[ccp4bb] Deprecation of MMTF-format files for the PDB archive

[Jose Duarte]

>From July 2024 the PDB file archive will not be offered in the compressed
MMTF format anymore. Users are strongly encouraged to switch to the BinaryCIF
format <https://github.com/molstar/BinaryCIF>, which has been available
since 2020. Details on how to access BinaryCIF (BCIF) data files for the
entire PDB archive are available here
<https://www.rcsb.org/docs/programmatic-access/file-download-services#pdb-entry-files>
.

RCSB PDB support is ready to assist with any issues or questions at
i...@rcsb.org.

Best wishes

Jose

---
Jose Duarte
RCSB Protein Data Bank
San Diego Supercomputer Center
UC San Diego
La Jolla CA, USA



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[ccp4bb] RCSB PDB file downloads DNS changes

[Jose Duarte]

RCSB PDB has recently introduced DNS names for programmatic access to PDB
archive downloads:

FTP: ftp://ftp.rcsb.org
HTTPS: https://files.wwpdb.org (replaces https://ftp.rcsb.org)
RSYNC: rsync://rsync.rcsb.org (replaces rsync://rcsb.org)

The File Download Services
<https://www.rcsb.org/docs/programmatic-access/file-download-services>
documentation
has detailed information.

Starting *September 19th 2023 (1 week from now)*, RCSB PDB will start
enforcing use of these updated DNS names. URLs in which the DNS name
doesn’t match the protocol (e.g., https://ftp.rcsb.org, ftp://files.rcsb.org)
will no longer work at that time.

Users who download PDB archive data programmatically are encouraged to
switch to the new DNS names as soon as possible. HTTPS protocol is
preferred (over FTP) for individual file downloads.

Please contact i...@rcsb.org with any questions.

Many thanks

Jose

---
Jose Duarte
RCSB Protein Data Bank
San Diego Supercomputer Center
UC San Diego
La Jolla CA, USA



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Re: [ccp4bb] Downloading individual chains from the PDB

[Jose Duarte]

Gary pointed me to a typo in the API reference link (thanks!). This is the
correct one: https://models.rcsb.org

On Thu, 7 Sept 2023 at 09:34, Jose Duarte  wrote:

> The ModelServer API is your friend. See the APIs help page at
> https://www.rcsb.org/docs/programmatic-access/web-services-overview and
> the full ModelServer API reference at https://modes.rcsb.org
>
> An example that retrieves chain A of 2trx (in CIF format):
> https://models.rcsb.org/v1/2trx/atoms?label_asym_id=A=cif_all_categories=false=false
>
> I'll also take this opportunity to advertise the upcoming RCSB PDB APIs
> crash course: https://iqb.rutgers.edu/node/279 . Though the course will
> mostly deal with other APIs (Data and Search).
>
> Hope this helps
>
> Jose
>
>
> On Thu, 7 Sept 2023 at 09:17, Whitley, Matthew (NIH/NCI) [C] <
> a8ed4e9d4a1a-dmarc-requ...@jiscmail.ac.uk> wrote:
>
>> Hello all,
>>
>>
>>
>> I have a script I use from time to time to batch download multiple PDB
>> files using curl.
>>
>>
>>
>> I have certain use cases in which I only need a specific chain from a PDB
>> file that contains multiple chains.  At present, I download the complete
>> PDB file and then use pdbtools to pull out the specific chain I want.
>>
>>
>>
>> Does anyone know a way to batch download *specific chains* from the PDB?
>>   I reviewed the “File Download Services” page at the RCSB PDB, but I
>> didn’t find anything about downloading specific chains, so I don’t know if
>> this functionality exists.
>>
>>
>>
>> Thanks for your suggestions.
>>
>> Matthew
>>
>>
>>
>> --
>>
>> To unsubscribe from the CCP4BB list, click the following link:
>> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
>>
>



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Re: [ccp4bb] Downloading individual chains from the PDB

[Jose Duarte]

The ModelServer API is your friend. See the APIs help page at
https://www.rcsb.org/docs/programmatic-access/web-services-overview and the
full ModelServer API reference at https://modes.rcsb.org

An example that retrieves chain A of 2trx (in CIF format):
https://models.rcsb.org/v1/2trx/atoms?label_asym_id=A=cif_all_categories=false=false

I'll also take this opportunity to advertise the upcoming RCSB PDB APIs
crash course: https://iqb.rutgers.edu/node/279 . Though the course will
mostly deal with other APIs (Data and Search).

Hope this helps

Jose


On Thu, 7 Sept 2023 at 09:17, Whitley, Matthew (NIH/NCI) [C] <
a8ed4e9d4a1a-dmarc-requ...@jiscmail.ac.uk> wrote:

> Hello all,
>
>
>
> I have a script I use from time to time to batch download multiple PDB
> files using curl.
>
>
>
> I have certain use cases in which I only need a specific chain from a PDB
> file that contains multiple chains.  At present, I download the complete
> PDB file and then use pdbtools to pull out the specific chain I want.
>
>
>
> Does anyone know a way to batch download *specific chains* from the PDB?
>   I reviewed the “File Download Services” page at the RCSB PDB, but I
> didn’t find anything about downloading specific chains, so I don’t know if
> this functionality exists.
>
>
>
> Thanks for your suggestions.
>
> Matthew
>
>
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
>



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[ccp4bb] Postdoctoral position at RCSB PDB San Diego

[Jose Duarte]

We are seeking a talented, highly motivated postdoctoral researcher to join
the multidisciplinary team of the RCSB Protein Data Bank at UC San Diego,
San Diego Supercomputer Center (SDSC).

Fast and accurate search of protein structures by 3-dimensional shape in
large databases continues to be a challenge in Bioinformatics. This has
been exacerbated by the recent appearance of accurate methods to predict
protein structures from sequence. Those methods, when applied to existing
protein sequence databases, produce numbers of structures many orders of
magnitude larger than the existing experimental knowledge in the PDB
database. The incumbent will research novel methods to compare
macromolecular structures that are scalable to the deluge of structural
data and that work at any level: domains, chains or assemblies. The
ultimate aim of this project is to improve the findability of data in the
PDB by building the next generation search engine for structural molecular
biology.

