Re: [ccp4bb] SMILES from PDB records (HELP-21524)
Dear Doeke,
Here is the process we recommend:
For now you can get the entire collection of ligand definitions at
http://www.wwpdb.org/data/ccd, using the file
https://files.wwpdb.org/pub/pdb/data/monomers/components.cif.gz
From there you would parse the SMILES from _pdbx_chem_comp_descriptor.
You can also use RCSB.org data API as described at
https://data.rcsb.org/#gql-example-7
Select "OPEN IN EDITOR" and add a chemical descriptor component search
as follows:
{
chem_comps(comp_ids:["NAG", "EBW"]) {
rcsb_id
chem_comp {
type
formula_weight
name
formula
}
pdbx_chem_comp_descriptor {
type
descriptor
}
rcsb_chem_comp_info {
initial_release_date
}
}
}
Then, you can get all IDs either using a "grep data_" command from the
file downloaded above, or by using the RCSB Advanced Search >> Chemical
Attributes >> Chemical IDs(s)>> "is not empty"
<https://www.rcsb.org/search?request=%7B%22query%22%3A%7B%22type%22%3A%22group%22%2C%22logical_operator%22%3A%22and%22%2C%22nodes%22%3A%5B%7B%22type%22%3A%22group%22%2C%22logical_operator%22%3A%22and%22%2C%22nodes%22%3A%5B%7B%22type%22%3A%22group%22%2C%22nodes%22%3A%5B%7B%22type%22%3A%22terminal%22%2C%22service%22%3A%22text_chem%22%2C%22parameters%22%3A%7B%22attribute%22%3A%22rcsb_chem_comp_container_identifiers.comp_id%22%2C%22operator%22%3A%22exists%22%2C%22negation%22%3Afalse%7D%7D%5D%2C%22logical_operator%22%3A%22and%22%7D%5D%2C%22label%22%3A%22text_chem%22%7D%5D%7D%2C%22return_type%22%3A%22entry%22%2C%22request_options%22%3A%7B%22paginate%22%3A%7B%22start%22%3A0%2C%22rows%22%3A25%7D%2C%22results_content_type%22%3A%5B%22experimental%22%5D%2C%22sort%22%3A%5B%7B%22sort_by%22%3A%22score%22%2C%22direction%22%3A%22desc%22%7D%5D%2C%22scoring_strategy%22%3A%22combined%22%7D%2C%22request_info%22%3A%7B%22query_id%22%3A%22757e2e66d52ec03ec085a0c4cc2ba0ba%22%7D%7D>
. Using the "Search API" button will then bring you to:
{
"query": {
"type": "terminal",
"label": "text_chem",
"service": "text_chem",
"parameters": {
"attribute": "rcsb_chem_comp_container_identifiers.comp_id",
"operator": "exists",
"negation": false
}
},
"return_type": "entry",
"request_options": {
"paginate": {
"start": 0,
"rows": 25
},
"results_content_type": [
"experimental"
],
"sort": [
{
"sort_by": "score",
"direction": "desc"
}
],
"scoring_strategy": "combined"
}
}
Please feel free to write to us at i...@rcsb.org if you have any questions.
Sincerely,
Rachel Green
-
*RACHEL KRAMER GREEN, PH.D.*
Scientific Support & Customer Service Lead
RCSB Protein Data Bank
Rutgers, The State University of New Jersey
174 Frelinghuysen Road, Piscataway NJ 08854
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On 9/13/2024 9:28 AM, Hekstra, Doeke Romke wrote:
Hi,
Does anyone have experience (or scripts!) to extract ligand SMILES
from macromolecular PDB records using the PDB data API or from a
library of PDB or mmCIF files? We would greatly appreciate any
pointers to get us started.
