Using your favorite editor, you can copy the LINK record from the pdb file
generated by Coot and paste it into the pdb file produced by Phenix. You can
also make a script to do this. This is what I did during the time LINK records
were not properly handled by coot, refmac and buster.
Best
I'm using a 24 BenQ XL2420TX (emitter builit-in; price 500€) monitor connected
to the DisplayPort of a Quadro FX 380 card. Works very well on 64bit
ScientificLinux 6.4 with the kmod-nvidia driver from ElRepo.
Please also see
http://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php/Stereo .
Dear bulletin board members,
A referee came back with a question about the accuracy of refined
group-occupancies. In the manuscript we describe 3 crystal structures with
resolutions between 2.1 and 2.4 Å. In all three cases, the inhibitor has been
fitted in two alternative conformations and
Thank you all for your suggestions.
Greetings,
On Thu, Nov 21, 2013 at 6:19 PM, Jim Pflugrath jim.pflugr...@rigaku.com wrote:
Here's an easy experiment to try:
What happens when you flash-cool your reservoir solution in Liquid Nitrogen?
Does it remains glass-clear at 100 K or lower?
-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1
Dear Herman,
you could apply random shifts to the occupancies, coordinates, and
B-values and refine a large number of times, e.g. with 50 variations.
Then you can calculate the mean occupancies with standard deviations.
That's give you an idea about
Dear CCP4ers,
apologies but the actual deadline for the advertised post is the 29th November
2013 (and not 2014). So only one week left to apply and not one year.
Best,
Alessandro
A post-doctoral position is available immediately in the laboratory of Dr.
Alessandro Vannini, within the
A 4-year Ph.D studentship in Structural Biology starting October 2014 is
available in the Research Group led by Dr. Christian Siebold. Our group, based
in the Division of Structural Biology (STRUBI) at the Wellcome Trust Centre for
Human Genetics, University of Oxford is primarily focused on
If you suspect your MR solution is crystallographically correct but it
does not represent the biological entity - eg - you will generate a
dimer if you move molecule B by a symmetry operator such -x,y-1/2,1-z
then the easy way is to submit the coordinates to PISA - either in the
CCP4 GUI or send
Thanks, Herman.
Zhijie, what is the difference between LINK and LINKR?
Maybe this will help somebody (though phenix-related):
phenix.link_edits parses the pdb for LINK records and outputs the pdb.edits
file.
Alternatively, phenix.ligand_linking can guess what should be bonded in the
absence of
Hi,
If you get the 0.8-pre prerelease version of coot, there's a fantastic new
feature that makes this much easier. Instead of File-Save Symmetry
Coordinates, you just center on the symmetry copy that you want to use as the
master copy and select Extensions-Modelling-Symm Shift Reference
Hi Dimetry,
The difference between LINK and LINKR can't be explained better:
http://www.mail-archive.com/ccp4bb@jiscmail.ac.uk/msg11865.html
Older versions of COOT used to not display the LINKR record, but now the
newer versions display both LINK and LINKR records as dotted bonds. I assume
that
http://portal.limon.gen.tr/gm/itfhmazeeuauqaqvqmzusuu.html
Rex Palmer
11/23/2013 2:52:00 AM
Dear all,
I am looking into ordering a stereo notebook to view 3D protein structure.
Which notebook can you recommended? I require that the 3D notebook will be
used with Linux and Windows, so support of the correspoding graphics card with
both systems is required.
In addition, I found that
13 matches
Mail list logo
