date:20171025

Re: [ccp4bb] blast pdb for a very short sequence (3 amino acids)

2017-10-25 Thread Michael Jarva

With the vast number of sequences available I doubt you’ll get any meaningful 
results with only 3 amino acids…
However, I believe the full list of sequences in the PDB is available here for 
download:
ftp://ftp.rcsb.org/pub/pdb/derived_data/pdb_seqres.txt

Using this you could run your own local scripts to do customised searches.

Cheers
Mike

From: CCP4 bulletin board > 
on behalf of Xiao Lei >
Reply-To: Xiao Lei >
Date: Thursday, 26 October 2017 at 14:40
To: "CCP4BB@JISCMAIL.AC.UK" 
>
Subject: [ccp4bb] blast pdb for a very short sequence (3 amino acids)

Dear CCP4BB members,

Sorry this post is off-topic. I am asking is there a way to blast pdb for a 
very short sequence like 2 or 3 amino acids?  I tried this for a positive 
control in pdb database but returned that "Your search parameters were adjusted 
to search for a short input sequence."  and "No significant similarity found. ".

[ccp4bb] blast pdb for a very short sequence (3 amino acids)

2017-10-25 Thread Xiao Lei

Dear CCP4BB members,

Sorry this post is off-topic. I am asking is there a way to blast pdb for a
very short sequence like 2 or 3 amino acids?  I tried this for a positive
control in pdb database but returned that "Your search parameters were
adjusted to search for a short input sequence."  and "No significant
similarity found. ".

[ccp4bb] Research Associate Position - Structure-based protein engineering - Hospital for Sick Children Research Institute, Toronto, Canada

2017-10-25 Thread Jean-Philippe Julien

Dr. Julien’s laboratory at The Hospital for Sick Children Research Institute 
(https://lab.research.sickkids.ca/julien/) is looking for a Computational 
Biologist to join our Structural Immunology team as a Research Associate. The 
successful candidate will participate in the design and engineering of antigens 
and antibodies in our quest to develop effective immunogens and 
immunotherapies. We are looking for a driven, enthusiastic and experienced 
scientist who demonstrates passion and creativity towards the 
structure/function study of important pathogenic targets and who can thrive in 
a highly-collaborative setting.

Roles & Responsibilities

  *   Use computational biology approaches to design and optimize proteins from 
available antibody-antigen crystal structures;
  *   Apply computational biology to engineer protein nanoparticles with 
optimal delivery properties;
  *   Interact across research teams to enhance computational biology 
applications related to vaccine design and antibody therapeutic development;
  *   Coordinate projects with international collaborators, including timely 
presentation of results and joint writing of reports.

Desired Skills and Experience

  *   Computational/Structural Biologist with a PhD in Biochemistry, 
Computational Biology, Molecular Biology, Immunology, or related field. 
Post-doctoral experience is a plus;
  *   Demonstrated ability to participate in collaborative and productive 
scientific projects;
  *   Organization skills, efficiency and meticulous record keeping;
  *   Experience in supervising and mentoring junior members of a research team;
  *   Practical experience in using protein evolution or yeast/mammalian 
display approaches to improve antibody-antigen binding interfaces is a plus;
  *   Strong knowledge of using structural biology to study pathogens, 
especially in a context of structure-based vaccine design is a plus;
  *   Experience in molecular biology, protein expression in various systems, 
purification and biophysical characterization is a plus.

How to Apply?
Send your CV and a letter of intent to 
jean-philippe.jul...@sickkids.ca 
before Nov 20th 2017. Successful candidates will be notified for interviews, at 
which time two letters of references will also be required. Anticipated start 
date is early 2018.

About Us
Dr. Julien's laboratory is interested in the structure/function study of B cell 
receptors and antibody interactions with antigens. A better understanding of 
the structures of B cell surface molecules and their secreted antibodies will 
serve towards the rational design of improved vaccine immunogens against a 
variety of pathogens, including malaria and HIV-1. Structure-based design is 
also applied to optimize antibody therapeutics to deplete dysregulated B cells 
in blood cancers and autoimmune disorders. Dr. Julien’s laboratory is located 
in The Peter Gilgan Centre for Research and Learning, a new 21-story, 750,000 
square-foot facility that incorporates an open-concept design, state-of-the-art 
research facilities, and collaborative work spaces.  As a member of the 
SickKids community, you will become part of a world-renowned organization 
dedicated to fulfilling a vision of Healthier Children, A Better World. For 
over 135 years, SickKids has worked hard to make the world a better place for 
children and their families. Each day, people around the organization are doing 
meaningful work that directly, and often indirectly, benefits children in 
Canada and around the world.