Thank you,
Doeke
=
Doeke Hekstra
Assistant Professor of Molecular & Cellular Biology, and of Applied
Physics (SEAS),
Director of Undergraduate Studies, Chemical and Physical Biology
Center for Systems Biology, Harvard University
52 Oxford Street, NW311
Cambridge, MA 02138
Office: 617-496-4740
Admin: 617-495-5651 (Lin Song)
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Re: [ccp4bb] search for similar complex structures (help-20620)
Dear Norbert, The structure search functionality at RCSB.org should help find AB complexes similar to yours: 1. Go to https://www.rcsb.org/search/advanced 2. In the "Structure Similarity" section, select "File upload" (using the pull-down menu that has "Entry ID" as the default) 3. Upload the coordinate file for your complex 4. Select "Search for" = "Assemblies" This should give you any assemblies in the PDB that have a globally similar shape to your AB complex. It will not give you locally similar matches (e.g. only one chain is similar or only a subdomain of each chain is similar) nor super assemblies (e.g. ABC where only AB is similar). Please feel to let us know at i...@rcsb.org if you have any questions. Sincerely, Rachel Green --------- *RACHEL KRAMER GREEN, PH.D.* Scientific Support & Customer Service Lead RCSB Protein Data Bank Rutgers, The State University of New Jersey 174 Frelinghuysen Road, Piscataway NJ 08854 rachel.gr...@rcsb.org rcsb.org <http://rcsb.org/>| facebook <https://www.facebook.com/RCSBPDB> | twitter <https://twitter.com/buildmodels>_ _ Coronavirus Resources: RCSB.org/covid19 <http://RCSB.org/covid19> Undergraduates and Graduates: Opportunities for Scientific Software-focused Summer Research, Gap Year, and Postdoctoral Research: www.rcsb.org/pages/jobs <http://www.rcsb.org/pages/jobs> On 1/29/2024 6:03 AM, Norbert Straeter wrote: Dear all, I have a heterodimeric complex AB and want to know if there are similar complexes between homologs of A and homologs of B or even any complex structures between such homologs. For the latter task, I could search for homologs of A and homologs of B by advanced PDB search or DALI etc. and next look for common PDB ids. Does anybody know a program or website that is dedicated to this kind of job? Best regards, Norbert To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/ To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
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Re: [ccp4bb] Absence of contact between layers in a crystal
Dear CCP4BB users,
For additional information on this matter, please see:
wwPDB Statement on Retraction of PDB Entries
http://www.wwpdb.org/documentation/UAB.php
and
Safeguarding the integrity of protein archive
/Nature/ (2010) *463*:425. doi:10.1038/463425c
<http://www.nature.com/nature/journal/v463/n7280/full/463425c.html>
Sincerely,
Rachel Green
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 2/6/2015 7:35 AM, Mark van Raaij wrote:
In our structures 1H6W (1.9Å) and 1OCY (1.5Å) we observed something
similar, I suspect the domain that makes the crystal contacts is
three-fold disordered, leading to layers of nothing. In our paper in
JMB 314, 1137 (doi 10.1006/jmbi.2000.5204) we tried to explain it a
bit, and describe what was done to try and "show up" the missing domain.
The 2HR0 structure was clearly made up, as were the data, apparently
the mathematical function used to calculate the sigmas could be
derived from the deposited data...It is indeed a pity that neither the
structure nor the paper have been rejected. Perhaps the PDB is waiting
for Nature, and Nature for the PDB...a joint letter to both might be
in order to get this sorted out.
On 6 Feb 2015, at 11:58, Kerff Fred wrote:
Hello,
Looking at structure 2HR0 ("The structure of complement C3b provides
insights into complement activation and regulation. »,Abdul Ajees,
A., Gunasekaran, K., Volanakis, J.E., Narayana, S.V., Kotwal,
G.J., Krishna Murthy, H.M.; (2006) Nature 444: 221-225), I noticed
the absence of contacts between layers in the crystal. Is it
something that has already been observed in other crystals?
Best regards,
Fred
-
Frédéric Kerff
Chercheur qualifié F.R.S.-FNRS
Cristallographie des protéines
Centre d'Ingénierie des Protéines
Université de Liège
17, Allée du 6 Août - Bat B5a
4000 Liège (Belgium)
Tel.: +32 (0)4 3663620
Fax: +32 (0)4 3663772
Le 6 févr. 2015 à 10:12, Tim Gruene <mailto:t...@shelx.uni-ac.gwdg.de>> a écrit :
-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1
Dear Smith,
The sca file most likely does not contain flags. pointless can read
the sca file, standardise it to ccp4 standards and freerflag marks
random reflections. You should use the maximum of 500 unique
reflections or 5% of the unique reflections, whichever is larger.
Best,
Tim
On 02/06/2015 09:49 AM, Smith Lee wrote:
Dear All, I have a sca file. Will you please tell me by which
software or how I can know whether the sca file contains R-free
tags? If not, by which software or how I can add the R-free tags?
