[ccp4bb] Acta Cryst. Endnote Output Style

[Jann-Patrick Pelz]

Dear all,

we are currently preparing a manuscript for publication in Acta Cryst.  
D. Neither the Output Style delivered with Endnote X7 nor the Outstyle  
we found on the IUCr Webpage contains the right abbreviations of the  
Journal names. Abbreviation 1 leads to full Journal names, while all  
other Settings lead to the same wrong abbreviations.

Did someone encounter the same problems and did you maybe find a solution?

Best regards,

Jann

Jann-Patrick Pelz
Lehrstuhl für Biochemie
Biozentrum - Am Hubland
97074 Würzburg
0931-31 83334
jann.p...@uni-wuerzburg.de

Re: [ccp4bb] Refmac refinement R factors going up..... TLS issue?

[Eleanor Dodson]

And I usually accept the TLS domain definition, but reset all B factors and
start B factor refinement again - ie dont use the actual TLS numbers
returned..
Ideally I guess the B reset could be done using TLSANL

There seems to be confusion over the interaction between the iso B and
those TLS generated ones..
Eleanor



On 18 June 2015 at 22:08, Boaz Shaanan  wrote:

> Hi Christian,
>
> I usually send the pdb back to the tlsmd server after any manipulation of
> the model just to be on the safe side. I'm not sure whether that'll make
> any difference in your case but it's perhaps worth trying.
>
>Cheers,
>
> Boaz
>
>
> Boaz Shaanan, Ph.D.
> Dept. of Life Sciences
> Ben-Gurion University of the Negev
> Beer-Sheva 84105
> Israel
>
> E-mail: bshaa...@bgu.ac.il
> Phone: 972-8-647-2220  Skype: boaz.shaanan
> Fax:   972-8-647-2992 or 972-8-646-1710
>
>
>
>
>
> 
> From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Christian
> Roth [christian.r...@bbz.uni-leipzig.de]
> Sent: Thursday, June 18, 2015 11:30 PM
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: [ccp4bb] Refmac refinement R factors going up. TLS issue?
>
> Hi all,
>
> I refine a structure with TLS and restrained refinement in Refmac. After
> the run finished, I fixed a few outliers manually in Coot, saved that
> file and used that with the original TLS file from TLSMD for the next
> round of refinement. As soon as the restrained refinement starts the
> R-factors are going up and stabilise than at a higher values compared to
> the previous run.
> If I switch of the TLS refinement and just do restrained refinement with
> the same input files the R-values start initially at a higher values and
> than decrease till they stabilise. Unfortunately the final values are
> about 1.5 % higher, compared to the run with TLS before manual
> rebuilding. So TLS seems to me beneficial and I would like to use it,
> but somehow a strange combination of wrong files?, wrong
> parametrization? or whatever prevent me of doing that.
> Has anyone an idea what might be the cause of that strange behaviour.
>
> Thank you very much in advance.
>
> Cheers
>
> Christian
>

[ccp4bb] FW: New ligand 3-letter code (help-7071)

[Sheriff, Steven]

All:

Since the original query was cross-posted on both the COOT mailing list and the 
CCP4BB Rachel Green gave me permission to forward this to both. She provides 
links about the mechanism of assignment of 3-letter codes. In the third link 
below, my original suggestion to the COOT mailing list that one could just use 
UNK is incorrect as that is reserved for unknown amino acids. According to this 
document, I should have suggested UNL for an unknown ligand.

Steven

From: Rachel Kramer Green [mailto:kra...@rcsb.rutgers.edu]
Sent: Tuesday, June 16, 2015 10:21 AM
To: Sheriff, Steven
Cc: info
Subject: Re: New ligand 3-letter code (help-7071)

Dear Steven,

During annotation of ligands, all chemical components present in the structure 
are compared against the definitions in the Chemical Component Dictionary 
(http://www.wwpdb.org/data/ccd). If the ligand is not in the dictionary, a 
three letter code is assigned. See 
http://www.wwpdb.org/documentation/policy#toc_assignment.  In the future, a 
group of three-letter codes may be set aside to be used during refinement to 
flag new ligands.