Note, this position is reviewed annually on the basis of performance and
can be renewed.
Requirements

Qualifications: Ph.D. in one of the following research areas

   -

   Computer Science with a focus on Bioinformatics
   -

   Structural Bioinformatics, or related field with a focus on software
   development
   -

   Structural Biology with a focus on software development


Demonstrated proficiency in a high-level programming language, such as
Java, Python, C++, and experience with state of the art software
engineering tools. Strong skills in problem solving and algorithm design
are required. Experience in Machine Learning/Deep Learning is desirable. A
background in NoSQL database technologies would be beneficial. Experience
in development of modern web applications, user interface design, or
scientific visualization would also be a plus. We expect candidates to have
shown high productivity demonstrated by publications and contributions to
open source software projects. Excellent written and oral communication
skills are required.
About the RCSB

Our group supports RCSB Protein Data Bank (PDB) operations at UC San Diego.
The RCSB PDB (http://www.rcsb.org) represents the preeminent source of
experimentally determined macromolecular structure information for research
and teaching in fundamental biology, biomedicine, bioenergy, and
biotechnology. With millions of unique users from over 160 countries around
the world, the RCSB PDB is one of the leading worldwide Biological
Databases.



As an Organized Research Unit of UC San Diego, SDSC is a world leader in
data-intensive computing and cyber infrastructure, providing resources,
services, and expertise to the national research community, including
industry and academia.

http://www.rcsb.org/pages/jobs




Jose Duarte
RCSB Protein Data Bank
San Diego Supercomputing Center, UC San Diego
9500 Gilman Drive
La Jolla CA 92093, USA



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[ccp4bb] More efficient delivery of sequence cluster files

[Jose Duarte]

The sequence cluster files offered at RCSB PDB's CDN server (see
https://www.rcsb.org/docs/programmatic-access/file-download-services#sequence-clusters-data)
are now offered using PDB polymer entity identifiers, removing much
redundancy and producing smaller file sizes. The previous chain-based
cluster files will be updated only until April 12 2022. If you use these
files, please consider migrating to the entity-based files as soon as
possible.

Please also note that more integrated access to the same data is available
via RCSB PDB's Data and Search APIs. See:

https://data.rcsb.org/#gql-example-3
https://search.rcsb.org/#dealing-with-redundancy

Best wishes

Jose

---
Jose Duarte
RCSB Protein Data Bank
San Diego Supercomputing Center
UC San Diego



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[ccp4bb] Enforcement of https for all RCSB PDB web services

[Jose Duarte]

Dear all

Starting May 10 2021, we will be enforcing https for all access to the
rcsb.org frontend or to any of RCSB's APIs.

The HTTPS protocol has been supported for a few years, but with this change
all users will be redirected to HTTPS so that secure communication is
always guaranteed.

Please note that all APIs (
https://www.rcsb.org/docs/programmatic-access/web-services-overview) will
also enforce use of HTTPS. Programmatic users are encouraged to switch to
HTTPS as soon as possible. Not all HTTP clients will necessarily follow
redirects automatically.

Please also note that the "HTTP Strict Transport Security" headers [
https://en.wikipedia.org/wiki/HTTP_Strict_Transport_Security] will also be
used, starting May 10 2021.

Best wishes

Jose

---
Jose Duarte
RCSB Protein Data Bank
SDSC, UC San Diego



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[ccp4bb] Positions at RCSB PDB, UC San Diego

[Jose Duarte]

We currently have 2 positions available at the RCSB PDB team in UC San
Diego:

- Scientific Software Developer (staff position)
- Postdoctoral Researcher

Please refer to our Careers page for more information and links to apply:
https://www.rcsb.org/pages/jobs

Best regards

Jose

---
Jose Duarte
RCSB Protein Data Bank
San Diego Supercomputing Center
UC San Diego
La Jolla, California



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Re: [ccp4bb] RCSB PDB legacy API shutdown, December 9 2020

[Jose Duarte]

A final reminder that the legacy RCSB PDB application will be shut down on
December 9 (next week).

Please note if you use any URL that starts with "rcsb.org/pdb" it will stop
working at that point. Instead it will return a 404 (not found) error.

That affects the search and fetch legacy APIs and other endpoints like the
FASTA downloads.

See the migration guides and the downloads page:

   - Data API migration guide: https://data.rcsb.org/migration-guide.html
   - Search API migration guide:
   https://search.rcsb.org/migration-guide.html
   - Downloads page with details about FASTA and other file download URLs:
   https://www.rcsb.org/pages/download/http

Jose


On Wed, 7 Oct 2020 at 16:49, Jose Duarte  wrote:

> Dear all
>
> The RCSB PDB legacy APIs are going to be discontinued on the 9th of
> December 2020.
>
> A month prior to the full shutdown, we will have a 1 week (November
> 3-10) brownout of the legacy APIs, when they will not be available. A 404
> http code will be returned instead. We hope this will help identify any
> remaining legacy API usage.
>
> All programmatic users are strongly encouraged to migrate to the new APIs
> before the final shutdown time in December.
>
> New json-based APIs are now available that provide more comprehensive
> search and fetch capabilities, see https://www.rcsb.org/pages/webservices.
> Highlights include :
>
>- A GraphQL interface for the Data API
>- Full boolean support for Search API
>- Integrated text + scientific searches (structure search, sequence
>search) in the Search API
>
> Documentation for the new services and a migration guide are available:
>
>- Data API tutorial: https://data.rcsb.org
>- Search API tutorial: https://search.rcsb.org
>- Data API migration guide: https://data.rcsb.org/migration-guide.html
>- Search API migration guide:
>https://search.rcsb.org/migration-guide.html
>
> As usual, for any questions you can use the "Contact Us" button at the
> rcsb.org website.
>
> Best wishes
>
> Jose
>
> ---
> Jose Duarte
> RCSB Protein Data Bank
> SDSC, UC San Diego
>



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[ccp4bb] Scientific Software Developer at RCSB PDB, UCSD

[Jose Duarte]

The RCSB PDB is seeking a Scientific Software Developer with skills as a
seasoned, experienced bioinformatics programming professional and a broad
understanding of computational algorithms.

