Dear Shveta,
I have seen similar trends with PRODRG. I recommend you to use
other molecular modeling programs like Hyperchem or Maestro to get more
consistent geometric parameters for small molecules. Once you know the
bondlengths and bond angles from aforesaid molecular modeling programs, you
On 09/01/12 06:13, Shveta Bisht wrote:
I need advise on the way I have run prodrg and the explanations for the results.
There is little room for manoeuvre when running prodrg.
Prodrg is not the Font of All Ligand Wisdom.
Prodrg makes mistakes.
If you think that the bond lengths are wrong,
Dear all,
Is there a mean to obtain statistics about R-Sym for deposited structures
databases ?
I know it is possible for R-Free values but is it the case also for R-Sym ?
Guillaume Gotthard, PhD student
Biocristallography, Biotechnology and Structural Enzymology Group
URMITE Laboratory - UMR
1) You say 3000 reflections - 400 parameters, but you arent including
the restraints as observations - refinement and rebuilding IS possible
at 3.2A..
2) B factors not unreasonable for the data.. You may want to use fixed
Bs with TLS or restrain Bs strictly..
3) How can your FreeR and r
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Dear Guillaume,
I am not sure which database you refer to, but for every structure
deposited at the PDB since 2007, the data are available, too.
The PDB-header might report R_sym as should the publication.
Buy the whey, you should better get used
Dont forget Rsym and Rmerge are one and the same I believe..
Eleanor
On 01/09/2012 11:05 AM, Tim Gruene wrote:
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Dear Guillaume,
I am not sure which database you refer to, but for every structure
deposited at the PDB since 2007, the data are
Thank you Shveta for NOTICING!!!
Please - everyone - check your restraints - programs make mistakes - you
(or the chemist who made the ligand) - are the experts
Eleanor
On 01/09/2012 10:05 AM, krish wrote:
Dear Shveta,
I have seen similar trends with PRODRG. I recommend you to use
On 08/01/12 10:36, ccp4 wrote:
Won't coot fix the nomenclature issue, then you can check whether you have
a real chirality problem - eg a squashed flattened VAL..
It will indeed [1]. So Afshan need only read in the file, Press OK and
then Save.
Robbie and I think that it is more likely
The problem with fixing the nomenclature problems in Coot is that they are
back again after the next round of refinement (or at least some of them are, if
they are right on the edge of an arbitrary distinction) - indeed irritating
Phil
On 9 Jan 2012, at 11:43, Paul Emsley wrote:
On 08/01/12
Hi Phil,
It is annoying problem especially for Phe and Tyr which have standard
rotamers close to the critical chi angles (-90 and +90). Asp and Glu do not
have standard rotamers near critical angles, so the problem should be much
smaller (but I still get them too often). If Val, Leu and Arg
That looks to me as if the critical Chi definitions are inappropriate for Phe
Tyr!
On 9 Jan 2012, at 12:24, Robbie Joosten wrote:
Hi Phil,
It is annoying problem especially for Phe and Tyr which have standard
rotamers close to the critical chi angles (-90 and +90). Asp and Glu do not
On 9 January 2012 06:13, Shveta Bisht shv...@mbu.iisc.ernet.in wrote:
Dear all
I have generated a refmac cif file for a molecule using PRODRG. I used
JME editor to draw the molecule and ran PRODRG online with the
options: Chirality-Yes, Charges-Reduced and EM-Yes. Please check the
I will second Ian's recommendation for GRADE from the Global Phasing group.
GRADE overcomes nearly all of the shortcomings we have encountered with other
approaches for ligand dictionary generation.
Best-
Steve
-Original Message-
From: CCP4 bulletin board
On Mon, 2012-01-09 at 10:28 +, Guillaume Gotthard wrote:
Is there a mean to obtain statistics about R-Sym for deposited
structures databases ?
1. It's actually quite easy to do on your own if you want. This
one-liner will get you the Rsym
wget
Also R cryst is sometimes used for the same number, I think (of course
there are historical reasons for the different terms, but...).