Clarification about the ligand ids assignment and in particular the usage of 
UNX/UNL/UNK residues can be found at 
http://www.wwpdb.org/documentation/procedure#toc_2.

Best wishes,
Rachel


Rachel Kramer Green, Ph.D.
RCSB PDB
kra...@rcsb.rutgers.edu

New! Deposit X-ray data with the wwPDB at:
http://deposit.wwpdb.org/deposition (NMR and 3DEM coming soon).
___
Twitter: https://twitter.com/#!/buildmodels
Facebook: http://www.facebook.com/RCSBPDB



On 6/5/2015 7:50 AM, Sheriff, Steven wrote:
All:

Why the concern for unassigned three-letter codes? The wwPDB isn’t going to let 
you assign a three-letter code, it will choose its own code.

At BMS (a pharmaceutical company), we do many hundreds of structures a year 
with ligands and we assign the same, already assigned, three-letter code for 
all of our ligands (unless we have two or more different ligands in a single 
structure, in which case we use two or more different already assigned 
three-letter codes).  COOT can mostly handle this.

However, I believe that if you want an unassigned code, the wwPDB has set aside 
UNK[nown] for this purpose.

Steven

From: Mailing list for users of COOT Crystallographic Software 
[mailto:c...@jiscmail.ac.uk] On Behalf Of Eleanor Dodson
Sent: Friday, June 05, 2015 6:28 AM
To: c...@jiscmail.ac.uk
Subject: Re: New ligand 3-letter code

I use your method - trial & error..
It would be nice if at least there was a list somewhere of unassigned codes!

On 5 June 2015 at 09:16, Lau Sze Yi (SIgN) 
mailto:lau_sze...@immunol.a-star.edu.sg>> 
wrote:
Hi,

What is the proper way of generating 3-letter code for a new ligand? As of now, 
I insert my ligand in Coot using smiles string and for the 3-letter code I 
picked a non-existent code by trial and error (not very efficient). A cif file 
with corresponding name which I generated using Phenix was imported into Coot.

I am sure there is a proper way of doing this. Appreciate your feedback.

Regards,
Sze Yi


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[ccp4bb] determine NCS operators from PDB coordinates

[Tobias Beck]

Dear all,

I have a PDB file that contains NCS in the asymmetric unit, probably point
group D3.

1.) What program is recommended for determining the symmetry operators from
PDB coordinates? I found findncs, but this uses only heavy atom coordinates
(I could probably use just the sulfurs from the PDB as a work around).

2.) Then I would like to compare the PDB file to a related structure. Here
I would like to align the symmetry operators determined above with symmetry
elements found in a different space group, for example align the twofold
axis from NCS with a twofold axis in found in a particular space group.
What is a good way to go about this?

I am aware that NCS is used in programs as restraints during refinement,
but here I am interested in obtaining the NCS symmetry operators and
aligning them to symmetry elements present in a new space group. Maybe I am
overlooking an obvious solution.

Any help is greatly appreciated.

Thanks and best wishes, Tobias.
-- 
___

Dr. Tobias Beck
- independent group leader -
RWTH Aachen University
Institute of Inorganic Chemistry
Landoltweg 1, office: 304N
52056 Aachen, Germany
phone:  +49-241-80-90057
fax:   +49-241-80-99003
web:  http://www.ac.rwth-aachen.de/extern/beck/
___

Re: [ccp4bb] Acta Cryst. Endnote Output Style

[Philip Kiser]

Hi Jan,

The problem is with your journals "terms list." That is ​where the journal
abbreviations are defined. You should be able to find some precompiled
lists from library websites for example.

