Hello,
I was wondering what people used to generate difference map images of,
say, a ligand in their structures?
e.g. Figure 2a here
http://journals.iucr.org/f/issues/2009/05/00/tt5012/tt5012.pdf
Cheers,
Andy
Andy,
One important thing if your complex crystals are isomorphous with apo is to
use nFo(complex) - Fo(apo). These maps give the maximum information as the
uninterpretable 'stuff' in the Fo-Fc map is likely quite similar in both
crystal forms so the difference signal should be cleaner.
Douglas
Andy,
on the practical point of view, you can create such images using Pymol
and the command 'carve'.
load composite_omit-ccp4.map, map-to-display, format=ccp4
isomesh mesh, map-to-display, 1.5, resi 45, carve=3
color blue, mesh
this will display the map at 1.5 sigma, at 3 angstroms around the
Wow, you can read too! Impressive.
Indeed, it seems Larson et al did use Pymol, as have I. The question
to the board was what they use, so that I might experiment with other
methods.
Any other helpful suggestions, please don't hesitate Jon.
Thanks to all for their responses.
A
2009/6/17
Hi Douglas
Do you have some references with examples of this technique? In my
experience this is a difficult experiment to perform routinely except in
a few special cases. The first problem is that soaking the ligand can
easily induce significant cell dimension changes, which if large enough
Ian,
I know that sometimes Fo(complex)-Fo(apo) cannot be done because of
nonisomorphism. We've had a lot of success with this with the dioxygenases
because there is no large scale alteration in the active site. As for the
technique itself, Brian Matthews drilled this into me when I was a postdoc
Post Doctoral Position in X-ray crystallography at University of
Colorado Denver
An NIH funded post-doctoral position in X-ray crystallography is
available in the Department of Pharmacology at the University of
Colorado Denver School of Medicine, working with Dr. David N. Jones
I get this:
read(5,100)xinten,siginten,fobs,sigfobs,itest
100 format(6x,3i5,3(6x,f10.3),/,25x,f10.3,6x,i10)
On 17 Jun 2009, at 4:18 PM, Francis E Reyes wrote:
INDE 00 -9 IOBS= 9062.000 SIGI= 200.300 FOBS=95.190
SIGMA= 1.060 TEST= 0
I know that sometimes Fo(complex)-Fo(apo) cannot be done because of
nonisomorphism. We've had a lot of success with this with the dioxygenases
because there is no large scale alteration in the active site. As for the
technique itself, Brian Matthews drilled this into me when I was a postdoc
in
I'd appreciate it if people could tell me their experiences with what I
would call phantom crystals, or ghost crystals. These are objects
that display the seeming morphology of crystals (clear facets, sharp
edges) but do not diffract X-rays AT ALL. I would not count objects
that diffract to 30 A
Dear Miri,
I cant find the FROFIT you mentioned.
sincerly
S.Jayashankar
Research Student
Institute for Biophysical Chemistry
Hannover Medical School
Germany.
On Tue, Jun 16, 2009 at 8:03 AM, Miri Hirshberg m...@ebi.ac.uk wrote:
Tue June. 16th 2009
EBI
For example, FROFIT, where you can
Do you include detergent artifacts in your query (even those containing
protein)? If so, you will be deluged...
Jacob Keller
***
Jacob Pearson Keller
Northwestern University
Medical Scientist Training Program
Dallos Laboratory
F. Searle 1-240
2240 Campus
You want my whole life story?
Briefly, RNA does this often, simply out of spite.
William G. Scott
contact info: http://chemistry.ucsc.edu/~wgscott
On Jun 17, 2009, at 3:11 PM, George DeTitta wrote:
I'd appreciate it if people could tell me their experiences with
what I
would call
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