Dear list,
Is there a way that for a binding site (defined as the protein surface
atoms N Angstroms around a ligand molecule) we can assign a (preferably
normalized) hydrophobicity score to the binding site?
- I would prefer something that I can run offline rather than
a webserver (but a we
Thank you everybody for your inputs. Already four suggested the QC server.
I think at this point we have enough ideas.
Once again, thanks for your attention.
Debasish
From: Kumar, Abhinav [mailto:abhin...@slac.stanford.edu]
Sent: Thursday, October 31, 2013 6:49 PM
To: Debasish Chattopadhyay
Cc:
Try JCSG QC server:
http://smb.slac.stanford.edu/jcsg/QC/
All our structures go through this server before submitted to the PDB and we
rarely get any issues back from PDB.
Thanks,
Abhinav
Abhinav Kumar, Ph.D.
Joint Center for Structural Genomics
SSRL, SLAC Nation
On 30/10/13 12:32, Tim Gruene wrote:
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Dear Andreas,
I am not sure there is a convention, but there has been a decision.
When you deposit a structure with the PDB, they place all ligands
including water molecules to the respective nearest macromolecul
The JCSG validation server is useful – it will run ADIT check, MolProbity,
real space CC, etc.
http://smb.slac.stanford.edu/jcsg/QC/
On Thu, Oct 31, 2013 at 2:22 PM, rjguan wrote:
> **
> we have a PSVS server, and welcome people to try and give back comments:
> http://psvs-1_5-dev.nesg.org/
>
we have a PSVS server, and welcome people to try and give back comments:
http://psvs-1_5-dev.nesg.org/
Rongjin Guan
From: Bosch, Juergen
Date: 2013-10-31 11:48
To: CCP4BB
Subject: Re: [ccp4bb] PDB structure validation
You do use Coot and look at the density plots right ?
Phenix will essentially
Hi Debasish,
Randy's update sounds fantastic! Absolutely fantastic because I suspect
many of us have gone through exactly what you described here, despite
running many other kinds of validations!
In the meantime, the PDB gave me two options as a workaround. One was to
either email them the update
Dear Colleagues:
Since the CCP4 OS X installer package installs 64-bit binaries and libraries,
and handles updates gracefully (and incrementally), there is no compelling
reason to continue to have a fink installer package for ccp4, and several
compelling reasons not to, so I have discontinued m
Are you talking about the Fig 3.1 in their book, "Laboratory-build
oscillation camera" (Arndt, Champness, Phizackerley and Wonacott, 1973)
On Thu, Oct 31, 2013 at 2:28 AM, Eleanor Dodson
wrote:
> one in their book, i am sure.
> eleanor
>
>
> On 30 Oct 2013, at 16:05, Gerard Bricogne wrote:
>
> >
Thanks Randy.
That would be fantastic.
From: Randy Read [mailto:rj...@cam.ac.uk]
Sent: Thursday, October 31, 2013 11:02 AM
To: Debasish Chattopadhyay
Cc: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] PDB structure validation
Yes, the intention at the PDB sites is to make available a standalone
val
Yes, the intention at the PDB sites is to make available a standalone
validation server that will run exactly the same validation tests that have
been introduced for recent depositions. My understanding is that this server
is currently being tested and will be rolled out to the community someti
Yes and I do.
I have to admit that for structures with many molecules in the asu, I have a
tendency to occasionally forget about checking the density fit plots for
non-water and unintentional ligands (crystallization reagents etc); I routinely
run the check/delete water option in coot.
Thanks
Hi Debashis,
you have "Density fit analysis" in the "Validate" menu in Coot, if it's just
that what you're looking for.
Ciao,
S
On Oct 31, 2013, at 4:43 PM, Debasish Chattopadhyay wrote:
>
> Yes, there remains many questions beyond Adit.
> I do want to emphasize that the new scrutiny in PDB
You do use Coot and look at the density plots right ?
Phenix will essentially do the same but in text form (unless you use the GUI).
You can also do this with Solve/Resolve and you can write your own script with
CCP4 available tools to do the same RSR fit diagram.
Jürgen
On Oct 31, 2013, at 11:4
No complaints about PDB stuff, they are always helpful.
Debasish
University of Alabama at Birmingham
CBSE-250
1025 18th Street South, Birmingham, Al-35294
USA
Ph: (205)934-0124; Fax: (205)934-0480
Yes, there remains many questions beyond Adit.
I do want to emphasize that the new scrutiny in PDB is very good since it now
includes a density fitting analysis (everything in the structure should be the
density, right) etc. But one has to go through the submission to generate the
report and
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Dear Debasish Chattopadhyay,
in my experience someone from the PDB always contacted me during the
deposition process and discussed the necessary modifications which
included (and possibly exceeded) the issues raised by the validation
report, i.e. the
Molprobity doesn't analyze density fit. New PDB validation now reports density
fit analysis etc.
From: Bosch, Juergen [mailto:jubo...@jhsph.edu]
Sent: Thursday, October 31, 2013 10:28 AM
To: Debasish Chattopadhyay
Cc: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] PDB structure validation
yes, ind
yes, indeed.
visit this site and make sure you get all green lights
http://molprobity.biochem.duke.edu
Jürgen
On Oct 31, 2013, at 11:25 AM, Debasish Chattopadhyay wrote:
I was wondering if there is a way to generate a PDB validation report before
depositing the coordinates so that one can go ba
I was wondering if there is a way to generate a PDB validation report before
depositing the coordinates so that one can go back and make necessary
corrections to the file before deposition. It will save a lot time and perhaps
would improve the quality of deposited structures.
Debasish Chattopa
Dear Thuy,
For blob1 you should also try to fit alternative conformations. Your maps are
good enough to give you a fair chance. You should also look for reasons behind
these alternative conformations: has a neighboring disulfide bond partially
opened? Is there a partially-occupied cadmium nearb
Dear Thuy,
It might be indeed a Cd2+ ion as suggested by Herman.
In this sense I would process the data assuming a false Friedel law and look if
there is some significant anomalous signal that superimposes to your mFo-DFc
positive peaks around the His you pointed out.
Best regards,
Philippe
Dear all,
The gly104 sequence is correct. This is the substrate complex structure. In
case of native structure, such strange of blob1 didnot appear
Also for the second blob, I follow your suggestion and the result is nice
I am still waitting for the suggestion of the first blob
Thank you a lot,
Can you exclude a sequencing error for Gly104?
Am 31.10.2013 um 08:40 schrieb thuy ngo:
> Dear all,
>
> I am dealing with two strange extra density map. One is connected from Cb of
> Proline to Ca of glycine (blob 1)
> and other is positioned between two symmetric molecules which is connected
Sorry, I meant glutamate.
HS
Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von
Schreuder, Herman R&D/DE
Gesendet: Donnerstag, 31. Oktober 2013 09:17
An: CCP4BB@JISCMAIL.AC.UK
Betreff: [ccp4bb] AW: [ccp4bb] help with strange density map
Dear Thuy,
I would try to model altern
Dear Thuy,
I would try to model alternative conformations. E.g. blob2 looks like a lower
occupancy cadmium ion coordinated to the glutamine, causing the histidine to
assume an alternative conformation, also coordinating the ion. Just try to
build different possibilities. If, after refinement it
one in their book, i am sure.
eleanor
On 30 Oct 2013, at 16:05, Gerard Bricogne wrote:
> Dear all,
>
> Apologies for such a "retro" and non-biological question, but would
> anyone have a photograph of an Arndt-Wonacott rotation camera that he/she
> would be willing to share? I collected dat
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