[ccp4bb] 1st CCP4/BGU Crystallography Workshop

[Anat Shahar]

Dear all,



We are very pleased to announce the 1st CCP4/BGU Crystallography Workshop, 
which will take place at Ben-Gurion University of the Negev (BGU) in 
Beer-Sheba, Israel between 18-23 February, 2018.



The workshop is limited to 25 participants, and everybody who is interested is 
welcome to apply.

The workshop program will be suitable for last-year PhD students, as well as 
postdoctoral researchers and young scientists in their first years of research.



Several of the leading protein crystallography software developers from around 
the world will present lectures and tutorials and will also be available to 
help participants with their crystallographic problems, such as processing own 
data and solving structures during hands-on sessions of the workshop.



More information, including “how to apply”, tentative program  and registration 
form, can be found at: https://lifeserv.bgu.ac.il/wp/ccp4workshop/



The closing date for application is 31.12.2017.



Best wishes,



Anat & Eugene






[cid:image001.jpg@01D1253D.4AF7ED90]
Anat Shahar, PhD
Macromolecular Crystallography Research Center (MCRC)
The National Institute for Biotechnology in the Negev Ltd.
Ben-Gurion University of the Negev
Beer-Sheva, Israel
Tel: +972-8-6461807
Fax: +972-8-6472970
Web: www.bgu.ac.il/crystallography

[ccp4bb] PDRA position at University of St Andrews

[Tracey Gloster]

The group of Rafael da Silva at the University of St Andrews has a position 
open for a 2 year PDRA, funded by the Wellcome Trust, in the area of enzymology 
and structural biology. Please see 
https://www.vacancies.st-andrews.ac.uk/Vacancies/W/4793/0/162476/889/research-fellow-in-biology-ar2000ml
 for more details, or contact Rafael directly (r...@st-andrews.ac.uk) with 
enquiries.

Re: [ccp4bb] Scripting for COOT

[Paul Emsley]

On 16/11/2017 13:28, Edward A. Berry wrote:

(set-go-to-atom-molecule 0)
(set-go-to-atom-chain-residue-atom-name "B" 42 " CA ")


Would those be also on the command line, or where?


You can use them on the command line like this:

coot --pdb input.pdb -c '(set-go-to-atom-molecule 0)(set-go-to-atom-chain-residue-atom-name 
"B" 42 " CA ")'

Re: [ccp4bb] Scripting for COOT

[Edward A. Berry]

(set-go-to-atom-molecule 0)
(set-go-to-atom-chain-residue-atom-name "B" 42 " CA ")


Would those be also on the command line, or where?

On 11/16/2017 07:19 AM, Paul Emsley wrote:

On 16/11/2017 08:08, Martín Martínez Ripoll wrote:


I am trying to write a long script that, among others, runs COOT, and for this 
purpose we use something like:

coot  --pdb  refmac-out.pdb--auto refmac-out.mtz

However, I do not know how to include in the script an instruction or keyword 
to centre at a particular
residue number.

Does anybody know how to do it?


Well, presuming that refmac-out.pdb creates a molecule with index 0, you could 
use

(set-go-to-atom-molecule 0)
(set-go-to-atom-chain-residue-atom-name "B" 42 " CA ")

Paul.

[ccp4bb] AW: [ccp4bb] Scripting for COOT

[Herman . Schreuder]

Dear Martin,

I use a script which invokes the coot command similar to what you describe with 
--script mapcent added on the same line. The mapcent script is attached. You 
can either go to a certain atom, or set hte rotation center in Å coordinates. 
You can add whatever commands to the script to get the view and options you 
like.

Best,
Herman

Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von Martín 
Martínez Ripoll
Gesendet: Donnerstag, 16. November 2017 12:09
An: CCP4BB@JISCMAIL.AC.UK
Betreff: [EXTERNAL] [ccp4bb] Scripting for COOT

Dear all,

I am trying to write a long script that, among others, runs COOT, and for this 
purpose we use something like:

coot  --pdb  refmac-out.pdb--auto refmac-out.mtz

However, I do not know how to include in the script an instruction or keyword 
to centre at a particular residue number.
Does anybody know how to do it?

Thanks in advance,
Martin
_
Dr. Martin Martinez-Ripoll
Research Professor Emeritus
xmar...@iqfr.csic.es
Department of Crystallography & Structural Biology
www.xtal.iqfr.csic.es
www.xtal.iqfr.csic.es/Cristalografia/
Telf.: +34 917459550
Consejo Superior de Investigaciones Científicas
Spanish National Research Council
[cid:image001.jpg@01D35EFD.59627D40]



mapcent
Description: mapcent

Re: [ccp4bb] Scripting for COOT

[Paul Emsley]

On 16/11/2017 08:08, Martín Martínez Ripoll wrote:


I am trying to write a long script that, among others, runs COOT, and for this 
purpose we use something like:

coot  --pdb  refmac-out.pdb    --auto refmac-out.mtz

However, I do not know how to include in the script an instruction or keyword to centre at a particular 
residue number.


Does anybody know how to do it?


Well, presuming that refmac-out.pdb creates a molecule with index 0, you could 
use

(set-go-to-atom-molecule 0)
(set-go-to-atom-chain-residue-atom-name "B" 42 " CA ")

Paul.

[ccp4bb] Scripting for COOT

[Martín Martínez Ripoll]

Dear all,

 

I am trying to write a long script that, among others, runs COOT, and for
this purpose we use something like:

 

coot  --pdb  refmac-out.pdb--auto refmac-out.mtz

However, I do not know how to include in the script an instruction or
keyword to centre at a particular residue number.

Does anybody know how to do it?

 

Thanks in advance,

Martin 

_

Dr. Martin Martinez-Ripoll

Research Professor Emeritus

  xmar...@iqfr.csic.es

Department of Crystallography & Structural Biology

  www.xtal.iqfr.csic.es

 
www.xtal.iqfr.csic.es/Cristalografia/ 

Telf.: +34 917459550

Consejo Superior de Investigaciones Científicas

Spanish National Research Council



 

[ccp4bb] search for the program RPScore

[Julian Pfahler]

Dear community,

sorry, for the slight off-topic question.

I am studying the complex of two human proteins. Till now, all 
co-crystallization trials (some dozen plates) were negative, but 
cross-linking and MST studies suggested a stable, mid-affinity complex. 
Therefore, I wanted to dock the proteins using these experimental 
information to get ideas for some more rational construct designs, e.g. 
fusion constructs.


After unsuccessfully trying Hex docking and Rosetta, I heard of the very 
old 3D-dock program which is unfortunately not maintained anymore. The 
package consists of FTDock, RPScore and MultiDock. We downloaded and 
installed it from the webpage 
(http://www.sbg.bio.ic.ac.uk/docking/download.html), but RPScore and 
MultiDock are not available. Also Google searches were negative ...


My questions are:
Does anybody may have a backup of RPScore (and MultiDock) somewhere and 
could drop me a copy?
Do you have any suggestions of protein docking programs which might be 
able to be constrained by my experimental results, especially the 
cross-linking results?


Thanks a lot in advance!

Best regards,
Julian Pfahler