Re: [ccp4bb] PDB search help

2017-10-04 Thread John Berrisford 
Dear Rajesh

 

 

This is possible with our search API

See:

http://www.ebi.ac.uk/pdbe/api/doc/search.html

 

For example 

https://www.ebi.ac.uk/pdbe/search/pdb/select?q=pfam_name:Lipocalin 
 
&wt=json

 

then for each result you will need to compare “number_of_polymer_residues” and 
“max_observed_residues”. This will give you the observed ratio for each 
molecule (results are per molecule, not per PDB entry) in your result.

 

To make your query you can use our standard search page (pdbe.org) and with a 
small amount of reformatting use the same query in our search API. 

For example:

If you did a search on a main page the URL would look something like this:

https://www.ebi.ac.uk/pdbe/entry/search/index?text:hemoglobin 

 
&molecule_name:%22Neural%20hemoglobin%22&assembly_composition:%22protein%20structure%22&molecule_type:Protein

with all the search parameters encoded in the URL.

To use this in the API – take the part after the ? and change & to “ AND “ – 
the spaces are important here. 

i.e. 

text:hemoglobin&molecule_name:"Neural%20hemoglobin"&assembly_composition:"protein%20structure"&molecule_type:Protein

becomes

text:haemoglobin AND molecule_name:"Neural%20hemoglobin" AND 
assembly_composition:"protein%20structure" AND molecule_type:Protein

then append this to our search API URL 
(https://www.ebi.ac.uk/pdbe/search/pdb/select?q=)

https://www.ebi.ac.uk/pdbe/search/pdb/select?q=text:hemoglobin AND 
molecule_name:"Neural%20hemoglobin" AND 
assembly_composition:"protein%20structure" AND molecule_type:Protein

and then if you prefer JSON format to XML add &wt=json to the end.  

https://www.ebi.ac.uk/pdbe/search/pdb/select?q=text:hemoglobin AND 
molecule_name:"Neural%20hemoglobin" AND 
assembly_composition:"protein%20structure" AND molecule_type:Protein&wt=json

By default this will get you 10 result – to get more add &rows=10 to the end 
and change 10 to a larger number. 

 

 

Hope this helps

 

John

 

From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Rajesh
Sent: 27 September 2017 23:48
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] PDB search help

 

Dear BB,

Sorry for the off topic. 

Does anyone know how to search the PDB for the entries that have the density 
only for part of the protein molecule rather than for the entire length of the 
protein attempted to crystallize?

 

 

Thanks,

Rajesh..

[ccp4bb] CCP4 series 7.0 update 045

2017-10-04 Thread Andrey Lebedev 
Dear All


updates 045 has been release.  This contains


shelxe (Mac, Linux 64 bit)
• update to 2017_1
• improved chain tracing at lower than 2A resolution
• further details at http://shelx.uni-ac.gwdg.de/SHELX/changes.php

coot (Mac, Linux)
• correctsions to some typos

molrep
• fix for bug in map read

sfcheck
• removed bug in reading ccp4 map

pointless
• 1.11.4 increase number of images from Scalepack file

lorestr
• fixed CCP4i2 compatibility issue with -p2 file names

ctruncate
• bug fixes, protect 0 value diagonal elements in hessian

hklfile
• bug fixes

acedrg
• bug fixes

ccp4i2
• new nautilus interface
• lorestr: fixed difference map import
• crank2: fixes for specific space groups
• arpwarp: added output xyz with dummy atoms removed
• added task interface for morda-mp

ccp4i
• jsrview set as the default viewer for crank2
• fixed termination of subprocesses

morda-mp (Mac, Linux)
• released python wrapper and i1 interface

crank2
• disabling ccp4i jsrview pop-up
• prasa fine-tuning
• fixes for specific space groups
• fixed flip-mem variant of charge flipping


All the best

CCP4 Core team

[ccp4bb] Implementation of PDB Entry Versioning and Better Revision History to Improve PDB Archive Management

2017-10-04 Thread John Berrisford 

Dear CCP4BB

The PDB is introducing versioning of PDB entries.
As part of this work a new FTP 
repository,ftp://ftp-versioned.wwpdb.org/now hosts versioned structural 
model files in PDBx/mmCIF and PDBML formats.
Asannounced 
on 
May 17, 2017, wwPDB has introduced a versioning system to enable 
depositor-initiated or wwPDB-initiated updates to previously released 
PDB entries while retaining the same PDB accession code. Updates to 
atomic coordinates, polymer sequence or chemical description in a PDB 
coordinate file will trigger a major version increment. Other changes 
will be classified as minor. All major versions of each PDB structure 
are retained in the new FTP archive.


