the debian utilities work (as does the crystallography software), so it is
just the fink perl wrapper script itself that doesn't work.
Here is a cheap and easy, but unoffic
Hi all,
After about a year of not working with XDS, I was a little surprised to see
that adding a REMOVE.HKL file to the current directory and running CORRECT does
not remove outliers. I still see the same reflections reported at the end of my
new CORRECT.LP file and I have grepped the XDS_ASCI
A postdoctoral position is available immediately in the group of
Ethan Merritt at the University of Washington - Seattle.
This project involves the structure-based design and development of
drugs targeting disease caused by eukaryotic parasites. It combines
crystal structure determination done i
Hi,
Does any one know which software could calculate and output
non-crystallography symmetry operator?
I am working on a structure with two molecules in one ASU, and two identical
subunits in each of one molecule. I would like to know the
non-crystallography operator of the two molecules, and al
On Mon, 2011-07-25 at 13:24 -0400, zhang yu wrote:
> which software could calculate and output non-crystallography symmetry
> operator?
LSQKAB, SUPERPOSE - there are other options, of course
--
Oh, suddenly throwing a giraffe into a volcano to make water is crazy?
Hello all-
(Paging Paul and Alexei)
I recently came across a difficulty in Coot and Molrep in parsing PDB
files containing insertion residues of the type where the residue number
is the same but with an A, B, etc appendage.
For example, PDB file 2CMR has several instances of the following type:
Thanks for all the reply. I am able to use "phenix.find_ncs" find NCS
operators for all the chains. But it doesn't give a NCS matrix between whole
molecules in ASU. Is that right or I missed something?
In "SUPERPOSE" of CCP4, How to ask the program to calculate the NCS
operator? It asks me to inpu
My favorite test for truth in molecular replacement solutions is whether or not
the map shows density for something that you know about but the computer
doesn't. Take out a base pair or two, or delete some nice fat side chains, and
see if they still show up in the density when you use that mode
Hi Engin,
I encountered the same issue a couple of months ago. As I understand,
the REMOVE.HKL file will only be used if you specify the spacegroup
and unit cell in the XDS.INP file.
Cheers,
Florian
On Jul 25, 2011, at 1:14 PM, Engin Özkan wrote:
Hi all,
After about a year of not worki
Thank you, Florian! That did it. This should be included in the docs.
Engin
On 07/25/2011 01:23 PM, Florian Schmitzberger wrote:
Hi Engin,
I encountered the same issue a couple of months ago. As I understand,
the REMOVE.HKL file will only be used if you specify the spacegroup
and unit cell i
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