The incumbent will develop, implement, and maintain complex scientific and
web-based software systems for the RCSB Protein Data Bank (PDB;
http://www.rcsb.org) at the University of California San Diego (UCSD).

The Scientific Software Developer will work closely and collaboratively
with other software developers and scientists at the San Diego
Supercomputer Center (SDSC) and the RCSB PDB partner sites to expand
RCSB.org's functionality and reliability as a premier biological data and
information resource. S/he will develop new scalable algorithms for the
mining and analysis of the rapidly growing PDB archive using leading edge
Big Data technologies, design and implement user interfaces for the query,
analysis, reporting, and visualization of 3D structural information and
associated annotations, as well as integrate external database resources
with RCSB PDB to provide a structural view of biology. The incumbent will
help lead the design of databases and data warehouses to store and aid in
the query of data and be actively involved in the software development
process, maintenance and system standards for analysis algorithms, tools,
and infrastructure.

Additionally, the incumbent will serve as an expert on relevant scientific
and technical aspects of the various web, web services, and database
components of the RCSB PDB. S/he will stay abreast of the latest
development in structural and computational biology and new technologies,
apply advanced bioinformatics concepts to design, develop, modify, debug,
and evaluate highly complex software programs and web tools, and translate
scientific problems into scalable and maintainable software solutions that
meet end-user needs. The incumbent will also further science through
Scientific Publications, written in collaboration with our team.

More information and how to apply at: https://www.rcsb.org/pages/jobs

---
Jose Duarte
RCSB Protein Data Bank
San Diego Supercomputing Center
UC San Diego



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[ccp4bb] RCSB PDB legacy API shutdown, December 9 2020

[Jose Duarte]

Dear all

The RCSB PDB legacy APIs are going to be discontinued on the 9th of
December 2020.

A month prior to the full shutdown, we will have a 1 week (November
3-10) brownout of the legacy APIs, when they will not be available. A 404
http code will be returned instead. We hope this will help identify any
remaining legacy API usage.

All programmatic users are strongly encouraged to migrate to the new APIs
before the final shutdown time in December.

New json-based APIs are now available that provide more comprehensive
search and fetch capabilities, see https://www.rcsb.org/pages/webservices.
Highlights include :

   - A GraphQL interface for the Data API
   - Full boolean support for Search API
   - Integrated text + scientific searches (structure search, sequence
   search) in the Search API

Documentation for the new services and a migration guide are available:

   - Data API tutorial: https://data.rcsb.org
   - Search API tutorial: https://search.rcsb.org
   - Data API migration guide: https://data.rcsb.org/migration-guide.html
   - Search API migration guide:
   https://search.rcsb.org/migration-guide.html

As usual, for any questions you can use the "Contact Us" button at the
rcsb.org website.

Best wishes

Jose

---
Jose Duarte
RCSB Protein Data Bank
SDSC, UC San Diego



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[ccp4bb] Scientific Software Developer position at RCSB PDB, UCSD

[Jose Duarte]

The RCSB PDB is seeking a Scientific Software Developer with skills as a
seasoned, experienced bioinformatics programming professional and a broad
understanding of computational algorithms.

The incumbent will develop, implement, and maintain complex scientific and
web-based software systems for the RCSB Protein Data Bank (PDB;
http://www.rcsb.org) at the University of California San Diego (UCSD).

The Scientific Software Developer will work closely and collaboratively
with other software developers and scientists at the San Diego
Supercomputer Center (SDSC) and the RCSB PDB partner sites to expand
RCSB.org's functionality and reliability as a premier biological data and
information resource. S/he will develop new scalable algorithms for the
mining and analysis of the rapidly growing PDB archive using leading edge
Big Data technologies, design and implement user interfaces for the query,
analysis, reporting, and visualization of 3D structural information and
associated annotations, as well as integrate external database resources
with RCSB PDB to provide a structural view of biology. The incumbent will
help lead the design of databases and data warehouses to store and aid in
the query of data and be actively involved in the software development
process, maintenance and system standards for analysis algorithms, tools,
and infrastructure.

Additionally, the incumbent will serve as an expert on relevant scientific
and technical aspects of the various web, web services, and database
components of the RCSB PDB. S/he will stay abreast of the latest
development in structural and computational biology and new technologies,
apply advanced bioinformatics concepts to design, develop, modify, debug,
and evaluate highly complex software programs and web tools, and translate
scientific problems into scalable and maintainable software solutions that
meet end-user needs. The incumbent will also further science through
Scientific Publications, written in collaboration with our team.

More information and how to apply at: https://www.rcsb.org/pages/jobs

---
Jose Duarte
RCSB Protein Data Bank
San Diego Supercomputing Center
UC San Diego



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Re: [ccp4bb] Thanks and outcome of ([ccp4bb] Looking for method to find similar oligomeric arrangement)

[Jose Duarte]

A further note on assembly search: since April the RCSB PDB offers
structure search for assemblies. See the "Structure Similarity" section in
https://www.rcsb.org/search/advanced. This works only for PDB-deposited
structures but we are working on making it available for 3D coordinates
submitted by users. The search is extremely fast (below a second) and it
will match the assembly globally. Additionally the search results can be
further filtered by other criteria such as resolution or organism.

The search is also available at Structure Summary Pages (e.g.
https://www.rcsb.org/structure/4HHB)  with the "Find Similar Assemblies"
link below the symmetry information on top left.

Jose


On Sun, 21 Jun 2020 at 07:58, Andrew Lovering  wrote:

> Dear All
>
>
> Many thanks to Johann for the suggestion of Topsearch - rather pleasingly
> our tetramer is novel in the tetrameric arrangement, but each of the dimers
> has its DNA recognition helices in agreement with several hits a win
> all round
>
>
> Bringing joy to my lockdown.
>
>
> Best
>
> Andy
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
>



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[ccp4bb] Deprecation of RCSB PDB legacy APIs

[Jose Duarte]

The RCSB PDB legacy APIs are going to be discontinued in November 2020, see
the news article from last week:

https://www.rcsb.org/news?year=2020=5eb18ccfd62245129947212a=true

Programmatic users are strongly encouraged to migrate to the new APIs
before November 2020.