JPK
On Mon, Jan 9, 2012 at 8:47 AM, Ed Pozharski epozh...@umaryland.edu wrote:
On Mon, 2012-01-09 at 10:28 +, Guillaume Gotthard wrote:
Is there a mean to
The Chook Lab (Department of Pharmacology, UT Southwestern, Dallas, TX;
http://www4.utsouthwestern.edu/chooklab/) is currently seeking a postdoctoral
fellow with expertise in protein biochemistry and structural biology. The
project involves molecular recognition of protein and nucleic acid
A CECAM/CCP4 Workshop will take place at the Spanish CECAM node in
Zaragoza from 19:00 on March 11th to 20:00 on March 16th 2012. The
overall objective of this course is to provide an intensive practical
training in all computational aspects of macromolecular structure
elucidation by X ray
Dear all,
The Alba Synchrotron (Barcelona, Spain), and in particular its MX beamline,
BL13-XALOC, is open for user applications for the first time. In order to
apply, please register at the Alba User Office Application (
http://useroffice.cells.es/ http://useroffice.cells.es ). Worldwide
Dear Bernhard,
a) will be fixed in the next release by changing %MMCIFDIC%; for now the
workaround is what you wrote. Thanks for reporting it.
d) it's ok, ccp4-6.2.2.msi is a new packages for version 6.2.0.
Someone else may address b) and c)
Regards,
Marcin
There is currently a position available within the Structure
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Please use the AstraZeneca Careers website to submit your application,
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The link to the job, with a role description can be found using the link
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Dear crystallographers
A theoretical question - can sub-angstrom resolution structures only be
obtained for a limited set of proteins? Is it impossible to achieve for
membrane proteins and large complexes?
Theresa
In theory, no: sub-angstrom resolution can be obtained for any and all
proteins, including membrane proteins, and for large complexes. In
reality, it becomes technically very difficult to achieve; you would need
ever-colder temperatures and ever-stronger irradiation sources.
P.S. In theory, the
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Hi,
in my opinion the resolution limit of crystals from large complexes/
membrane proteins is more likely due to lattice imperfections and
long-range disorder, and cold neither cold temperatures nor stronger
radiation sources would circumvent this
The word theory in this thread/question has to be clarified better.
Jacob
On Mon, Jan 9, 2012 at 1:27 PM, Tim Gruene t...@shelx.uni-ac.gwdg.de wrote:
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Hi,
in my opinion the resolution limit of crystals from large complexes/
membrane proteins is
On Mon, 2012-01-09 at 18:15 +, Theresa H. Hsu wrote:
Dear crystallographers
A theoretical question - can sub-angstrom resolution structures only be
obtained for a limited set of proteins? Is it impossible to achieve for
membrane proteins and large complexes?
Theresa
On the matter
On Monday, January 09, 2012 11:37:23 am Ed Pozharski wrote:
On Mon, 2012-01-09 at 18:15 +, Theresa H. Hsu wrote:
Dear crystallographers
A theoretical question - can sub-angstrom resolution structures only be
obtained for a limited set of proteins? Is it impossible to achieve for
On Fri, Jan 06, 2012 at 04:23:03PM +0800, ?? wrote:
Also, there is one more information I forgot to mention---I also have the
NMR assignment(HNCACB spectrum) of the protein, is it possible to combine
the NMR data in my refinement?
Yes - we did something a few years back for the structure
To elaborate further on software packages available that do a reasonable job of
fitting small molecules and outputting reasonable dictionaries, one could
consider Afitt from OpenEye Scientific Software. They have academic as well as
commercial licenses to their software.
Cheers, tom
I like that animation a lot, as it shows the gradual nature of the
lattice effect, but it is not exactly what I am looking for. I am
actually just curious what the pattern behind the spots looks like for
various molecules, and would like to see an image of that in various
orientations. I guess one
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