@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Comparison of Water Positions across PDBs
On Tue, Nov 5, 2013 at 12:22 AM, Bernhard Rupp hofkristall...@gmail.com
wrote:
Given their otherwise almost paranoid sensitivity to ultimate author
authority
(resulting in things like still having 2hr0 etc
On Wed, Nov 6, 2013 at 12:39 AM, Bernhard Rupp hofkristall...@gmail.comwrote:
Hmmm….does that mean that the journals are now the ultimate authority of
what stays in the PDB?
I find this slightly irritating and worthy of change.
http://www.wwpdb.org/UAB.html
It is the current wwPDB
I've remained silent as this thread evolved into a discussion of how the PDB deals with
water names and numbers. But Nat's comment about the PDB not advertising itself as
anything other than an archival service finally prodded me into saying something.
Something I've slowly come to realize is
@JISCMAIL.AC.UK
Sent: Monday, 4 November 2013, 14:50
Subject: Re: [ccp4bb] Comparison of Water Positions across PDBs
As far as confusion as a result of PDB renumbering is concerned: It was
useful to run the old REM525 standalone program (I think I got it from
PDBe/Kim Hendrick) at the end
On Tue, Nov 5, 2013 at 12:22 AM, Bernhard Rupp hofkristall...@gmail.comwrote:
Given their otherwise almost paranoid sensitivity to ultimate author
authority
(resulting in things like still having 2hr0 etc in the bank because
certain authors go AWOL or ignore major issues)
In defense of the
standard:
polymer - heterogen - water?
Yours perplexedly
Martyn
From: Rachel Kramer Green kra...@rcsb.rutgers.edu
To: CCP4BB@JISCMAIL.AC.UK
Sent: Friday, 1 November 2013, 20:18
Subject: Re: [ccp4bb] Comparison of Water Positions across PDBs
In PDB format
: Re: [ccp4bb] Comparison of Water Positions across PDBs
Thank you for that, Rachel
Even though the tone of your comment does not suggest that you want to carry
on a dialogue about this, I thought I would reply in any case - since
dialogue is what this forum is supposed to be about.
Thing
From: Bernhard Rupp hofkristall...@gmail.com
To: CCP4BB@JISCMAIL.AC.UK
Sent: Monday, 4 November 2013, 14:50
Subject: Re: [ccp4bb] Comparison of Water Positions across PDBs
As far as confusion as a result of PDB renumbering is concerned: It was useful
to run
In PDB format files, each polymer is assigned a unique chain ID. Chain
IDs for all bound moieties and waters are assigned based on their
proximity (number of contacts) to the nearest polymer. Once the polymers
and non-polymer residues associated with them are assigned chain IDs,
they are also
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
For detailed examination of this topic, see:
Koellner, G., Kryger, G., Millard, C. B., Silman, I., Sussman, J. L. Steiner,
T. (2000).
Active-site gorge and buried water molecules in crystal structures of
acetylcholinesterase from Torpedo californica. Journal of Molecular Biology
296, 713-735.
Well - years ago I wrote a program called watertidy to do just this -
but it asigned waters as OH0 OH1 OH2 with a according to what atom it
was H bonded too, and those names are not now permitted..
My way now is to read in a completed homologous structure - use SSM to
fit it over the new one -
...@weizmann.ac.il
To: CCP4BB@JISCMAIL.AC.UK
Sent: Wednesday, 30 October 2013, 6:49
Subject: Re: [ccp4bb] Comparison of Water Positions across PDBs
For detailed examination of this topic, see:
Koellner, G., Kryger, G., Millard, C. B., Silman, I., Sussman, J. L. Steiner,
T. (2000).
Active
Dear all,
this water discussion is flowing increasingly towards a place where I
feel a bit out of my depth.
What is the convention for numbering water molecules? Is there
preference for:
- putting waters into a separate chain (W for water or S for solvent)?
- splitting waters according to
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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 macromolecular
chain. I found this rather annoying
Dear Elise,
Try the 3Dss server (http://cluster.physics.iisc.ernet.in/3dss/). You can
superimpose up to 20 structures and look for invariant waters.
Cheers,
Uli
---
dr ulrich gohlke
staff scientist - macromolecular
This is to be answered by PDB people, who definitely read BB :)
Would be nice to have a tool common between CCP4/Phenix and the PDB which sorts
this out
Eugene
On 30 Oct 2013, at 12:09, Andreas Förster wrote:
Dear all,
this water discussion is flowing increasingly towards a place where I
Elise - after looking into a related problem for some time, I've come
to the conclusion it's a bit harder than it seems. Two obstacles:
(1) there is no good coordinate system for partitioning the overall
solvent volume (fraction of unit cell not occupied by protein density)
into suitable
Hello,
I am working on a project with several (separate) structures of the same
protein. I would like to be able to compare the solvent molecules between
the structures, and it would be best if the waters that exist in roughly
the same position in each PDB share the same residue number.
Downloading structures of the same homologous family with blast. Then
superimpose them on a reference structure. You may then try to look at over
lapping water molecules
On 30 Oct 2013 02:23, Elise B ek...@case.edu wrote:
Hello,
I am working on a project with several (separate) structures of
of Water Positions across PDBs
Downloading structures of the same homologous family with blast. Then
superimpose them on a reference structure. You may then try to look at over
lapping water molecules
On 30 Oct 2013 02:23, Elise B ek...@case.edumailto:ek...@case.edu wrote:
Hello,
I am working
[mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Dom
Bellini
Sent: Tuesday, October 29, 2013 3:34 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Comparison of Water Positions across PDBs
Hi Elise,
How about taking the homologue structure with highest number of waters and use
it to run molecular
http://www.ccp4.ac.uk/html/watertidy.html
On 10/29/2013 04:43 PM, Elise B wrote:
Hello,
I am working on a project with several (separate) structures of the
same protein. I would like to be able to compare the solvent molecules
between the structures, and it would be best if the waters that
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