Philip

On Fri, Jun 19, 2015 at 5:55 AM, Jann-Patrick Pelz <
jann.p...@biozentrum.uni-wuerzburg.de> wrote:

> Dear all,
>
> we are currently preparing a manuscript for publication in Acta Cryst. D.
> Neither the Output Style delivered with Endnote X7 nor the Outstyle we
> found on the IUCr Webpage contains the right abbreviations of the Journal
> names. Abbreviation 1 leads to full Journal names, while all other Settings
> lead to the same wrong abbreviations.
> Did someone encounter the same problems and did you maybe find a solution?
>
> Best regards,
>
> Jann
>
> Jann-Patrick Pelz
> Lehrstuhl für Biochemie
> Biozentrum - Am Hubland
> 97074 Würzburg
> 0931-31 83334
> jann.p...@uni-wuerzburg.de
>

Re: [ccp4bb] Acta Cryst. Endnote Output Style

[Jann-Patrick Pelz]

Hi Philip,

thank you, that is exactly my problem. Now I just have to find a correct list!

Jann


Zitat von Philip Kiser :


Hi Jan,

The problem is with your journals "terms list." That is ​where the journal
abbreviations are defined. You should be able to find some precompiled
lists from library websites for example.

Philip

On Fri, Jun 19, 2015 at 5:55 AM, Jann-Patrick Pelz <
jann.p...@biozentrum.uni-wuerzburg.de> wrote:


Dear all,

we are currently preparing a manuscript for publication in Acta Cryst. D.
Neither the Output Style delivered with Endnote X7 nor the Outstyle we
found on the IUCr Webpage contains the right abbreviations of the Journal
names. Abbreviation 1 leads to full Journal names, while all other Settings
lead to the same wrong abbreviations.
Did someone encounter the same problems and did you maybe find a solution?

Best regards,

Jann

Jann-Patrick Pelz
Lehrstuhl für Biochemie
Biozentrum - Am Hubland
97074 Würzburg
0931-31 83334
jann.p...@uni-wuerzburg.de





Jann-Patrick Pelz
Lehrstuhl für Biochemie
Biozentrum - Am Hubland
97074 Würzburg
0931-31 83334
jann.p...@uni-wuerzburg.de

[ccp4bb] AW: [ccp4bb] determine NCS operators from PDB coordinates

[Herman . Schreuder]

Dear Tobias,

If you have coordinates available for the different space groups, the obvious 
solution is to first generate complete NCS units in the different space groups, 
using appropriate crystallographic symmetry and then superimpose the whole unit 
with something like lsqkabs. You have to watch out though, that equivalent 
molecules are used for the superposition.

Best,
Herman

Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von Tobias 
Beck
Gesendet: Freitag, 19. Juni 2015 15:07
An: CCP4BB@JISCMAIL.AC.UK
Betreff: [ccp4bb] determine NCS operators from PDB coordinates

Dear all,
I have a PDB file that contains NCS in the asymmetric unit, probably point 
group D3.
1.) What program is recommended for determining the symmetry operators from PDB 
coordinates? I found findncs, but this uses only heavy atom coordinates (I 
could probably use just the sulfurs from the PDB as a work around).
2.) Then I would like to compare the PDB file to a related structure. Here I 
would like to align the symmetry operators determined above with symmetry 
elements found in a different space group, for example align the twofold axis 
from NCS with a twofold axis in found in a particular space group.
What is a good way to go about this?
I am aware that NCS is used in programs as restraints during refinement, but 
here I am interested in obtaining the NCS symmetry operators and aligning them 
to symmetry elements present in a new space group. Maybe I am overlooking an 
obvious solution.
Any help is greatly appreciated.
Thanks and best wishes, Tobias.
--
___

Dr. Tobias Beck
- independent group leader -
RWTH Aachen University
Institute of Inorganic Chemistry
Landoltweg 1, office: 304N
52056 Aachen, Germany
phone:  +49-241-80-90057
fax:   +49-241-80-99003
web:  http://www.ac.rwth-aachen.de/extern/beck/
___

Re: [ccp4bb] AW: [ccp4bb] determine NCS operators from PDB coordinates

[Eleanor Dodson]

Well - I would begin by submitting both sets of coordinates to pisa which
will attempt to group the NCS into the "best" complex.