New json-based APIs are now available that provide more comprehensive
search and fetch capabilities, see https://www.rcsb.org/pages/webservices.
Highlights include :

   - A GraphQL interface for the Data API
   - Full boolean support for Search API
   - Integrated text + scientific searches (structure search, sequence
   search) in the Search API

Best wishes

Jose

---
Jose Duarte
RCSB Protein Data Bank
SDSC, UC San Diego



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[ccp4bb] Postdoctoral position at RCSB PDB San Diego

[Jose Duarte]

We are seeking a talented, highly motivated postdoctoral researcher to join
the multidisciplinary team of the RCSB Protein Data Bank at UC San Diego,
San Diego Supercomputer Center (SDSC).

The successful applicant will work on research projects that drive next
generation search tools at rcsb.org. Dealing with redundancy within the
Protein Data Bank (PDB) is an important challenge in face of the ~10%
year-on-year growth in structural data stored in the PDB. Tackling the
redundancy problem requires understanding of similarities and differences
among macromolecules at many different levels. She/he will be expected to
contribute to this project by devising new and improved algorithms for
protein family classification at levels such as biological assemblies. The
ultimate aim of this project is to improve the findability of data in the
PDB by building the next generation search engine for structural molecular
biology.

Note, this position is reviewed annually on the basis of performance and
can be renewed.

Requirements

Qualifications: Ph.D. in one of the following research areas
● Computer Science with a focus on Bioinformatics
● Structural Bioinformatics, or related field with a focus on software
development
● Structural Biology with a focus on software development

Demonstrated proficiency in a high-level programming language, such as
Java, Python, C++, and experience with state of the art software
engineering tools. Strong skills in problem solving and algorithm design
are required. A background in NoSQL database technologies would be
beneficial. Experience in development of modern web applications, user
interface design, or scientific visualization would also be a plus. We
expect candidates to have shown high productivity demonstrated by
publications and contributions to open source software projects. Excellent
written and oral communication skills are required.

About the RCSB
Our group supports RCSB Protein Data Bank (PDB) operations at UC San Diego.
The RCSB PDB represents the preeminent source of experimentally determined
macromolecular structure information for research and teaching in
fundamental biology, biomedicine, bioenergy, and biotechnology. With
millions of unique users from over 160 countries around the world, the RCSB
PDB is one of the leading worldwide Biological Databases.

As an Organized Research Unit of UC San Diego, SDSC is a world leader in
data-intensive computing and cyber infrastructure, providing resources,
services, and expertise to the national research community, including
industry and academia.

http://www.rcsb.org/pages/jobs

All applications must be submitted electronically via
https://apol-recruit.ucsd.edu/JPF02453



Jose Duarte
RCSB Protein Data Bank
San Diego Supercomputing Center, UC San Diego
9500 Gilman Drive
La Jolla CA 92093, USA



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Re: [ccp4bb] Mixed oligomeric states in crystallo

[Jose Duarte]

Here's a few examples:

https://www.rcsb.org/structure/1A2K
The crystal has an A3B2 stoichiometry. The paper describes how they find
A2B2 in solution, concluding the extra A molecule comes from "fortuitous
packing" in the crystal

https://www.rcsb.org/structure/2RBL
A design protein, but with very similar crystal packing as described in the
original post: a domain-swapped dimer and a non-swapped monomer.

https://www.rcsb.org/structure/1A99
Both dimers and monomers in the crystal



On Fri, 31 Jan 2020 at 09:46, Diana Tomchick <
diana.tomch...@utsouthwestern.edu> wrote:

> Here’s two examples of heterooligomers that crystallized in a lattice with
> an extra monomer of one of the proteins. In both cases this was an
> unexpected result, but easily explained due to the low micro molar
> affinities for the complex.
>
> 4PKY
> 2CJS
>
> Diana
>
> **
> Diana R. Tomchick
> Professor
> Departments of Biophysics and Biochemistry
> UT Southwestern Medical Center
> 5323 Harry Hines Blvd.
> Rm. ND10.214A
> Dallas, TX 75390-8816
> diana.tomch...@utsouthwestern.edu
> (214) 645-6383 (phone)
> (214) 645-6353 (fax)
>
> On Jan 31, 2020, at 9:23 AM, Kluenemann, Thomas <
> thomas.kluenem...@helmholtz-hzi.de> wrote:
>
>
> EXTERNAL MAIL
>
> Dear all,
>
> We recently solved a the structure of a small c-type cytochrome. We
> observed, that of the eleven chains in the asymmetric unit ten form 3D
> domain swapped dimers by exchanging an α-helix. The eleventh  chain is
> present as a monomer. Based on the anomalous iron signal and the chain
> tracing we are sure that no chain was missed.
> I tried to find other examples in the PDB, were one crystal is made of
> different homo- or heterooligomers.  I only found proteins with partial
> occupied peptide binding sites, which is not what I am looking for. Does
> anyone know of a case were the presence of different homo- or
> heterooligomers is required to form the crystal?
>
> Best regards,
> Thomas Klünemann
>
>
>
> --
>
> Helmholtz-Zentrum für Infektionsforschung GmbH | Inhoffenstraße 7 | 38124
> Braunschweig | www.helmholtz-hzi.de
>
> Vorsitzende des Aufsichtsrates: Frau MinDir'in Prof. Dr. Veronika von
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>
> CAUTION: This email originated from outside UTSW. Please be cautious of
> links or attachments, and validate the sender's email address before
> replying.
>
>
> --
>
> UT Southwestern
>
> Medical Center
>
> The future of medicine, today.
>
> --
>
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>



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Re: [ccp4bb] Generating symmetry mates using python

[Jose Duarte]

BioJava is another library that can do this. Not python but perhaps it can
still help.

