Re: [ccp4bb] Scripting for COOT

[B.Lohkamp]

Just for completeness the pythonic command line way:

coot --pdb input.pdb --auto input.mtz --python -c 
'set_go_to_atom_molecule(0); set_go_to_atom_chain_residue_atom_name("B", 
42, " CA ")'


Bernhard

On 17/11/2017 09:00, Martín Martínez Ripoll wrote:

We have used it in this way...

coot --pdb  input.pdb   ---auto  input.mtz   --script  script.com

and then, in file "script.com", you write the corresponding instructions...

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

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


-Mensaje original-
De: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] En nombre de Paul
Emsley
Enviado el: jueves, 16 de noviembre de 2017 17:32
Para: CCP4BB@JISCMAIL.AC.UK
Asunto: Re: [ccp4bb] Scripting for COOT

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

[Martín Martínez Ripoll]

We have used it in this way...

coot --pdb  input.pdb   ---auto  input.mtz   --script  script.com

and then, in file "script.com", you write the corresponding instructions...

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

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


-Mensaje original-
De: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] En nombre de Paul
Emsley
Enviado el: jueves, 16 de noviembre de 2017 17:32
Para: CCP4BB@JISCMAIL.AC.UK
Asunto: Re: [ccp4bb] Scripting for COOT

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

[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<mailto:xmar...@iqfr.csic.es>
Department of Crystallography & Structural Biology
www.xtal.iqfr.csic.es<https://urldefense.proofpoint.com/v2/url?u=http-3A__www.xtal.iqfr.csic.es_=DwMFAw=Dbf9zoswcQ-CRvvI7VX5j3HvibIuT3ZiarcKl5qtMPo=HK-CY_tL8CLLA93vdywyu3qI70R4H8oHzZyRHMQu1AQ=kU7E2X2Pk1OIZPrH3Jv3BdMeufRvkl9y06XUojOiKj0=yiNG__jT6YRPhqgIOO3x6BCoYuqwi-1o4FK-t4MkBts=>
www.xtal.iqfr.csic.es/Cristalografia/<https://urldefense.proofpoint.com/v2/url?u=http-3A__www.xtal.iqfr.csic.es_Cristalografia_=DwMFAw=Dbf9zoswcQ-CRvvI7VX5j3HvibIuT3ZiarcKl5qtMPo=HK-CY_tL8CLLA93vdywyu3qI70R4H8oHzZyRHMQu1AQ=kU7E2X2Pk1OIZPrH3Jv3BdMeufRvkl9y06XUojOiKj0=BzUGq7oLSRRIIfx651bTf6sDG9GgHdRPMT6qF9fMrb8=>
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