In the 2018 phase of the project, wwPDB will enable depositor-initiated 
updates of coordinates.


File names in the versioned FTP archive conform to a new naming scheme, 
which allows users to easily see the major and minor version numbers:

__v-..
The familiar 4-character PDB accession code is extended to 8 characters 
prefixed with “pdb”. Thus PDB accession code for entry 1abc becomes 
pdb_1abc. This new format of PDB accession code will be included in 
the model files at a later date. For example, the first initial release 
of PDB entry 1abc would have the following form under the new 
file-naming scheme:

pdb_1abc_xyz_v1-0.cif.gz
where xyz stands for coordinate content; cif indicates the file format; 
and gz indicates a compressed UNIX archive file.
The first minor revision of PDB entry 1abc would then have the following 
name:

pdb_1abc_xyz_v1-1.cif.gz
If PDB entry 1abc then had a major update, it would have the following name:
pdb_1abc_xyz_v2-0.cif.gz (N.B.: The minor update number will be 
reset to zero every time a new major update is made.)
The versioned data files for a particular entry are stored in single 
directory following a 2-character hash from the two penultimate 
characters of the PDB code:

../pdb_versioned/data/entries///
For example, major version 1 with minor version 2 file for entry 1ABC 
would have the following path:

../pdb_versioned/data/entries/ab/pdb_1abc/pdb_1abc_xyz_v1-2.cif.gz
Different views of the repository are provided for content type and 
format as a convenience for repository users. The wwPDB provides a link 
to the absolutely latest version files as well as latest version of each 
major version in the entries directories.
For example, users can access the absolute latest version of each 
coordinate mmCIF file (e.g. 1ABC) via below file path.

../pdb_versioned/views/latest/coordinates/mmcif/ab/pdb_1abc/pdb_1abc_xyz.cif.gz
→../pdb_versioned/data/entries/ab/pdb_1abc/pdb_1abc_xyz_v2-0.cif.gz
Or users can access all major versions of coordinate mmCIF files for 
entry 1ABC via below file path.

../pdb_versioned/views/all/coordinates/mmcif/ab/pdb_1abc/pdb_1abc_xyz_v1.cif.gz
→../pdb_versioned/data/entries/ab/pdb_1abc/pdb_1abc/pdb_1abc_xyz_v1-2.cif.gz
../pdb_versioned/views/all/coordinates/mmcif/ab/pdb_1abc/pdb_1abc/pdb_1abc_xyz_v2.cif.gz
→../pub/pdb_versioned/data/entries/ab/pdb_1abc/pdb_1abc_xyz_v2-0.cif.gz
Data files in the current archive location 
ftp://ftp.wwpdb.org/pub/pdb/data/structures/ will continue to use the 
familiar naming style and will continue to contain only the latest 
version for every entry.



John

--
John Berrisford
PDBe
European Bioinformatics Institute (EMBL-EBI)
European Molecular Biology Laboratory
Wellcome Trust Genome Campus
Hinxton
Cambridge CB10 1SD UK
Tel: +44 1223 492529

http://www.pdbe.org
http://www.facebook.com/proteindatabank
http://twitter.com/PDBeurope

[ccp4bb] Postdoctoral Felloship available

2017-10-04 Thread Richard Baxter 
A postdoctoral opportunity exists in the laboratory of Richard Baxter at the 
Temple University School of Medicine in Philadelphia to investigate the 
structure and function of complement-like proteins in insects, their roles in 
immunity, development, and the transmission of infectious diseases. You will 
join an interdisciplinary group using biochemistry, biophysics, structural 
biology, and cell-based assays in collaboration with experts at the organismal 
level. Your objective will be to elucidate novel molecular mechanisms of 
immunity, and new connections between invertebrate and vertebrate immune 
responses, that can be leveraged to predict and disrupt disease.

For recent publications and current projects, please visit 
http://sites.temple.edu/baxterlab

Applicants should have a Ph.D. in chemistry, biochemistry, biophysics, 
biochemistry or related disciplines, a record of peer-reviewed publication, and 
familiarity with standard laboratory techniques of molecular cloning, protein 
expression and purification, and structural techniques such as x-ray 
crystallography, electron microscopy, small angle x-ray scattering, and/or mass 
spectrometry. Interested applicants please send (i) cover letter, (ii) 
curriculum vitae, and (iii) name and contact information for three references 
to Prof. Richard Baxter by email: rbax...@temple.edu.