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[ccp4bb] ERC funded postdoc position - Cryo-EM of complexes involved in gene expression

2017-10-25 Thread Albert Weixlbaumer

Dear members of the structural biology community,

I am looking for postdoctoral researchers interested to do single particle 
Cryo-EM on complexes involved in gene expression. The position will be funded 
through an ERC starting grant and I would be grateful if you could bring the 
following ad to the attention of potential candidates.

Thanks, Albert

 
Postdoc position in the laboratory of Albert Weixlbaumer available at the IGBMC 
in Strasbourg, France.

We are inviting applications for a postdoc position, which is available in the 
laboratory of Albert Weixlbaumer, PI in the Department of Integrated Structural 
Biology, at the Institute of Genetics and Molecular and Cellular Biology 
(IGBMC), in Strasbourg, France.
The position is funded through an ERC starting grant for several years. The 
successful candidate will study the regulation of transcription elongation by 
protein or non-coding RNA transcription factors using a combination of 
biochemical and biophysical techniques. To gain detailed mechanistic insights, 
you will study complexes of RNA polymerase bound to regulatory factors using 
structural approaches (mostly single particle cryo-EM). IGBMC is one of the 
European INSTRUCT (Integrated Structural Biology in Europe) centers and 
therefore provides state of the art facilities (Titan KRIOS with K2 direct 
electron detector) and technology platforms that will support your project in 
every aspect. Further information can be found at: 
http://www.igbmc.fr/research/department/3/team/119/

Please download the ad for more details on the team, the institute, and the 
surroundings: 
https://www.dropbox.com/s/62qfyyt8pq2iurs/Postdoc_Ad_Weixlbaumer_lab_2017.pdf?dl=0

Highly motivated candidates with PhD degrees in structural biology, chemical 
biology, biochemistry, molecular biology, or related fields are encouraged to 
apply. Although not strictly required, preference will be given to candidates 
with prior experience in single particle Cryo-EM. Applications including a 
cover letter outlining research interests, CV, list of publications, and names 
of three references should be sent via e-mail to Albert Weixlbaumer: 
albert.weixlbau...@igbmc.fr

Re: [ccp4bb] MrBUMP error

2017-10-25 Thread Nishant Varshney

Dear Derek and CCP4bb community,

Sorry for not posting the solution. The issue have got solved with the help
from Felix, Ronan and Jens.

Adding # in front of *locale.setlocale(locale.LC_NUMERIC, "") *(near the
top), in 
"/Applications/ccp4-7.0/share/mrbump/include/output/MRBUMP_printTable.py"
worked for me.


many thanks

Nishant



On Wed, Oct 25, 2017 at 1:23 PM, Derek Logan  wrote:

> Dear Nishant,
>
> Did you ever get an answer to your question? I came across it while
> looking through old e-mails. This has happened to me on every Mac I have
> run MrBUMP on in recent years (always in Sweden). You need to go to
>
> /Applications/ccp4-7.0/Frameworks/Python.framework/
> Versions/2.7/lib/python2.7/locale.py
>
> and comment out lines 576-579, i.e.
>
> #if locale and type(locale) is not type(""):
> ## convert to string
> #locale = normalize(_build_localename(locale))
> #return _setlocale(category, locale)
>
>  I don't know if this is the most elegant solution, but it works and it
> doesn't seem to break anything else.
>
> /Derek
>
> On 5 Sep 2017, at 13:17, Nishant Varshney  wrote:
>
> Dear Crystallographer,
>
> I will be grateful if you help me with what may be a simple problem. While
> trying MrBUMP with my mtz file , I am currently getting the following
> error. Similar error I am getting while trying AMPLE as well.
>
> "CCP4I VERSION CCP4Interface 7.0.044
> #CCP4I SCRIPT LOG mrbump
> #CCP4I DATE 01 Sep 2017  15:58:19
> #CCP4I USER apple
> #CCP4I PROJECT Josephin
> #CCP4I JOB_ID 45
> #CCP4I SCRATCH /tmp/apple
> #CCP4I HOSTNAME Apples-iMac.local
> #CCP4I PID 933
>
> http_proxy not specified in environemnt
> 
> ***
> * Information from CCP4Interface script
> 
> ***
> The program run with command: /Applications/ccp4-7.0/bin/mrbump HKLIN
> /Users/apple/Documents/Nishant/Josephin_data/ccp4/XDS_ASCII_scaled1.mtz
> SEQIN /Users/apple/Documents/Nishant/Josephin_data/Phenix/Q15040.fasta
> HKLOUT /Users/apple/Documents/Nishant/Josephin_data/ccp4/
> XDS_ASCII_scaled1_mrbump_soln1.mtz XYZOUT /Users/apple/Documents/
> Nishant/Josephin_data/ccp4/XDS_ASCII_scaled1_mrbump_soln1.pdb KEYIN
> /tmp/apple/Josephin_45_1_com.tmp
> has failed with error message
> Traceback (most recent call last):
>   File "/Applications/ccp4-7.0/Frameworks/Python.framework/
> Versions/2.7/lib/python2.7/runpy.py", line 162, in _run_module_as_main
> "__main__", fname, loader, pkg_name)
>   File "/Applications/ccp4-7.0/Frameworks/Python.framework/
> Versions/2.7/lib/python2.7/runpy.py", line 72, in _run_code
> exec code in run_globals
>   File "/Applications/ccp4-7.0/lib/py2/mrbump/__main__.py", line 85, in
> 
> import MRBUMP_master
>   File 
> "/Applications/ccp4-7.0/share/mrbump/include/initialisation/MRBUMP_master.py",
> line 17, in 
> import Matches
>   File "/Applications/ccp4-7.0/share/mrbump/include/structures/Matches.py",
> line 29, in 
> import Write_MR_results
>   File 
> "/Applications/ccp4-7.0/share/mrbump/include/output/Write_MR_results.py",
> line 20, in 
> import printTable
>   File "/Applications/ccp4-7.0/share/mrbump/include/output/printTable.py",
> line 5, in 
> locale.setlocale(locale.LC_NUMERIC, "")
>   File "/Applications/ccp4-7.0/Frameworks/Python.framework/
> Versions/2.7/lib/python2.7/locale.py", line 579, in setlocale
> return _setlocale(category, locale)
> locale.Error: unsupported locale setting
> 
> ***
>
>
> #CCP4I TERMINATION STATUS 0 "Traceback (most recent call last):   File
> "/Applications/ccp4-7.0/Frameworks/Python.framework/
> Versions/2.7/lib/python2.7/runpy.py", line 162, in _run_module_as_main
>   "__main__", fname, loader, pkg_name)   File "/Applications/ccp4-7.0/
> Frameworks/Python.framework/Versions/2.7/lib/python2.7/runpy.py", line
> 72, in _run_code exec code in run_globals   File
> "/Applications/ccp4-7.0/lib/py2/mrbump/__main__.py", line 85, in 
> import MRBUMP_master   File "/Applications/ccp4-7.0/share/
> mrbump/include/initialisation/MRBUMP_master.py", line 17, in 
> import MatchesFile "/Applications/ccp4-7.0/share/
> mrbump/include/structures/Matches.py", line 29, in  import
> Write_MR_results   File "/Applications/ccp4-7.0/share/
> mrbump/include/output/Write_MR_results.py", line 20, in 
> import printTable   File "/Applications/ccp4-7.0/share/
> mrbump/include/output/printTable.py", line 5, in 
> locale.setlocale(locale.LC_NUMERIC, "")   File "/Applications/ccp4-7.0/
> Frameworks/Python.framework/Versions/2.7/lib/python2.7/locale.py", line
> 579, in setlocale return _setlocale(category, locale) locale.Error:
> unsupported locale setting"
> #CCP4I TERMINATION TIME 01 Sep 2017  15:58:20
> #CCP4I TERMINATION OUTPUT_FILES   /Users/apple/Documents/
>

Re: [ccp4bb] MrBUMP error

2017-10-25 Thread Derek Logan

Dear Nishant,

Did you ever get an answer to your question? I came across it while looking 
through old e-mails. This has happened to me on every Mac I have run MrBUMP on 
in recent years (always in Sweden). You need to go to

/Applications/ccp4-7.0/Frameworks/Python.framework/Versions/2.7/lib/python2.7/locale.py

and comment out lines 576-579, i.e.

#if locale and type(locale) is not type(""):
## convert to string
#locale = normalize(_build_localename(locale))
#return _setlocale(category, locale)

 I don't know if this is the most elegant solution, but it works and it doesn't 
seem to break anything else.

/Derek

On 5 Sep 2017, at 13:17, Nishant Varshney 
> wrote:

Dear Crystallographer,

I will be grateful if you help me with what may be a simple problem. While 
trying MrBUMP with my mtz file , I am currently getting the following error. 
Similar error I am getting while trying AMPLE as well.