This part of the tutorial covers how to find all contacts in the crystal:

https://github.com/biojava/biojava-tutorial/blob/master/structure/crystal-contacts.md

Definitely I'd follow Marcin's advice to use existing solutions. The basic
task might seem quite simple, but working out all the details can be very
time consuming.

Jose



On Sun, 12 Jan 2020 at 07:59, Marcin Wojdyr  wrote:

> Hi Zhijie,
>
> it's good and instructive to implement such things from the ground up,
> but there are many special cases that one would be discovering while
> testing this procedure, so if the time is limited it may be better to
> use an existing solution.
>
> For instance, here one may find out that using the SCALE1 record
> doesn't give the sufficient accuracy. In the example in your script
> you have 6 significant digits in the unit cell lengths in CRYST1, but
> only 4 significant digits in SCALE1. (The accuracy of SCALE1 is
> problematic in general; sometimes it needs to be manually removed when
> a program reads it in preference to CRYST1.)
>
> Then one may find out that the 3x3x3 supercell is not sufficient. If
> the molecule is far from the origin, symmetry operations send it far
> away. For example, 5M3H annotates (in the mmCIF format) hydrogen bond
> between 1_555 and 2_11516 - the symmetry mate is shifted 16 unit cells
> in the z direction. Since you already use fractional coordinates in
> your script you could tell directly from the center-of-mass
> coordinates how many unit cells it should be shifted. Say, you have
> x=3.1, so to shift it near the origin you shift it by 3 unit cells
> along x.
>
> But even if all the molecules are shifted near the origin, the 3x3x3
> cell is still not sufficient to find contacts.
> See 3NWH – a homo-4-mer in P2 (4 x 2 chains per unit cell). Here it in
> its unit cell, colored by the chain id:
> https://gemmi.readthedocs.io/en/latest/_images/3nwh.png
> Or 5XG2 – a monomer in P21. Two copies of the chain are rainbow-colored
> here:
> https://gemmi.readthedocs.io/en/latest/_images/5xg2.png
> These chains span over more than 4 unit cells in one direction. One
> could use big enough supercell, but it'd be slow. I suppose that even
> using a 3x3x3 supercell is slow. The alternative is to do the distance
> calculation in fractional coordinates modulo 1.
>
> Then you needs to consider atoms on special positions. If you apply
> symmetry operations to an atom on a 4-fold symmetry axis you get 4
> atoms in the same place. So this needs to be handled. The atom may not
> be exactly on the axis, because the refinement program may not
> constrain its position. So the symmetry operations should produce, I
> think, 4 alternative locations of the same atom. But you could also
> have an atom near the symmetry axis bonded to its symmetry mate - then
> the symmetry operations should produce different atoms. So the
> procedure requires a cut-off distance or a heuristics to distinguish
> the two cases.
>
> Then, if you'd like to expand non-crystallographic symmetry from the
> MTRIX records - this is another complication. And so on...
>
> So I'd recommend using one of many available programs for finding
> contacts or interactions. If none of them is suitable - then try
> crystallographic libraries.
> I didn't document yet how to find the contacts using gemmi, but I'll
> do it in the coming weeks (or months). Cctbx and clipper are other
> (more mature) libraries worth checking.
>
> Best wishes,
> Marcin
>
>
> On Sat, 11 Jan 2020 at 02:11, Zhijie Li  wrote:
> >
> > Hi Orly,
> >
> > REMARK 290 should be the easiest way for generating symmetry mates.
> Other routes are just going to give you the same results. As Jonathan
> already pointed out, the symm ops do not garantee that the symm copies are
> close to each other.  The most simple-minded solution to this problem would
> be simply generating 3x3x3 unit cells so that the unit cell in center will
> be complete. An upgrade to this is to compute the center of mass of the
> symmetry copies in each of the 3x3c3 cells and find which one is closest to
> the orignal 1555 copy.  Just for fun, I wrote a little python script that
> does this (attached). In this script for unit cell translation and
> calculating center-center distances, I converted the Cartesian coordinates
> to fractional coords first. Then after the translation,I used the inverse
> of the SCALE1 matrix to get the shifted Cartesian coords. This way I don't
> need to read wikipedia on geometry . But as noted in the script the
> distances should better be calculated in Cartesian.
> >
> > Zhijie
> >
> > 
> > From: CCP4 bulletin board  on behalf of orly
> avraham 
> > Sent: Friday, January 10, 2020 3:30 PM
> > To: CCP4BB@JISCMAIL.AC.UK 
> > Subject: [ccp4bb] Generating symmetry mates using python
> >
> > Hi all,
> >
> > I am a crystallographer currently employing computational 

Re: [ccp4bb] Java based structural database websites

[Jose Duarte]

Indeed java in the browser was killed a long time ago.

But the good news is that plenty of alternatives exist, written in native
(to the browser) javascript. Wikipedia has a nice compilation of the
different viewers, under the "Web-based systems" section:

https://en.wikipedia.org/wiki/List_of_molecular_graphics_systems

I would particularly recommend the Mol* project:

https://molstar.org/

Jose


On Tue, 19 Mar 2019 at 10:37, Robbie Joosten 
wrote:

> Hi Nick,
>
> A bit of a hack I suppose, but you could use a (single use) VM with some
> old windows version that still works.
> E-mailing the developers directly is the way to go to figure out whether
> you can expect an update.
>
> We had a similar problem with our own webserver (the Crystallographic
> Construct Designer ccd.rhpc.nki.nl) which was completely a java applet.
> The only real solution was a full rewrite. But that requires funding which
> we luckily got from the West-Life project.
> Keeping websites online is is not easy with changing technology and
> getting funding is hard because it is not new science.
>
> Cheers,
> Robbie
>
>
>
> On 19 Mar 2019 17:43, Nicholas Keep  wrote:
>
> This is slightly off topic but I suspect people from PDBe etc read this
> bulletin board.
>
> Quite a number of very useful structural biology web sites (Olderado,
> Vivaldi, EMDB to name but a few) require java based viewers and hence no
> longer have full (or in the case of vivaldi any) functionality on up to
> date browsers.
>
> On a new computer it may prove hard or even impossible to find a browser
> that will work
>
> Are there plans to update these websites and is there any suggeted time
> scale?
>
> Any work rounds?
>
> Best wishes
>
> Nick
>
> --
> Prof Nicholas H. Keep
> Executive Dean of School of Science
> Professor of Biomolecular Science
> Crystallography, Institute for Structural and Molecular Biology,
> Department of Biological Sciences
> Birkbeck,  University of London,
> Malet Street,
> Bloomsbury
> LONDON
> WC1E 7HX
>
> email n.k...@mail.cryst.bbk.ac.uk
> Telephone 020-7631-6852  (Room G54a Office)
>020-7631-6800  (Department Office)
> Fax   020-7631-6803
> If you want to access me in person you have to come to the crystallography
> entrance
> and ring me or the department office from the internal phone by the door
>
> 
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
>
>
>
> --
>
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>



