The RCSB PDB Validation server will also report this info for you.
Diana
**
Diana R. Tomchick
Associate Professor
Department of Biochemistry
University of Texas Southwestern Medical Center
5323 Harry Hines Blvd.
Rm. ND10.214B
Dallas, TX 75390-8816
d
According to the PDB Format document, entries with missing
atoms should have a parsable REMARK 470. You might want
to write some quick code to look for that REMARK.
The PDB staff could comment about the accuracy of REMARK
470 in its entries.
Frances Bernstein
===
Hi Ed,
On Tue, Aug 23, 2011 at 12:39 PM, Ed Pozharski wrote:
> I would be pretty sure there is something like
> phinix.which_atoms_are_missing or such :)
>
good idea! I can turn the script that I just sent into this command so it is
available in a couple of days -:)
Pavel.
Hi Tiago,
easy, two steps:
1) Save the lines between *** into a file say called run.py:
***
import os,sys
from mmtbx.monomer_library import pdb_interpretation
from mmtbx import monomer_library
import mmtbx.monomer_library.server
from cStringIO import StringIO
def exercise(args):
file_name = a
David Schuller wrote:
On 08/23/11 15:01, Ed Pozharski wrote:
On Tue, 2011-08-23 at 12:36 -0600, Francis E Reyes wrote:
Seems to be a quiet day on the BB
So you need an earthquake :)
Had one already, thanks.
Apparently sent from the vicinity of U. Maryland and JHSPH, thanks.
On 08/23/11 15:01, Ed Pozharski wrote:
On Tue, 2011-08-23 at 12:36 -0600, Francis E Reyes wrote:
Seems to be a quiet day on the BB
So you need an earthquake :)
Had one already, thanks.
--
===
All Things Serve the Beam
=
On Tue, 2011-08-23 at 12:19 -0700, Tiago Barros wrote:
> Does anyone know a program that will check a PDB file for missing
> atoms and output a list of the corresponding residues?
REFMAC reports a (truncated?) list in the log file. Coot can also
identify missing atoms. I would be pretty sure th
Dear all,
Does anyone know a program that will check a PDB file for missing atoms and
output a list of the corresponding residues?
Many thanks in advance,
Tiago
***
Tiago Barros, PhD
Kuriyan lab - Molecular and Cellular Biolo
On Tuesday, August 23, 2011 11:15:46 am Engin Özkan wrote:
> I distinctly remember reading a paper where B factors were predicted
> based on the location of the atoms (core vs exposed, main chain vs side
> chain) and the predicted values were not that far off. I wonder if B
> factors could actua
(3a) You could give GraphENT a shot first and see if you can do magic on
visualizing the remaining bits of density.
You could also have multiple conformations, try refining with a low occupancy
first and see what you get back.
(3b) use AFitt
Jürgen
P.S. I would set the occupancy to zero for th
On Tue, 2011-08-23 at 12:36 -0600, Francis E Reyes wrote:
> Seems to be a quiet day on the BB
So you need an earthquake :)
This is similar, imho, to the issue of disordered side chains:
https://docs.google.com/spreadsheet/gform?key=0Ahe0ET6Vsx-kdHVNa3VodUtfbVQtZ2pnUFcxQkx6RHc&hl=en_US&gridId=0#c
Seems to be a quiet day on the BB, so I propose this question:
Suppose you have a ligand in the binding pocket and some mediocre data (3 A or
so), the 'core' of the ligand is well defined in 2Fo-Fc map using the model
phases of your protein, however there are 'chains/tails' of the ligand whic
I distinctly remember reading a paper where B factors were predicted
based on the location of the atoms (core vs exposed, main chain vs side
chain) and the predicted values were not that far off. I wonder if B
factors could actually be restrained at low resolution towards values
reasonable/expe
On Tue, 2011-08-23 at 11:30 -0600, Francis E Reyes wrote:
> What's a way to determining a B-factor to set for all residues of a
> model at low resolution (4A)?
Why not refine the overall B-factor? Even at 4A it should still be
legitimate.
--
Oh, suddenly throwing a giraffe into a volcano to mak
Hi all
What's a way to determining a B-factor to set for all residues of a model at
low resolution (4A)? How valid is the wilson B at this resolution? (better than
nothing?)
I'm in the process of fitting whole domains into some rasty experimental
density maps and was thinking of doing a rigid
Dear Tongqing
No there is no such option in CCP4's PISA, but I put this on the list for
further developments. Regrettably PDBe changed the interface after I moved out
and I cannot help you with that. However, you may ask them to put that option
back.
Sorry,
Eugene.
On 23 Aug 2011, at 17:16,
Dear CCP4bb,
We are trying to get some detailed interface information from an
antibody:antigen complex, PDBePISA used to have an option to select atomic
level details, now the new web interface only gives residue level information.
Is there a way to run PISA (in the CCP4 package) with a differe
Look at AP-2 alpha-appendage. And for that matter, the beta appendage too.
Alpha appendage binds ~30 different proteins using two sites on one domain.
J Biol Chem. 2004 Oct 29;279(44):46191-203. Epub 2004 Aug 2.
Dual engagement regulation of protein interactions with the AP-2 adaptor alpha
appen
Calmodulin
Poul
On 23/08/2011, at 16.55, Pete Meyer wrote:
>> We know one protein can interact with different partners by different
>> domains or different parts. Is there a protein that it could interact
>> with different proteins by the same part (maybe the same part but in
>> different conform
We know one protein can interact with different partners by different
domains or different parts. Is there a protein that it could interact
with different proteins by the same part (maybe the same part but in
different conformations?)? Thank you in advance!!
The RNA Polymerase II rpb1 CTD intera
Dear all,
see below for a PDRA opportunity at Imperial college to work on the structural
basis of Photosystem II assembly and repair.
James
http://www.jobs.ac.uk/job/ADC906/research-associate/
Research Associate
Imperial College London - Faculty of Natural Sciences, Division of Molecular
This is very common among the small GTP-binding proteins of the Ras
superfamily. For an interesting analysis (although doubtless there are
lots of more recent examples) you might look at:
Corbett and Alber, TIBS 26 (12) 710-716 (2001)
Evette S. Radisky, Ph.D.
Assistant Professor
Mayo Clinic Canc
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On Tue, 2011-08-23 at 09:44 -0400, Yamei Yu wrote:
> Is there a protein that it could interact
> with different proteins by the same part (maybe the same part but in
> different conformations?)?
Lysozyme interacts with two antibodies, HyHel-5 and D44.1 via the same
epitope but different set of in
What about polyclonal antibody? I am sure that you find some
structures in the PDB.
Petr
2011/8/23 Yamei Yu :
> HI all,
>
> We know one protein can interact with different partners by different
> domains or different parts. Is there a protein that it could interact
> with different proteins by th
HI all,
We know one protein can interact with different partners by different
domains or different parts. Is there a protein that it could interact
with different proteins by the same part (maybe the same part but in
different conformations?)? Thank you in advance!!
yamei
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