To avoid excessive excitement potentially caused by such a list, people
should also indicate the time spent with a model just good enough to
initially justify the eventually futile effort.
Andreas
On 9/21/07, Bryan W. Lepore <[EMAIL PROTECTED]> wrote:
>
> would anyone be willing to share storie
would anyone be willing to share stories of the worst molecular
replacement search probes they used to get the correct solution purely
with MR?
perhaps in terms of %-scattering, RMSD, Z-score, LLG, or other possibly
specific scoring values.
-bryan
Some of you may be interested in applying to a tenure track Structural
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teaching and research at
A PhD bursary position is available at the University of Groningen to
study the structure and function of LysM (peptidoglycan/chitin-binding)
domains in eukaryotic proteins. The aim of this project is to obtain
in-depth structural knowledge of eukaryotic LysM domain repeats and
their interactio
OK, I'm properly chastised - "outlier" does not equal "bad".
However, residues which are not flagged as problematic or unusual
during validation should not be flagged in the final pdb file.
And I have read Gerard's paper, and the molprobity paper. Recently.
Sue
On Sep 21, 2007, at 9:57 AM,
Has anyone successfully fought this "bad residue" listing? I understand that
the pdb wishes to flag problem regions, but this is not a valid way of doing
so. I can tell them where the problem regions are in the structure if they
wish.
oh dear, oh dear - touchy, touchy!
coordinate-based valida
On Friday 21 September 2007 09:03:56 am Sue Roberts wrote:
> Yes, and I just got a pdb file back from the pdb that they flagged
> with over forty bad residues.
>
> The Molprobity plot from the RCSB validation server shows zero
> residues in disallowed regions. ( I got lucky, I didn't "fix" any bad
Yes, and I just got a pdb file back from the pdb that they flagged
with over forty bad residues.
The Molprobity plot from the RCSB validation server shows zero
residues in disallowed regions. ( I got lucky, I didn't "fix" any bad
residues.)
For many of these "bad" residues, the position o
Hi,
If you checked the Ramachandran plot using PROCHECK, you may think
almost all residues belong to the most favoured, additional allowed,
or generously allowed regions of the Ramachandran plot that is the
part 1 of the PROCHECK output PostScript file.
But if you checked the part 2 of the PROCHE
Klaus,
I can only assume that the pointed comment below was directed at me so I'll
reply. Oh no, everything matters. I was just giving an example of how to use
the pymol command. What distance cutoff is ultimately used is up to the
crystallographer and the problem at hand. Note also the pot
The eCheminfo Autumn Community of Practice meeting (2007) will take
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The following conference sessions will be
The answer to your question is called Phaser. Using Phaser, you can input
multiple search models in one search routine to look for
solutions.
You should read the online manual and tutorials, if you are not already
familiar with Phaser. You can also 'modify' or appropriately
'trim' your search
Hi All,
I heard about a way of preparing crystals - presented at the BSR recently as
"Crystals to go" - which allows them to be carried at room temperature then
cooled for data collection i.e. for beamline testing. Please could someone
point me in the right direction for the instructions on ho
Hi all,
Can anyone tell me, why ADIT Validation server says that residues that
are in the generously allowed regions of Ramachandran plot are outside
the expected regions? Is there something new in the validation tools of
the server? Two days ago I validated the same pdb and in the validation
summ
Deep-View (Swiss PDB Viewer) allows to calculate (and visualise) a
'contact surface'
between two subunits, by loading the subunits into different layers.
Residues contributing to the contact surface can be selected by CTRL-
click
on the contact surface line in the 'Cavities' menu, available un
http://www.ebi.ac.uk/msd/
Go to msdpisa
E
Xiaoyi Deng wrote:
Dear all:
I used moleman2 to calculate the contacts between chain A and B. Can
anyone suggest a program to calculate the contacts between the
interface of dimer-dimer?
Thank you,
Xiaoyi
Graduate student
University of Nebraska
Faculty Positions in the Area of Structural and Computational Biology are
Available at the Department of Biological Sciences & BioEngineering, Indian
Institute of Technology, KANPUR.
Biological
Sciences and Bioengineering (BSBE) was established at IIT-Kanpur in
September 2001 as a
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