picking. If you happen to have an automated
ligand-fitting technology you can throw that in also.
I use this script all the time for projects (usually cocrystals or fragment
screening) where I have many data sets and I want an efficient route to the
first maps.
Thanks
John Badger
is not made very
often but that is more a shame on the reviewers than the willingness of the
journal at this point in time.
Of course, it is a confusing situation when you only see density for a part of
a ligand and it comes up all the time.
Thanks
John Badger
.
MIFit and MIExpert will continue to be developed and improved. Feedback is
welcomed.
Bradley A. Smith, Ph.D., MIFit Project Manager
John Badger, Ph.D., MIExpert Author
I would echo Ethan on this metric being something of a relic and add a bit
more data.
Several years ago I tried to get a practical solution to the questions:
- when is a refinement finished?
- how to detect the correctable abnormalities (errors) in a structure so they
can all be corrected
Hi Ethan,
Your effort to play devils advocate is appreciated - I have not seen much
debate on the applicability of TLS so at risk of diverging into a separate
thread:
I would not argue that TLS is necessarily a valid model for correlated motion
in
proteins because it 'works' in fitting the
, 1995.
From this perspective it is quite surprising that crystallographers are so keen
on using TLS models for fitting displacement amplitudes.
John Badger
The SDsearch software is used to search compound libraries in the form
of SD files over chemical properties and chemical substructures.
SDsearch 2.0 now adds multi-conformer docking to check the steric
compatibility of compounds that contain positioned subfragments within
protein target sites.
The SDsearch application is intended to allow crystallographers and other
structure analysts quickly find analogs of known ligands or build small
fragment/scaffold libraries without incurring the cost or requiring the
technical
resources needed to establish commercial database software. For
Simple test is to vary the occupancy (say increments of 0.1) and check for
residual densities following quickie refinements on each. Then at least you
know if you can make a conclusion or not.
I suppose you could also try refining coupled occupancies on ligand-sized
chunks of the protein to
Many people responded with questions following our first
announcement of a ready-to-use small fragment screening library
designed for protein crystallographic screening. Given suitable crystals,
the methodology is of interest to anyone wishing to probe ligand
binding interactions and motifs
For MIFit downloads stats are 63% windows, 27% Linux (no fully functional
Mac port yet).
I have been doing crystallography on moderately high-end Windows laptops
for a few years now - mostly MIFit with CCP4 but SHELX, MOSFLM, d*TREK
etc are also fine. Performance is NOT a practical issue as
If you mean that you have many structure files for the same protein but with
different ligands you can automatically align them all based on just the target
site CA atoms (i.e. defined as those close to one of the ligands) using the
Job/Cocrystal superposition application in MIFit8
/deprecated/src/arp_waters_
If you type make in $CCP4/deprecated/src you should get it back.
We are examining alternatives for water-picking that workable in the context
of automated refinement and are not aware of any other incompatibilities at
this time.
Thanks
John Badger
as it is one of the more unique programs, perhaps without a direct
substitute.
As a sidebar, Windows interoperability and reduction of cost/complexity in the
crystallographic computing environment is the main reason for preserving
arp-waters in CCP4.
Thanks
John Badger, Director of Structural Biology
. There is an
installer for Windows and gzipped tar file for Linux
http://mi.active-sight.com/download.html
There is a lot of flexibility in rendering and image export.
Thanks
John Badger, Director of Structural Biology, ActiveSight
are now being accepted for poster presentations.
Please see http://fbld2008.com/ for more details.
Individual inquiries may be address to Mary Canady at
[EMAIL PROTECTED]
Thanks
John Badger, Director of Structural Biology, ActiveSight
16 matches
Mail list logo