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Re: [ccp4bb] Generating rotation/translation matrices for biological assemblies

[Jose Duarte]

Try EPPIC (http://eppic-web.org), it will give you all possible symmetric
assemblies in your crystal and their constituent interfaces, listing the
symmetry operators too. See some help here http://eppic-web.org/ewui/#help

Jose

On Sat, 2 Feb 2019 at 16:42, Ricardo Padua  wrote:

> Hi Erik,
>
> Have you tried Achesym?
>
> http://achesym.ibch.poznan.pl
>
> Kowiel, M., Jaskolski, M. & Dauter, Z. (2014). ACHESYM: an algorithm and
> server for standardized placement of macromolecular models in the unit cell.
> Acta Cryst. D70, doi:10.1107/S1399004714024572.
>
> Best
>
> Ricardo Padua
>
> On Sat, Feb 2, 2019 at 4:06 PM Klontz, Erik 
> wrote:
>
>> Hi all,
>>
>>
>> I'm working on a protein that I believe is tetrameric based on AUC, gel
>> filtration, and crystallography. However, although my asymmetric unit has 4
>> chains, I cannot form the tetramer within the asymmetric unit. Instead, the
>> asymmetric unit has two half-tetramers ('dimers'), and each full tetramer
>> is completed by pairing up with another half-tetramer from a symmetry mate.
>> If I load this structure into PISA, it recognizes that each of the 'dimers'
>> forms a stable assembly, but cannot seem to assemble the tetramer. However,
>> if I the generate symmetry mates in pymol to create a new PDB for the
>> biological tetramer and give this to PISA, it recognizes a stable tetramer.
>>
>>
>> Specifically, chains A and C in the original PDB pair with chains A and C
>> of the second symmetry mate generated in pymol, while chains B and D in the
>> original pair with chains B and D of the third symmetry mate. How do I use
>> this knowledge to generate a 3x4 rotation with translation matrix for
>> PDB deposition?
>>
>>
>> Thanks,
>> Erik Klontz
>>
>>
>> --
>>
>> To unsubscribe from the CCP4BB list, click the following link:
>> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
>>
> --
> Ricardo Padua
> HHMI Research Associate
> Kern Lab
> Dept. of Biochemistry, MS009
> Brandeis University
> Waltham, MA 02454, USA
>
> E-mail: rpa...@brandeis.edu
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
>



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[ccp4bb] Postdoc positions at RCSB PDB, UC San Diego

[Jose Duarte]

Two postdoctoral positions are available for talented and highly motivated
individuals interested in joining our multidisciplinary team at UC San
Diego/San Diego Supercomputer Center.


*Postdoctoral Fellow: 3D Visualization and Analysis*

Develop innovative scientific visualization and analysis tools for 3D
biomolecular structures to help accelerate research in biology, medicine,
and related disciplines. Your work will extend Mol* and MolQL to reach a
wide audience when deployed as interactive features.

Areas of focus include:

Innovative representations for 3D structural data from integrative/hybrid
methods
Visualizations for comparative analyses of molecular structures and
sequences
GPU acceleration of analysis and visualization algorithms
Multiscale rendering and data delivery for exploring large
structures/complexes

Requirements

PhD: Structural Bioinformatics or related field with a focus on software
development or
PhD: Computer Science with a focus on scientific visualization and/or
biology
Demonstrated proficiency in JavaScript/TypeScript as a general-purpose
programming language and experience with state-of-the-art software
development. Strong skills in problem solving and algorithm design are
required. High productivity and independence demonstrated by publications
and contributions to open source software projects is a plus. Experience in
the development of modern web applications, user interface design, or
scientific visualization is a plus. Experience with writing GPU shaders a
plus. Good written and oral communication skills.


*Postdoctoral Fellow: Bioassembly/Machine Learning*

Improve the representation and findability of biological assemblies in the
PDB, using innovative algorithms to build the next generation search engine
for molecular biology.

Areas of focus include:

Machine learning
Efficient search algorithms
Scalability of solutions across large datasets

Requirements

PhD: Computer Science with a focus on bioinformatics or machine learning or
PhD: Structural Bioinformatics or Biology, or related field with a focus on
software development
Demonstrated proficiency in a high-level programming language, such as
Java, Python, C++ and experience with state of the art software engineering
tools. Strong skills in problem solving and algorithm design are required.
A background in NoSQL database technologies would be beneficial. Experience
in the development of modern web applications, user interface design, or
scientific visualization is a plus. We expect candidates to have shown high
productivity demonstrated by publications and contributions to open source
software projects. Excellent written and oral communication skills are
required.


*About RCSB PDB*
RCSB Protein Data Bank is a world-renowned, scientific organization focused
on serving technical, educational and other programmatic needs of
scientific and research communities worldwide. RCSB.org serves more than 1
million users in academia and industry. The RCSB PDB development team
creates leading edge web technologies targeted for scientific and
educational audiences.

*About UCSD/SDSC*
RCSB PDB is located in the Skaggs School of Pharmacy at UC San Diego.