"CCP4I VERSION CCP4Interface 7.0.044
#CCP4I SCRIPT LOG mrbump
#CCP4I DATE 01 Sep 2017  15:58:19
#CCP4I USER apple
#CCP4I PROJECT Josephin
#CCP4I JOB_ID 45
#CCP4I SCRATCH /tmp/apple
#CCP4I HOSTNAME Apples-iMac.local
#CCP4I PID 933

http_proxy not specified in environemnt
***
* Information from CCP4Interface script
***
The program run with command: /Applications/ccp4-7.0/bin/mrbump HKLIN 
/Users/apple/Documents/Nishant/Josephin_data/ccp4/XDS_ASCII_scaled1.mtz SEQIN 
/Users/apple/Documents/Nishant/Josephin_data/Phenix/Q15040.fasta HKLOUT 
/Users/apple/Documents/Nishant/Josephin_data/ccp4/XDS_ASCII_scaled1_mrbump_soln1.mtz
 XYZOUT 
/Users/apple/Documents/Nishant/Josephin_data/ccp4/XDS_ASCII_scaled1_mrbump_soln1.pdb
 KEYIN /tmp/apple/Josephin_45_1_com.tmp
has failed with error message
Traceback (most recent call last):
  File 
"/Applications/ccp4-7.0/Frameworks/Python.framework/Versions/2.7/lib/python2.7/runpy.py",
 line 162, in _run_module_as_main
"__main__", fname, loader, pkg_name)
  File 
"/Applications/ccp4-7.0/Frameworks/Python.framework/Versions/2.7/lib/python2.7/runpy.py",
 line 72, in _run_code
exec code in run_globals
  File "/Applications/ccp4-7.0/lib/py2/mrbump/__main__.py", line 85, in 
import MRBUMP_master
  File 
"/Applications/ccp4-7.0/share/mrbump/include/initialisation/MRBUMP_master.py", 
line 17, in 
import Matches
  File "/Applications/ccp4-7.0/share/mrbump/include/structures/Matches.py", 
line 29, in 
import Write_MR_results
  File 
"/Applications/ccp4-7.0/share/mrbump/include/output/Write_MR_results.py", line 
20, in 
import printTable
  File "/Applications/ccp4-7.0/share/mrbump/include/output/printTable.py", line 
5, in 
locale.setlocale(locale.LC_NUMERIC, "")
  File 
"/Applications/ccp4-7.0/Frameworks/Python.framework/Versions/2.7/lib/python2.7/locale.py",
 line 579, in setlocale
return _setlocale(category, locale)
locale.Error: unsupported locale setting
***


#CCP4I TERMINATION STATUS 0 "Traceback (most recent call last):   File 
"/Applications/ccp4-7.0/Frameworks/Python.framework/Versions/2.7/lib/python2.7/runpy.py",
 line 162, in _run_module_as_main "__main__", fname, loader, pkg_name)   
File 
"/Applications/ccp4-7.0/Frameworks/Python.framework/Versions/2.7/lib/python2.7/runpy.py",
 line 72, in _run_code exec code in run_globals   File 
"/Applications/ccp4-7.0/lib/py2/mrbump/__main__.py", line 85, in  
import MRBUMP_master   File 
"/Applications/ccp4-7.0/share/mrbump/include/initialisation/MRBUMP_master.py", 
line 17, in  import MatchesFile 
"/Applications/ccp4-7.0/share/mrbump/include/structures/Matches.py", line 29, 
in  import Write_MR_results   File 
"/Applications/ccp4-7.0/share/mrbump/include/output/Write_MR_results.py", line 
20, in  import printTable   File 
"/Applications/ccp4-7.0/share/mrbump/include/output/printTable.py", line 5, in 
 locale.setlocale(locale.LC_NUMERIC, "")   File 
"/Applications/ccp4-7.0/Frameworks/Python.framework/Versions/2.7/lib/python2.7/locale.py",
 line 579, in setlocale return _setlocale(category, locale) locale.Error: 
unsupported locale setting"
#CCP4I TERMINATION TIME 01 Sep 2017  15:58:20
#CCP4I TERMINATION OUTPUT_FILES   
/Users/apple/Documents/Nishant/Josephin_data/ccp4/search_45
#CCP4I MESSAGE Task failed


Looking forward for your help

Regards
Nishant

--
Dr. Nishant Kumar Varshney,
Research Associate,
C/O Dr. Sameena Khan,
Drug Discovery Research Center,
Translational Health Science and Technology Institute (THSTI)
NCR Biotech Science Cluster,
3rd Milestone, Faridabad – Gurgaon Expressway,
Faridabad – 121001 (HARYANA), India
Ph: +91- 0129-2876477
Mob: 8390564690
<45_mrbump.log>

Re: [ccp4bb] blast pdb for a very short sequence (3 amino acids)

[ccp4bb] blast pdb for a very short sequence (3 amino acids)

[ccp4bb] Research Associate Position - Structure-based protein engineering - Hospital for Sick Children Research Institute, Toronto, Canada

[ccp4bb] ERC funded postdoc position - Cryo-EM of complexes involved in gene expression

Re: [ccp4bb] MrBUMP error

Re: [ccp4bb] MrBUMP error

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