Once you have that you can use any of the SUPERPOSE options to fit A to B,
A to C , B to C etc. for each molecule and from that deduce your NCS class.

eg: Hexamers - 6 fold rotations-  teramers - 2 2 2 symmetry etc etc..

Then SSM will probably fit the two different structures together and you
can see  where the differences are

Eleanor



On 19 June 2015 at 14:46,  wrote:

>  Dear Tobias,
>
>
>
> If you have coordinates available for the different space groups, the
> obvious solution is to first generate complete NCS units in the different
> space groups, using appropriate crystallographic symmetry and then
> superimpose the whole unit with something like lsqkabs. You have to watch
> out though, that equivalent molecules are used for the superposition.
>
>
>
> Best,
>
> Herman
>
>
>
> *Von:* CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] *Im Auftrag von
> *Tobias Beck
> *Gesendet:* Freitag, 19. Juni 2015 15:07
> *An:* CCP4BB@JISCMAIL.AC.UK
> *Betreff:* [ccp4bb] determine NCS operators from PDB coordinates
>
>
>
> Dear all,
>
> I have a PDB file that contains NCS in the asymmetric unit, probably point
> group D3.
>
> 1.) What program is recommended for determining the symmetry operators
> from PDB coordinates? I found findncs, but this uses only heavy atom
> coordinates (I could probably use just the sulfurs from the PDB as a work
> around).
>
> 2.) Then I would like to compare the PDB file to a related structure. Here
> I would like to align the symmetry operators determined above with symmetry
> elements found in a different space group, for example align the twofold
> axis from NCS with a twofold axis in found in a particular space group.
>
> What is a good way to go about this?
>
> I am aware that NCS is used in programs as restraints during refinement,
> but here I am interested in obtaining the NCS symmetry operators and
> aligning them to symmetry elements present in a new space group. Maybe I am
> overlooking an obvious solution.
>
> Any help is greatly appreciated.
>
> Thanks and best wishes, Tobias.
>
> --
>
> ___
>
> Dr. Tobias Beck
> - independent group leader -
> RWTH Aachen University
> Institute of Inorganic Chemistry
> Landoltweg 1, office: 304N
> 52056 Aachen, Germany
> phone:  +49-241-80-90057
> fax:   +49-241-80-99003
> web:  http://www.ac.rwth-aachen.de/extern/beck/
> ___
>

Re: [ccp4bb] determine NCS operators from PDB coordinates

[Pavel Afonine]

phenix.simple_ncs_from_pdb will detect NCS from input PDB file, write out
NCS operators (matrices) and atom selections for NCS related groups.

On Fri, Jun 19, 2015 at 6:07 AM, Tobias Beck  wrote:

> Dear all,
>
> I have a PDB file that contains NCS in the asymmetric unit, probably point
> group D3.
>
> 1.) What program is recommended for determining the symmetry operators
> from PDB coordinates? I found findncs, but this uses only heavy atom
> coordinates (I could probably use just the sulfurs from the PDB as a work
> around).
>
> 2.) Then I would like to compare the PDB file to a related structure. Here
> I would like to align the symmetry operators determined above with symmetry
> elements found in a different space group, for example align the twofold
> axis from NCS with a twofold axis in found in a particular space group.
> What is a good way to go about this?
>
> I am aware that NCS is used in programs as restraints during refinement,
> but here I am interested in obtaining the NCS symmetry operators and
> aligning them to symmetry elements present in a new space group. Maybe I am
> overlooking an obvious solution.
>
> Any help is greatly appreciated.
>
> Thanks and best wishes, Tobias.
> --
> ___
>
> Dr. Tobias Beck
> - independent group leader -
> RWTH Aachen University
> Institute of Inorganic Chemistry
> Landoltweg 1, office: 304N
> 52056 Aachen, Germany
> phone:  +49-241-80-90057
> fax:   +49-241-80-99003
> web:  http://www.ac.rwth-aachen.de/extern/beck/
> ___
>
>

