the 5AX entries
should be arranged.
Yours (not holding his breath),
Martyn
From: Rachel Kramer Green
To: CCP4BB@JISCMAIL.AC.UK
Sent: Wednesday, 6 November 2013, 16:49
Subject: Re: [ccp4bb] Problematic PDBs
Dear Martyn,
wwPDB staff regularly reviews
ing and redepositing their PDB entry. The
test for obsoleting would then be the same as for a paper - that the change
invalidates a fundamental interpretation of the data.
All the best
Martyn
From: Pavel Afonine
To: CCP4BB@JISCMAIL.AC.UK
Sent: Sunday, 20
Hello,
just for the sake of completeness: this paper lists a bunch of known
pathologies (I would not be surprised if they've been remediated by now):
http://www.phenix-online.org/papers/he5476_reprint.pdf
Pavel
On Thu, Oct 17, 2013 at 6:51 AM, Lucas wrote:
> Dear all,
>
> I've been lecturing
@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Problematic PDBs
Hi Lucas,
this book
(http://www.amazon.com/Structural-Bioinformatics-Methods-Biochemical-Analysi
s/dp/0471201995/ref=sr_1_2?s=books
<http://www.amazon.com/Structural-Bioinformatics-Methods-Biochemical-Analysi
s/dp/0471201995/ref=sr_1_
Hi Lucas,
this book (
http://www.amazon.com/Structural-Bioinformatics-Methods-Biochemical-Analysis/dp/0471201995/ref=sr_1_2?s=books&ie=UTF8&qid=1382044405&sr=1-2&keywords=structural+bioinformatics)
brings nice examples of protein structures with "unusual features" in the
structure validation chapt
Yikes! This cuts close to my area. We occasionally have undergrads solve
and refine carbonic anhydrase-sulfonamide structures as a part of a
4-hour biochemistry teaching lab. (We have a whole shelf-full of
sulfonamides that make excellent teaching projects.)
I use 2QNS for teaching. It is an egregious case of modeling ligand into noise.
Also, the structure has many close contacts (e.g. HOH A351), poor
stereochemistry (e.g. A58-A61), and incorrectly built water. Turn on symmetry
to see the steric clash of the peptide ligand with itself. You can g
I would start with 1E4M (residue 361 of chain M) and 1QW9 (170 of
chain B). First show the model and then reveal the electron density.
This promotes a healthy skepticism of PDB models and enforces the
importance of always looking at a model in the context of the map.
For model building I wo
On Thursday, 17 October, 2013 10:51:08 Lucas wrote:
> Dear all,
>
> I've been lecturing in a structural bioinformatics course where graduate
> students (always consisting of people without crystallography background to
> that point) are expected to understand the basics on how x-ray structures
> a
From the original ABC transporter retraction:
http://www.sciencemag.org/content/314/5807/1875.2.full
"The Protein Data Bank (PDB) files 1JSQ, 1PF4, and 1Z2R for MsbA and
1S7B and 2F2M for EmrE have been moved to the archive of obsolete PDB
entries"
You can get your hands on them via URLs like
On Thu, Oct 17, 2013 at 6:51 AM, Lucas wrote:
> I wonder if there's a list of problematic structures somewhere that I
> could use for that practice? Apart from a few ones I'm aware of because of
> (bad) publicity, what I usually do is an advanced search on PDB for entries
> with poor resolution a
Sorry, it is acta cryst F69, not 96!
Herman
Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von
Schreuder, Herman R&D/DE
Gesendet: Donnerstag, 17. Oktober 2013 16:11
An: CCP4BB@JISCMAIL.AC.UK
Betreff: [ccp4bb] AW: [ccp4bb] Problematic PDBs
Dear Lucas,
I recently came acc
@JISCMAIL.AC.UK] Im Auftrag von Lucas
Gesendet: Donnerstag, 17. Oktober 2013 15:51
An: CCP4BB@JISCMAIL.AC.UK
Betreff: [ccp4bb] Problematic PDBs
Dear all,
I've been lecturing in a structural bioinformatics course where graduate
students (always consisting of people without crystallography background to
Dear all,
I've been lecturing in a structural bioinformatics course where graduate
students (always consisting of people without crystallography background to
that point) are expected to understand the basics on how x-ray structures
are obtained, so that they know what they are using in their bioi
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