I have noticed renaming chains in the sequence ID's but not in the coordinates:
2FBW_3|Chains C, G[auth P]|Succinate dehydrogenase cytoch
MATTAKEEMARFWEKNTKSSRPLSPHISIYKWSLPMAMSITHRGTGVALSLGVSLFSL
2FBW_4|Chains D, H[auth Q]|Succinate dehydrogenase [ubiqu
GSSKAASLHWTSERAVSALLLGLLPAAYLYPGPAVDYSL
Hi David,
Why not do all those things with Rwork? It is much less noisy than
Rfree. Have you ever seen a case in such analysis where Rwork didn't
tell you the same thing Rfree did? If so, did you believe the difference?
Once when I was playing with lossy image compression if I picked just
t
Dear John Helliwell,
I should have been more clear in addressing my email. It was in response to
John Berrisford’s answer.
Regards,
Vaheh
From: John R Helliwell
Sent: Monday, November 1, 2021 3:13 PM
To: Oganesyan, Vaheh
Cc: CCP4BB@jiscmail.ac.uk
Subject: Re: [ccp4bb] renaming chains
Dear V
Dear Valeh
Apologies, I was solely replying to the numbering/labelling of waters
observation/query of Mohamed, ie as a function of in situ parameter (time,
temperature and pressure).
Best wishes
John
Emeritus Professor John R Helliwell DSc
> On 1 Nov 2021, at 18:39, Oganesyan, Vaheh
> wrot
Hi John,
Thank you for explanation.
The most recent encounter I had on this issue was with 3DMM and 3B9K. You would
know better what caused chain renaming here, but it doesn't look like any of
the two scenarios you describe. Whatever the reason was I'm glad to hear that
this is not a widespread
Dear Mohamed,
The situation you describe applies also to multiple crystal structures studied
as a function not only of time but also of temperatures and pressures. I
enquired if the numberings of discussed waters and so on could be retained
across the related crystal structures in the PDB. The r
Dear Vaheh
Usually we do not rename chains as part of the curation procedure.
There are instances when we do, for example when a chain has to be split
into two chains and a new chain has to be defined, but this isn't
typical.
Because of this the wwPDB mmCIF file for each entry will usually co
Hi All,
I have a very similar question; why can't we retain the same water
numbering as the deposited files. For articles that discuss waters, it is a
considerable challenge. For example, for serial crystallography structures,
it becomes confusing and harder for the readers to follow the water
num
Hi All,
This question is mostly for RCSB and PDBe: why are you renaming chains in the
deposited PDB files? Why does it matter what letter is assigned to the chain?
For 1,2 or 3 chain structures it is manageable, but for more chains and/or many
complexes per asu this becomes quite a challenge. A
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Hi James,
What you wrote makes lots of sense. I had not heard about Rsleep, so that
looks like interesting reading, thanks.
I have often used Rfree as a simple tool to compare two protocols. If I am
not actually optimising against Rfree but just using it for a one-off
comparison then that is okay
Dear Mark
The keyword you want is
pdbout format mmcif
This is described here:
https://www.wwpdb.org/deposition/PDBxDeposit
Regards
John
On 2021-10-30 00:03, Mark J. van Raaij wrote:
Dear All,
this may be something simple but I can’t find it in the CCP4i GUI or
online.
Is there a keyword
Dear all,
We are expanding our Crystallography team within the Discovery Biology
department at Exscientia and we currently have open positions for
“Crystallographer” and “Crystallography Research Assistant”.
The Discovery Biology team in Exscientia is responsible for enabling
small-molecule t
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