Re: [ccp4bb] determine NCS operators from PDB coordinates

[Edward A. Berry]

A number of superposition programs allow to superimpose specified atoms (such 
as CA).
Once you get the operator, comparing two different operators is not a job
for a conventional superposition program, since you are superimposing a
line on a line which has the extra degree of freedom- rotation about the line.
If you express the operator in spherical polar coordinates, which the 
superposition
program may provide or you can get from the matrix using ccp4 "rotmat",
you should be able to work out the relation between the axes.

Using the Uppsala sofware factory programs:

#This is superimposing parts of chains C, A, B on P, N, O (and vice versa - 
it's proper 2-fold)
lsqman -b < 
* if you use the .odb file outside of the USF software, be aware the matrix is the transpose

(or more accurately it is written by columns). In ccp4 this is taken care of withthe 
keyword "odb".

On 06/19/2015 09:07 AM, Tobias Beck wrote:

Dear all,

I have a PDB file that contains NCS in the asymmetric unit, probably point 
group D3.

1.) What program is recommended for determining the symmetry operators from PDB 
coordinates? I found findncs, but this uses only heavy atom coordinates (I 
could probably use just the sulfurs from the PDB as a work around).

2.) Then I would like to compare the PDB file to a related structure. Here I 
would like to align the symmetry operators determined above with symmetry 
elements found in a different space group, for example align the twofold axis 
from NCS with a twofold axis in found in a particular space group.
What is a good way to go about this?

I am aware that NCS is used in programs as restraints during refinement, but 
here I am interested in obtaining the NCS symmetry operators and aligning them 
to symmetry elements present in a new space group. Maybe I am overlooking an 
obvious solution.

Any help is greatly appreciated.

Thanks and best wishes, Tobias.
--
___

Dr. Tobias Beck
- independent group leader -
RWTH Aachen University
Institute of Inorganic Chemistry
Landoltweg 1, office: 304N
52056 Aachen, Germany
phone:  +49-241-80-90057
fax:   +49-241-80-99003
web: http://www.ac.rwth-aachen.de/extern/beck/
___

Re: [ccp4bb] Refmac refinement R factors going up..... TLS issue? update

[Christian Roth]

Hi all,

I looked again careful in the respective files and it turns out that all 
B-Factors of the protein chains which are treated with TLS are refined 
to the lowest possible value of 2.00 for all atoms!
A workaround is to use the option to set the initial B-factor to 20.0 in 
the GUI and than the refinement finally works. I haven't yet figured out 
what goes wrong in Refmac, but it seems in the B-Factor refinement step 
something gets not treated quite right.


Cheers

Christian


Am 18.06.2015 um 21:58 schrieb Shane Caldwell:

Hi Christian, I've seen this behaviour as well. I'm not an expert but I
rationalized the situation as the TLS parameters for an incomplete model
getting overfit as the missing/wrong parts of the model pull on the TLS
parameters. REFMAC doesn't alternate between TLS and coordinate
refinement, so you can get stuck in a local minimum that moving atoms
and refining individual B-factors won't get you out of. As more of the
model is built correctly, the drift of this refinement gets less and less.

I've found that refining comparatively few TLS cycles (I usually do 3)
before the restrained refinement tends to avoid this problem most of the
time - don't let the TLS refinement converge. Sometimes I'll let the
coordinate step converge, then run another TLS refinement to bootstrap
things along, but usually the stats only marginally improve at that
point. In cases where I've made substantial rebuilds, it's sometimes
been necessary to turn off TLS and refine without it like you do, then
re-introduce the same TLS groups, setting the B-factors to fixed values.
Not really ideal, but it gets there. Hopefully others have some more
theoretically-sound advice.