And how much of the reflections I add the R-free tags? I am looking
forward to getting your reply. Smith
- --
- --
Dr Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen
GPG Key ID = A46BEE1A
-BEGIN PGP SIGNATURE-
Version: GnuPG v1.4.12 (GNU/Linux)
iD8DBQFU1IWVUxlJ7aRr7hoRAmZHAJ4+6wREnwkFN0EhfErAA0tPSopKKwCgiLdi
j0JFZac4kAh8twpov71MG84=
=XN57
-END PGP SIGNATURE-
Mark J van Raaij
Lab 20B
Dpto de Estructura de Macromoleculas
Centro Nacional de Biotecnologia - CSIC
c/Darwin 3
E-28049 Madrid, Spain
tel. (+34) 91 585 4616
http://www.cnb.csic.es/~mjvanraaij <http://www.cnb.csic.es/%7Emjvanraaij>
[ccp4bb] "NEW! Try depositing X-ray data using the wwPDB deposition system"
Depositing a new X-ray crystal structure to the PDB archive?Try the new and improved wwPDB Deposition system at http://deposit.wwpdb.org/deposition/. Since the new system went live on January 27^th , 2014, ~700 structures have been deposited and promptly annotated.Detailed information on the system can be found at http://www.wwpdb.org/system_info.html.The new system was developed to allow the wwPDB partners to meet the evolving needs of the scientific community over the next decade, including support for very large systems, complex chemistry, and joint use of multiple experimental methods. The system replaces all current deposition and annotation systems in use at the wwPDB deposition centers, and will lead to improved efficiency and consistency. New or enhanced features of the deposition system include the generation of X-ray validation reports (following the recommendations of the wwPDB X-ray Validation Task Force), improved capture and review of ligand information, the ability to replace coordinate and/or experimental data files pre- and post-submission, improved communication process between depositors and wwPDB curators, and the ability to preview and download the PDBx/mmCIF entry file prior to submission. Depositors will have the option to use the new system or one of the legacy deposition tools (ADIT, AutoDep) for most of 2014. After the transition to the new system, the legacy tools will be available for a limited period of time to complete any unfinished deposition sessions. The wwPDB continues to improve the deposition interface and supporting functionality as it receives more submissions and input.Questions, comments, and suggestions should be sent to: http://deposit-feedback.wwpdb.org_._ -- 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
Re: [ccp4bb] Comparison of Water Positions across PDBs
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 assigned unique residue numbering with the order polymer residues, ligands and then waters. Please see: http://www.wwpdb.org/procedure.html#toc_4 The wwPDB has established this rule to improve the usability and interpretation of the structural data. Assigning the same chain ID for all moieties associated with a polymer enables rapid and uniform identification of feature analysis. Sincerely, Rachel Green Rachel Kramer Green, Ph.D. RCSB PDB kra...@rcsb.rutgers.edu Twitter: https://twitter.com/#!/buildmodels Facebook: http://www.facebook.com/RCSBPDB On 10/30/2013 8:09 AM, Eugene Krissinel wrote: 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 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 the peptide chains in the structure? - appending all waters to chain A? Thanks. Andreas On 30/10/2013 11:57, MARTYN SYMMONS wrote: At deposition the PDB runs a script that renumbers authors' waters according to a scheme based on the residue they are nearest from N to C terminus along each chain. This renumbering started when waters were assigned to macromolecular chains rather than getting a chain id of their own. I have failed to find the rationale explained in any PDB documents - but it could be motivated by this sort of consideration when waters from different chains or entries are to be compared. Having said that I do not know if there are any cases where this approach has successfully matched waters. .. However an associated step which is certainly a help is that, in the case of multiple chains, the crystal symmetry is applied to replace waters with their symmetry equivalent position if it is closer to a different chain. I believe a freely available program implementing a similar approach is WATERTIDY in CCP4 which might be a good place to start. It gives a pretty complete output, detailing residues actually H-bonded to the waters, and you could parse that for further analysis and comparisons. Best wishes. Martyn -- Andreas Förster Crystallization and Xray Facility Manager Centre for Structural Biology Imperial College London
Re: [ccp4bb] "Formageddon" is upon us... Important news from wwPDB! (help-4246)
