To reply to the original question, "can the calculated Matthews coefficient be
wrong?":
have you read the paper by Matthews? There is a distribution of solvent content
in macromolecular (protein)
crystals. It has a "peak" and tails on both sides. Meaning that there are
"outliers" in the distrib
Hi everyone:
Thanks for all the responses.
The Matthaws-cell content analysis programe in CCP4 package gives the
results: 47% solvent content and 3 molecules in asu with 87% confidence.
the space group is P3121. how to carry out self rotation function? can
phaser do that work? If there a
hi CCPeers
The Matthews coefficient of my protein is 3 calculated with matthews-cell
content analysis CCP4 programe with 87% confidence , but when doing the
refinement the third molecular couldn't get into the unit cell because of
too many clashes.Deletion of the clashed AA did not work well, T
Hello,
I used this script once just to have a look
at some NMA-moved structures:
---
#!/bin/bash
if [ "$#" -ne "1" ] ; then
#0 1
echo "usage: phaser_nma.sh INPUT.PDB"
exit 1
fi
name=`echo $1 | sed "s/\.pdb$//g"`
phaser << EOF
TITLE moved by some low frequen
In your run with the option "residues are close only" refmac also
should generate a pdb file with link records added. In very simple
form you can edit this pdb file and remove all unnecessary links and
leave link you want. Then you can rerun with normal options and
generated library.
Better
Dear Dr. Murshudov,
I am working on the heme protein with a surface Cys residue
covalenlty linked to another molecule through its SG atom.
Here is a part of log file.
--
INFO: link is found (not be used) dist= 2.188 ideal_dist=
2.300
ch:AA res: 400 C
Dear all,
A position has become available for a Post-doctoral Refsearch Fellow
in the Department of Pharmacology, at Baylor College of Medicine in
Houston. The focus of our work is on structural and biochemical
characterization of Serine/Threonine protein kinases. The successful
candidate will be
I am getting an error in running Phaser in NMA mode based on the usage in
the Phaser document.
#
#
##
Hi Ian:
There was an issue with the environment setup of my PBS script, which has
just been fixed and everything back to normal. Anyway, thanks a lot for
all the help!
Best Regards, Hailiang
> On Thu, Jun 24, 2010 at 4:15 AM, Hailiang Zhang wrote:
>> Hi Tim:
>>
>> Thanks a lot for suggeting "ex
It might be instructive to draw a precession-like diagram of your
reflections in reciprocal space. Remember that reciprocal space dimensions
are generally in reciprocal Angstrom and volumes raise those dimensions to
the third power. Thus (1/12)^3 to (1/15)^3 is not a big volume.
How many reflect
Francis E Reyes wrote:
Sorry a late comer to this thread but the OP mentioned "tweaking the
error model" in HKL2000. I have heard this before.What's the validity
in this? Does it actually help or does it only help the integration
numbers but you'll pay for it during refinement?
FR
There is n
That was quick. They are all taken.
Frances
=
Bernstein + Sons
* * Information Systems Consultants
5 Brewster Lane, Bellport, NY 11713-2803
* * ***
*Frances C. Bernst
Improved Version of ADIT Available
An updated and enhanced version of ADIT is now available for
depositing new entries at http://deposit-beta.rcsb.org/adit/. We
encourage depositors to use this new tool and send feedback to
depo...@deposit.rcsb.org.
ADIT is used to validate and submit st
Dear CCP4bb,
I am still playing around scaling two datasets together and have
noticed another interesting behavior in scala. If I scale all my data
(from 1.5A to 51A) I get 100% completeness in my outer shell, 98% in
my inner shell and 99.9% overall, stats that I am normally quite happy
w
If anyone can use any of these, please let me know. The only thing
I ask is postage reimbursement.
Vol. 16 1980"Structure and Bonding Relationships Between Quantum
Chemistry and Crystallography", T.F. Koetzle, Ed.
Vol. 17 1981"Diffraction Aspects of Orientationally Disor
GRADUATE PROGRAMS IN BIOLOGICAL SCIENCES:
BIOCHEMISTRY-IMMUNOLOGY & PHYSIOLOGY-PHARMACOLOGY
Institute of Biological Sciences Universidade Federal de Minas Gerais - Brazil
"Fellowship available"
The coordinators of the Graduate Programs in Biochemistry-Immunology and
Physiology-Pharmacology of th
On Thu, Jun 24, 2010 at 4:15 AM, Hailiang Zhang wrote:
> Hi Tim:
>
> Thanks a lot for suggeting "exec" in my shell script. It really works
> under both shell and PBS; however, the running was just terminated right
> after "exec ${DIR}/lx_mapman" was excutated. I am not sure why this
> happens:-(
Matheus, Ian, Frank, Jonathan
Thanks for all the comments.
It is easy to calculate the amount of splitting of the spots once the
cell dimensions of each component are known. For the P212121 case, with
a-b twinning, splitting will be zero in the c* direction. The splitting
will increase as h and k
Hi there,
If there are a few clashes (acceptable - usually surface loops that
"enter" the surface part of another molecule or subunit) then you can
delete the parts of loops that usually have poor density and that clash,
refine, compute a new map and see if the loop can be traced (usually it
Rfactors can vary a lot for equally good results it seems. You need to
look at your Rfactor v resolution to see if there are any problems - ice
rings? low resolution stuff? etc etc
Have you used TLS sensibly - this can help..
etc etc
But if the maplooks good you should be happy.
Eleanor
Tim G
If this is happening something is wrong!
REFMAC can certainly use multiple NCSR requests..
I usually check the agreement with the Superpose molecules task
(Coordinate utilities) matching all atoms just to make sure that AC does
match A'C' and B matches B'. If the RMS difference is greater than
Dear All,
I am trying to resolve a protein structure with the use of Molecular
Replacement. However, some part of protein are overlap in the interface of
homodimer. Would someone please give me suggestions? Thank you!
--
Best regards,
WuXH
Or download the latest refmac 6.6, and it will do NCS fully
automatically, and handle conformational flexibility too.
David Schuller wrote:
I think you should be able to specify two different "NCSR" lines, one to
cover chains A&A' and C&C', and another to cover chains B&B'.
On 06/23/10 18:51
23 matches
Mail list logo