A good thing to look at doing, especially if TLS is behaving weirdly, is
to check with the PARVATI server
(http://skuld.bmsc.washington.edu/parvati/). If your TLS group
boundaries set off flags, you have some more work to do on the refinement.


Shane Caldwell
McGill University

On Thu, Jun 18, 2015 at 4:30 PM, Christian Roth
mailto:christian.r...@bbz.uni-leipzig.de>> wrote:

Hi all,

I refine a structure with TLS and restrained refinement in Refmac.
After the run finished, I fixed a few outliers manually in Coot,
saved that file and used that with the original TLS file from TLSMD
for the next round of refinement. As soon as the restrained
refinement starts the R-factors are going up and stabilise than at a
higher values compared to the previous run.
If I switch of the TLS refinement and just do restrained refinement
with the same input files the R-values start initially at a higher
values and than decrease till they stabilise. Unfortunately the
final values are about 1.5 % higher, compared to the run with TLS
before manual rebuilding. So TLS seems to me beneficial and I would
like to use it, but somehow a strange combination of wrong files?,
wrong parametrization? or whatever prevent me of doing that.
Has anyone an idea what might be the cause of that strange behaviour.

Thank you very much in advance.

Cheers

Christian




--
Christian Roth
Strukturanalytik von Biopolymeren
Fakultät für Chemie und Mineralogie
Universität Leipzig
Deutscher Platz 5
04103 Leipzig

Email christian.r...@bbz.uni-leipzig.de

Re: [ccp4bb] FW: New ligand 3-letter code (help-7071)

[Martyn Symmons]

By oversimplifying the situation here the PDB does not answer my
related point about competing crystallographers:
My scenario:

Group A deposits structure with new drug - gets their three-letter
code for example ZA3
 they then get to check the coordinates and chemical definition of this ligand.

But suppose a little after that a competing group B deposits their
structure with the same drug which they think is novel - but no...
they get assigned the now described ZA3 which has been checked by the
other group.

 Then it is a race to see who gets to publish and release first. And
if it is the second group B who wins then they are publishing the work
of their A competitors - who have done the depositing and checking of
the ligand  description.

 Sounds unlikely? Well, it actually happened in 2011 for my exact
example ZA3 - present in 2Y2I and in 2Y59 from competing groups.

 From the dates in the mmcif it was 2Y2I depositors who set up and had
a chance to review the description of ZA3 ligand. Only to see it
released a week before their crystal structure, when their ZA3
appeared to accompany competing 2Y59! It is amazing that the PDB did
not spot this and arrange a suitable workaround.

Just to check:
mmcif for ZA3 shows it was created for 2Y2I:
...
_chem_comp.pdbx_model_coordinates_db_code2Y2I
...
But it was modified for release:
...
_chem_comp.pdbx_modified_date2011-07-22
...
corresponding to the early 2011-07-27 release date of the competing
structure: 2Y59 even though this PDB was  _deposited_ second.

The ZA3 ligand definition released with 2Y59 actually embodies the
atomic coordinates from the 2Y2I structure:


ZA3 O6   O6   O 0  1 N N N 8.279  7.165  40.963 0.311  -1.061 -0.920
O6   ZA3 1
ZA3 C5   C5   C 0  1 N N N 9.132  8.047  40.908 0.147  -0.205 -0.073
C5   ZA3 2  ...

HETATM 3598  O6  ZA3 A1000   8.279   7.165  40.963  1.00 41.25   O
HETATM 3599  C5  ZA3 A1000   9.132   8.047  40.908  1.00 63.20
  C ...

Surely a better approach would be to allow both groups a chance to
work through and sign off on independent ligand descriptions?