Dear Robbie, We will continue the practice that any structure deposited as a single PDBx/mmCIF file will be divided into SPLIT files and added to the ftp archive as usual, in all supported formats (PDB, PDBx/mmCIF, PDBML/XML). Entries are split only for reasons of size. SPLIT entries currently in the archive will remain as they are until sometime in 2014 when we plan to consolidate all existing and new SPLIT entries into single large files. Regards, Rachel Rachel Kramer Green, Ph.D. RCSB PDB kra...@rcsb.rutgers.edu Twitter: https://twitter.com/#!/buildmodels Facebook: http://www.facebook.com/RCSBPDB On 5/24/2013 12:41 PM, Robbie Joosten wrote: Perhaps a silly question: will old entries with SPLIT records be superseded by consolidated entries? And what about entries split for other reasons than size (there are only a few of those, and they are old)? Cheers, Robbie Van: Gerard DVD Kleywegt Verzonden: 24-5-2013 20:21 Aan: CCP4BB@JISCMAIL.AC.UK Onderwerp: [ccp4bb] "Formageddon" is upon us... Important news from wwPDB! Dear colleagues, I would like to draw your attention to a notification from the wwPDB partners about "Deposition and Release of PDB Entries Containing Large Structures" - see: http://www.wwpdb.org/news/news_2013.html#22-May-2013 There are major changes afoot in the way large structures are handled in the PDB, as well as in the deposition and annotation procedures and software used by the wwPDB sites. This is of immediate relevance for depositors and users of large structures, but also for software developers and anyone who routinely processes the entire PDB archive or its weekly releases (bioinformatics resources, etc.). From 2014, it will affect essentially everyone who deposits, uses or processes PDB entries. If you have any questions about the new deposition system or the procedures for handling large structures or any of the other changes, please contact: i...@wwpdb.org Please pass on this information to anyone likely to be affected by the upcoming changes. Thanks! On behalf of the Worldwide Protein Data Bank, --Gerard Kleywegt --- Gerard J. Kleywegt, PDBe, EMBL-EBI, Hinxton, UK ger...@ebi.ac.uk . pdbe.org Secretary: Pauline Haslam pdbe_ad...@ebi.ac.uk
Re: [ccp4bb] Vitamin B12 (cobalamin) geometry issues (help-3615)
Dear Oliver, The representation of B12 has been updated in the wwPDB's Chemical Component Dictionary and related PDB entries. They will be available with next week's update of the archive. Sincerely, Rachel Green ******* Rachel Kramer Green, Ph.D. RCSB PDB kra...@rcsb.rutgers.edu On 10/12/2012 4:31 AM, Oliver Smart wrote: If you are working on a protein that binds vitamin B12 (cobalamin) then you may be interested that there appears to be an issue with geometry of the B12 dictionary currently distributed by ccp4. The problem is that atom C19 in the corrin ring is defined as being SP2, planar with no hydrogen atom attached. Small molecule structures of B12 clearly show this atom is tetrahedral (as do high resolution protein complexes). A survey of 53 PDB structures containing B12 reveals that 19 have C19 atoms that are not sufficiently chiral. All are recent - structures prior to 2008 are all OK. The problem also effects the PDB chemical components definition of B12. Please see https://www.globalphasing.com/buster/wiki/index.cgi?B12Dictionary This page provides a dictionary for B12 with the problem fixed. Hope this proves useful. Regards, Oliver | Dr Oliver Smart | | Global Phasing Ltd., Cambridge UK | | http://www.globalphasing.com/people/osmart/ |
Re: [ccp4bb] TLS and ANISOU/RESIDUAL B-FACTORS - doubt
Dear Catarina, When TLS is involved in refinement using a script, the keyword "tlsout addu" should be added to produce a coordinate file containing the full B factor. The latest REFMAC interface (in CCP4i) has a button "Add TLS contribution to XYZOUT" in the folder of TLS Parameters which will add this keyword. There are three ways to convert file so it contains full B factors: 1. You can convert your PDB file so it contains full B factors using the server at http://deposit.rcsb.org/adit/REFMAC.html 2. Convert locally using the script at http://deposit-beta.rcsb.org/tlsanl/tlsanl_script.csh Run tlsanl_script.csh pdbfile (note: CCP4 should be installed on your local machine prior to running the script) 3. Convert using CCP4i package * Find the file of TLS parameters TLSOUT that corresponds to the coordinate file, or if necessary extract the TLS parameters from the PDB file using the CCP4 program tlsextract * Use CCP4's tlsanl to put the full B factor in the PDB coordinate file, available in the GUI interface as the task "Analyse TLS parameters". Be sure to set the keyword BRESID T in this interface. Please let us know if we can be of any further help. Sincerely, Rachel Green *********** Rachel Kramer Green, Ph.D. RCSB PDB kra...@rcsb.rutgers.edu __ PDB 40: Celebrate four decades of innovation in structural biology Oct 28-30, 2011 at Cold Spring Harbor Laboratory http://meetings.cshl.edu/meetings/pdb40.shtml ** On 8/3/2011 1:47 PM, Catarina Silva wrote: Dear all, I am trying to deposit a pdb containing TLS groups. PDB instructions states: "As we have mentioned on the start page for autodep, entries refined using REFMAC with TLS parameters must now contain the full B-factor in ATOM/HETATM records, with the TLS contribution coded into ANISOU records." I did run Refmac with TLS parameters and, as such, I would expect that all the values necessary to pdb deposition would be on the pdb coming out from refmac. However, when I deposit the pdb a 'serious error' comes up, not allowing me to deposit the coordinates: "You will NOT be allowed to proceed for deposition unless these issues are corrected. *TLS and ANISOU/RESIDUAL B-FACTORS.* As we have mentioned on the start page for autodep, entries refined using REFMAC with TLS parameters must now contain the full B-factor in ATOM/HETATM records, with the TLS contribution coded into ANISOU records.Your entry contains TLS records but no ANISOU records OR Residual B-factors. Please correct this and reupload your structure for validation" I don't really understand why these supposed missing values are not already contained in the pdb file, and I can't figure out how to get them. Does anyone knows how to fix this situation? Thanks in advance! Catarina Silva