UC San Diego is recognized as one of the largest employers in San Diego
county with outstanding benefits and a diverse community of faculty, staff
and students. As an Organized Research Unit of UC San Diego, the San Diego
Supercomputer Center (SDSC) is a world leader in data-intensive computing
and cyber infrastructure, providing resources, services, and expertise to
the national research community, including industry and academia.

Details of UC San Diego's Postdoc compensation, including salary ranges,
are online. UC San Diego is an equal opportunity employer and both foreign
and domestic applicants are encouraged to apply.



More information and how to apply at http://www.rcsb.org/pages/jobs

Re: [ccp4bb] biological molecule?

[Jose Duarte]

Dear Charlie

There's good documentation here:

https://pdb101.rcsb.org/learn/guide-to-understanding-pdb-data/biological-assemblies

Hope it helps

Jose



On Mon, Apr 9, 2018 at 2:55 PM, Carter, Charlie  wrote:

> I knew this would happen one day. I loathed the cif versions of the
> coordinates, but fortunately, I’ve never had to use a .cif file.
>
> Now, the pdb no longer offers anything but…
>
> I cannot find in the .cif file where the instructions are to generate the
> biological molecule from the asymmetric unit. How does one do this please?
>
> Thanks,
>
> Charlie

[ccp4bb] 3D Visualization Postdoc at RCSB PDB: San Diego, California

[Jose Duarte]

The University of California, San Diego seeks to fill an opening for a
Postdoctoral Researcher in the RCSB Protein Data Bank.

*Job description*

Your challenge is to develop web-based, innovative scientific visualization
tools for 3D biomolecular structures to help accelerate research and
training in biology, medicine, and related disciplines.

Areas of focus include:

• Innovative representations for 3D structural data

• Visualizations for comparative analyses

• Multiscale rendering for exploring large structures



Your work will reach an audience of more than 1 million RCSB PDB Data
Consumers when deployed as interactive features for the RCSB PDB website (
http://www.rcsb.org).

*Requirements*

The successful candidate holds a Ph.D. in one or more of the following
research areas:

• Structural Bioinformatics, or related field with a focus on software
development

• Computer Science with a focus on scientific visualization



-Demonstrated proficiency in JavaScript as a general-purpose programming
language and experience with state of the art software development tools.

-Strong skills in problem solving and algorithm design are required.

-High productivity demonstrated by publications and contributions to open
source software projects.

-Experience in the development of modern web applications, user interface
design, or scientific visualization is a plus.

-Excellent written and oral communication skills.

*Compensation*

Compensation depends on postdoctoral experience level in accordance with UC
Salary Scale (12/1/16). Please see chart at
http://postdoc.ucsd.edu/appointment-guidelines/index.html

*About UC San Diego, San Diego Supercomputer Center and the Protein Data
Bank*

The position is available immediately in the San Diego Supercomputer Center
(SDSC).
As an Organized Research Unit of UC San Diego, SDSC is a world leader in
data-intensive computing and cyber infrastructure, providing resources,
services, and expertise to the US national research community, including
industry and academia.

The RCSB PDB (http://www.rcsb.org) represents the preeminent source of
experimentally determined macromolecular structure information for research
and teaching in fundamental biology, medicine, and bioenergy. With more
than 1 million users from over 160 countries around the world, the RCSB PDB
is one of the leading worldwide Biological Databases. Our group is
responsible for RCSB Protein Data Bank (PDB) west-coast operations.

*Application*

To be considered, please submit your CV and cover letter (optional) with
contact information to Cole Christie at cole.chris...@rcsb.org.

UC San Diego is an equal opportunity employer, both foreign and domestic
applicants are encouraged to apply.

Re: [ccp4bb] How to determine Quaternary symmetry

[Jose Duarte]

You can try http://www.eppic-web.org. It will give you a full enumeration
of all symmetric assemblies present in the crystal. If the assembly you are
looking at is not symmetric (within a certain approximation) it will not be
listed in the results.

Hope it helps

Jose


On Mon, Jul 10, 2017 at 12:18 PM, Vands  wrote:

> Hi ,
>I have a protein which has A4 stoichiometry. I am trying to
> find symmetry component which should be D2 but one axis looks like
> translated which does not make it perfect D2. I am wondering if there is
> any tool which I can use to determine Quaternary symmetry.
> thanks
>
>
>
>
>
>
>
>
>
> --
> Vandna Kukshal
> Senior Scientist
> Dept. oncology
> Washington University School of Medicine
> 660 S. Euclid, Campus Box 8231
> St. Louis, MO 63110
>

Re: [ccp4bb] 3D graphics linux compatibility question

[Jose Duarte]

Hi Emmanuel

Here we have tried the nvidia Quadro 2000 with two different monitors 
(both with the built-in IR emitter, thus with synching through DVI): 
ASUS VG278HR and BenQ XL2420TX. The setup works perfectly well in Linux, 
both pymol and coot work without issues. Unfortunately we have no 
experience with other nvidia cards, so can't comment on that.


Hope it helps

Jose


---
Jose Duarte
Laboratory of Biomolecular Research
Paul Scherrer Institute
5232 Villigen PSI
Switzerland




On 09/17/2013 12:09 PM, Emmanuel Saridakis wrote:

Dear BB,
We are still a bit confused about compatibility of graphics cards with 
3D Coot/PyMol in Linux:
(a) In previous CCP4bb discussions, it was stated that only Quadro 
cards are compatible with Linux setups. But could someone tell me what 
the minimum standard really is: is it Quadro FX380, 2000, 3800 or 
something else ? The nVidia site lists Quadro 3700 and 3800 as the two 
lowest (cheapest) options compatible with Linux 3D. However, different 
CCP4ers have in the past mentioned the other two options as working 
perfectly or with little trouble.
(b) If a monitor such as the ASUS VG278H 
http://www.asus.com/Monitors_Projectors/VG278H/#overview , which has 
an in-built nVidia 3D vision emitter which takes its stereo synch from 
a DVI cable is used, can we even use the simpler GeForce GTX670 or 680 ?
As you might imagine, we are on a rather tight budget. Any info would 
be greatly appreciated!