Then whoever releases first would release both a novel structure and
the ligand definition _they_ deposited and checked. Their priority can
then be asserted and the other group contacted to ask if they agree to
accept this definition. This also has the advantage of better
confidentiality pre-publication.

Another problem from any cross-linking of definitions is that say
group A are motivated by reviewers' reports to change the definition
of ZA3 pre-release. Well now the change impinges on the chemical
meaning of other group B's deposited structure. For example ZA3 mmcif
has a statement:

ZA3 "Modify aromatic_flag" 2011-06-04 RCSB

so this change was pre-release - but we cannot be sure what motivated
this - whether it was signed off by the 2Y2I authors or the 2Y59
authors (or both?)

With the accelerating pace of drug discovery for sure this sort of
uncertainty is going to happen again.Unless the PDB have changed their
practice for ligand deposition?

All the best
 Martyn

Cambridge.

On Fri, Jun 19, 2015 at 1:49 PM, Sheriff, Steven  wrote:
> All:
>
>
>
> Since the original query was cross-posted on both the COOT mailing list and
> the CCP4BB Rachel Green gave me permission to forward this to both. She
> provides links about the mechanism of assignment of 3-letter codes. In the
> third link below, my original suggestion to the COOT mailing list that one
> could just use UNK is incorrect as that is reserved for unknown amino acids.
> According to this document, I should have suggested UNL for an unknown
> ligand.
>
>
>
> Steven
>
>
>
> From: Rachel Kramer Green [mailto:kra...@rcsb.rutgers.edu]
> Sent: Tuesday, June 16, 2015 10:21 AM
> To: Sheriff, Steven
> Cc: info
> Subject: Re: New ligand 3-letter code (help-7071)
>
>
>
> Dear Steven,
>
> During annotation of ligands, all chemical components present in the
> structure are compared against the definitions in the Chemical Component
> Dictionary (http://www.wwpdb.org/data/ccd). If the ligand is not in the
> dictionary, a three letter code is assigned. See
> http://www.wwpdb.org/documentation/policy#toc_assignment.  In the future, a
> group of three-letter codes may be set aside to be used during refinement to
> flag new ligands.
>
> Clarification about the ligand ids assignment and in particular the usage of
> UNX/UNL/UNK residues can be found at
> http://www.wwpdb.org/documentation/procedure#toc_2.
>
> Best wishes,
> Rachel
>
>
>
> 
>
> Rachel Kramer Green, Ph.D.
>
> RCSB PDB
>
> kra...@rcsb.rutgers.edu
>
>
>
> New! Deposit X-ray data with the wwPDB at:
>
> http://deposit.wwpdb.org/deposition (NMR and 3DEM coming soon).
>
> ___
>
> Twitter: https://twitter.com/#!/buildmodels
>
> Facebook: http://www.facebook.com/RCSBPDB
>
>
>
>
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> On 6/5/2015 7:50 AM, Sheriff, Steven wrote:
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Re: [ccp4bb] FW: New ligand 3-letter code (help-7071)

[Edward A. Berry]

You raise some good points, but as far as better confidentiality 
pre-publication goes. unreleased entries are not secret in any case- if the 
second group is at all nervous about competition, they will be searching the 
unreleased entries database (http://www.rcsb.org/pdb/search/searchStatus.do), 
with the name of their protein or ligand, or suspected competing authors names, 
on a weekly basis.
We deposited 1yq3 and 1yq4 in Feb 2005, well before we were ready to 
publish. Regularly searching our protein in the unreleased entries, we saw 1zoy 
and 1zp0 deposited in May. And even so,they beat us to publication, but with 
lower resolution structures. I sometimes wonder if they would have waited for 
better data had they not known we were about to publish.

