I prepared this on Sunday, here it is now:-
Well, I was 'shaken but not stirred' to see a program 'fake_Fobs'. However
James' posting on the Rfactor gap in MX is a more respectable, Sunday morning,
topic. I tried to find the previous threads on this via google and couldn't. So
apologies to all
Dear all,
I run a twin refinement using Refmac,
but it was in failure saying the message below;
Why did it happen?
H. Miyatake
-
free R flag 0
Number of free reflections 12993
Number
It seems you cannot read either your data or a scratch mtz file - the
log file should tell you its name.
There is obviously something funny - see the discussion of free r reflections..
You dont say your pointgroup - presumably P/mmm or P3m or P6/mmm -
they have that twin law.
But with perfect
I don't know of such a program, but I would think that an algorithm that
considered solvent-exposed ionizable residues only (and everything
ionizable in any disordered/missing loops) of a PDB structure, and
applied the typical pKa values of side chains from Thurlkill et al.
(2006) Protein Sci.
Dear CCP4bbers,
I was wondering whether anyone knew of a program that would calculate
the pI of a protein based on its structure rather than its sequence and
whether such a calculation might correlate better with the measured pI
Dave
David Hargreaves
Associate Principal Scientist
CCP4 STUDY WEEKEND 2014
The next CCP4 study weekend will be held on 4th and 5th January 2014 at the
University of Nottingham. The meeting is entitled Two Way Street -
Complementary Methods and the aim is to explore methods that can be used to
complement X-ray structure analysis and to learn
ANNOUNCEMENT
SECOND RESEARCH COORDINATION MEETING (RCM) ON
UTILIZATION OF ACCELERATOR - BASED, REAL - TIME METHODS IN INVESTIGATION
OF MATERIALS WITH HIGH TECHNOLOGICAL IMPORTANCE
_24-27
SEPTEMBER
Hi all:
If have used SC previously to calculate shape complimentarity for
macromolecular complexes. Can this also be used to calculate shape
complimentarity for a (say) protein/small molecule inhibitor complex? Or is
there some other metric/software that can/should be used to quantitate how
Hi Tom,
Yes, SC can be used for calculating protein-small molecule ligand SC. Simply
put the ligand and protein on two separate chains. You probably need to edit
the $CLIBD/sc_radii.lib file to add some atom radii for your ligand. For
example:
ABC N* 1.65
ABC C* 1.90
Zhijie
Hello Everyone,
PHASER is returning the following error Input Error: No Mode Set when called
from MRBUMP.
CCP4-6.3.0 running on Centos5-x64.
Any help , ideas, comment would be greatly appreciated.
Thanks,
Doug
Hi Brett, SC was not developed for this purpose and hence may not be very
useful with its default parametrization. Nevertheless, it could be useful for
cross-comparing the complementarity of different inhibitors to the same site,
but I have not experimented this. The TRIM parameter may need to
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