Emmanuel Saridakis

N.C.S.R. DEMOKRITOS
Athens 15 310 Greece
esari...@chem.demokritos.gr mailto:esari...@chem.demokritos.gr
tel. +30-210-6503793

Re: [ccp4bb] Pisa application

[Jose Duarte]

Hi Careina

To my knowledge PISA by itself is not able to do interface prediction. 
In any case there are a few methods available for protein-protein 
interface prediction. See for example this nice compilation:


http://rosettadesigngroup.com/blog/58/10-protein-protein-interface-prediction-servers/

Hope it helps

Jose


On 08/08/2012 08:33 AM, Careina Edgooms wrote:

Dear ccp4ers

I just wonder whether anybody knows if the PISA software could be 
used/modified to detect potential interfaces of interaction of 
different proteins? This would be very useful as a tool to validate 
protein-protein interactions detected by in vivo methods such as yeast 
2 hybrid screens. If PISA is not quite there yet, does anyone know of 
other software that could do a similar thing?


Best
Careina

Re: [ccp4bb] Fwd: [ccp4bb] Did anyone here know how to config a local protein secondary structure prediction server?

[Jose Duarte]

Then probably PFAM does what you want

http://pfam.sanger.ac.uk

Best

Jose


On 12/07/2011 11:43 AM, 商元 wrote:



-- Forwarded message --
From: *商元* shangyuan5...@gmail.com mailto:shangyuan5...@gmail.com
Date: Wed, Dec 7, 2011 at 6:41 PM
Subject: Re: [ccp4bb] Did anyone here know how to config a local 
protein secondary structure prediction server?

To: Jose Duarte jose.dua...@psi.ch mailto:jose.dua...@psi.ch


Dear Jose,
   Thanks for you kind replies and they are very helpful.
   Both HSSP and consurf are based on known structures on PDB 
database. However, I want to scan for a certain motif, and use the 
conservation information as a filter to narrow down my searched 
results. In this case, most of these motifs exists in the linker 
region between domains and may not appears in the pdb database. Do you 
have any suggestions?


Best regards,
Yuan SHANG


On Wed, Dec 7, 2011 at 4:31 PM, Jose Duarte jose.dua...@psi.ch 
mailto:jose.dua...@psi.ch wrote:


HSSP has it. Have a look: http://swift.cmbi.kun.nl/swift/hssp/

also the consurf server will give you conservation values mapped
to structure positions

Cheers

Jose




On 12/07/2011 09:24 AM, 商元 wrote:

By the way, do you know any available protein database with the
sequence conservation annotation information included?

Regards,
Yuan

On Sun, Dec 4, 2011 at 11:32 PM, Jose Duarte jose.dua...@psi.ch
mailto:jose.dua...@psi.ch wrote:

You can run psipred yourself locally by downloading the
software available here:

http://bioinfadmin.cs.ucl.ac.uk/downloads/psipred/

You will also require blast and a local sequence database
(usually uniref90). Have a look at the README

http://bioinfadmin.cs.ucl.ac.uk/downloads/psipred/README

This gives you a local command line application to run
psipred, not a graphical web interface. Anyway if you really
want to run a lot of secondary structure prediction jobs
that's really what you want.

Hope this helps

Jose


Jose Duarte
Laboratory of Biomolecular Research
Paul Scherrer Institute
5232 Villigen PSI
Switzerland




On 12/04/2011 04:22 PM, Boaz Shaanan wrote:

Hi,

I would just submit your sequence to Phyre
(http://www.sbg.bio.ic.ac.uk/~phyre/
http://www.sbg.bio.ic.ac.uk/%7Ephyre/). You'll get, among
other good things, the secondary structure predictions,
perhaps even a 3-D structure prediction, depending on the
similarity of your sequence to that of known structures.

   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 mailto: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
mailto:CCP4BB@JISCMAIL.AC.UK] on behalf of 商元
[shangyuan5...@gmail.com mailto:shangyuan5...@gmail.com]
*Sent:* Sunday, December 04, 2011 2:00 PM
*To:* CCP4BB@JISCMAIL.AC.UK mailto:CCP4BB@JISCMAIL.AC.UK
*Subject:* [ccp4bb] Did anyone here know how to config a
local protein secondary structure prediction server?

Hi, everyone,
   I want to run plenty secondary structure prediction works
and online prediction costs a lot of time. So I expect local
software for secondary structure prediction will greatly
help to my work.
Has anyone ever configed such local secondary structure
prediction server?

Any suggestion will be welcome.

Thanksregards,
Yuan SHANG

Re: [ccp4bb] Did anyone here know how to config a local protein secondary structure prediction server?

[Jose Duarte]

You can run psipred yourself locally by downloading the software 
available here:


http://bioinfadmin.cs.ucl.ac.uk/downloads/psipred/

You will also require blast and a local sequence database (usually 
uniref90). Have a look at the README


http://bioinfadmin.cs.ucl.ac.uk/downloads/psipred/README

This gives you a local command line application to run psipred, not a 
graphical web interface. Anyway if you really want to run a lot of 
secondary structure prediction jobs that's really what you want.


Hope this helps

Jose


Jose Duarte
Laboratory of Biomolecular Research
Paul Scherrer Institute
5232 Villigen PSI
Switzerland



On 12/04/2011 04:22 PM, Boaz Shaanan wrote:

Hi,

I would just submit your sequence to Phyre 
(http://www.sbg.bio.ic.ac.uk/~phyre/). You'll get, among other good 
things, the secondary structure predictions, perhaps even a 3-D 
structure prediction, depending on the similarity of your sequence to 
that of known structures.


   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 商元 
[shangyuan5...@gmail.com]

*Sent:* Sunday, December 04, 2011 2:00 PM
*To:* CCP4BB@JISCMAIL.AC.UK
*Subject:* [ccp4bb] Did anyone here know how to config a local protein 
secondary structure prediction server?


Hi, everyone,
   I want to run plenty secondary structure prediction works and 
online prediction costs a lot of time. So I expect local software for 
secondary structure prediction will greatly help to my work.

Has anyone ever configed such local secondary structure prediction server?

Any suggestion will be welcome.

Thanksregards,
Yuan SHANG