Elsewhere in the thread: I don't think you want to call your new ligand UNL. 
From what I understand that indicates the authors were unable to identify it, 
and by default it will remain UNL in the final released entry (although some 
back-and forth with the annotator would put things right).

eab

On 06/19/2015 08:38 PM, Martyn Symmons wrote:

By oversimplifying the situation here the PDB does not answer my
related point about competing crystallographers:
My scenario:

Group A deposits structure with new drug - gets their three-letter
code for example ZA3
  they then get to check the coordinates and chemical definition of this ligand.

But suppose a little after that a competing group B deposits their
structure with the same drug which they think is novel - but no...
they get assigned the now described ZA3 which has been checked by the
other group.

  Then it is a race to see who gets to publish and release first. And
if it is the second group B who wins then they are publishing the work
of their A competitors - who have done the depositing and checking of
the ligand  description.

  Sounds unlikely? Well, it actually happened in 2011 for my exact
example ZA3 - present in 2Y2I and in 2Y59 from competing groups.

  From the dates in the mmcif it was 2Y2I depositors who set up and had
a chance to review the description of ZA3 ligand. Only to see it
released a week before their crystal structure, when their ZA3
appeared to accompany competing 2Y59! It is amazing that the PDB did
not spot this and arrange a suitable workaround.

Just to check:
mmcif for ZA3 shows it was created for 2Y2I:
...
_chem_comp.pdbx_model_coordinates_db_code2Y2I
...
But it was modified for release:
...
_chem_comp.pdbx_modified_date2011-07-22
...
corresponding to the early 2011-07-27 release date of the competing
structure: 2Y59 even though this PDB was  _deposited_ second.

The ZA3 ligand definition released with 2Y59 actually embodies the
atomic coordinates from the 2Y2I structure:


ZA3 O6   O6   O 0  1 N N N 8.279  7.165  40.963 0.311  -1.061 -0.920
O6   ZA3 1
ZA3 C5   C5   C 0  1 N N N 9.132  8.047  40.908 0.147  -0.205 -0.073
C5   ZA3 2  ...

HETATM 3598  O6  ZA3 A1000   8.279   7.165  40.963  1.00 41.25   O
HETATM 3599  C5  ZA3 A1000   9.132   8.047  40.908  1.00 63.20
   C ...

Surely a better approach would be to allow both groups a chance to
work through and sign off on independent ligand descriptions?

Then whoever releases first would release both a novel structure and
the ligand definition _they_ deposited and checked. Their priority can
then be asserted and the other group contacted to ask if they agree to
accept this definition. This also has the advantage of better
confidentiality pre-publication.

Another problem from any cross-linking of definitions is that say
group A are motivated by reviewers' reports to change the definition
of ZA3 pre-release. Well now the change impinges on the chemical
meaning of other group B's deposited structure. For example ZA3 mmcif
has a statement:

ZA3 "Modify aromatic_flag" 2011-06-04 RCSB

so this change was pre-release - but we cannot be sure what motivated
this - whether it was signed off by the 2Y2I authors or the 2Y59
authors (or both?)

With the accelerating pace of drug discovery for sure this sort of
uncertainty is going to happen again.Unless the PDB have changed their
practice for ligand deposition?

All the best
  Martyn

Cambridge.

On Fri, Jun 19, 2015 at 1:49 PM, Sheriff, Steven  wrote:

All:



Since the original query was cross-posted on both the COOT mailing list and
the CCP4BB Rachel Green gave me permission to forward this to both. She
provides links about the mechanism of assignment of 3-letter codes. In the
third link below, my original suggestion to the COOT mailing list that one
could just use UNK is incorrect as that is reserved for unknown amino acids.
According to this document, I should have suggested UNL for an unknown
ligand.



Steven



From: Rachel Kramer Green [mailto:kra...@rcsb.rutgers.edu]
Sent: Tuesday, June 16, 2015 10:21 AM
To: Sheriff, Steven
Cc: info
Subject: Re: New ligand 3-letter code (help-7071)



Dear Steven,

During annotation o