Re: [ccp4bb] [EXTERNAL] Re: [ccp4bb] Modeling ATP/ADP

2020-07-24 Thread Oleg Kovalevskiy - UKRI STFC 

Dear Reza,

We had a case when two phosphate ions and magnesium ion have been bound to the 
ATP-binding site (300mM sodium phosphate in the crystallisations conditions). 
However, your ATP/ADP may not have full occupancy and therefore electron 
density might be lower. You may consider calculation of a blurred map (bring up 
contributions from low-resolution terms) and see whether there is any density 
for the nucleotide.
But first of all I would calculate omit map (without ligand) and would start to 
worry if there is no density for nucleotide part.

All the best,
Oleg

--
Dr Oleg Kovalevskiy
CCP4 team
UKRI Science and Technology Facilities Council
Rutherford Appleton Laboratory
Harwell Campus
Didcot, Oxfordshire
OX11 0QX
UK

From: CCP4 bulletin board  on behalf of Reza Khayat 

Reply to: Reza Khayat 
Date: Thursday, 23 July 2020 at 21:13
To: ccp4bb 
Subject: Re: [ccp4bb] [EXTERNAL] Re: [ccp4bb] Modeling ATP/ADP


Tried the homologues thing. There are homologues and I've done the fitting, but 
this is what I consider to be subjective. I'm certain the referee will ask: 
Given the quality of density for the nucleotide, how certain are the authors 
that a different fit is not possible? Have other fit poses been considered?



Reza


Reza Khayat, PhD
Assistant Professor
City College of New York
Department of Chemistry and Biochemistry
New York, NY 10031

From: CCP4 bulletin board  on behalf of Jon Cooper 
<488a26d62010-dmarc-requ...@jiscmail.ac.uk>
Sent: Thursday, July 23, 2020 1:07 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [EXTERNAL] Re: [ccp4bb] Modeling ATP/ADP

Hello, do you have any homologues in the PDB with ATP, etc, bound as a guide? 
Coot is pretty good at fitting known ligands, and unknown ones, too!


 Original Message 
On 23 Jul 2020, 17:53, Reza Khayat < rkha...@ccny.cuny.edu> wrote:


Hi,



Can folks suggest programs for objectively docking ATP/ADP molecules into 
density? Our density is not so good, probably because of occupancy, and we'd 
like a less subjecting approach for modeling. Thanks.



Best wishes,
Reza


Reza Khayat, PhD
Assistant Professor
City College of New York
Department of Chemistry and Biochemistry
New York, NY 10031



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Re: [ccp4bb] CCP4 update manager command line options?

2019-12-14 Thread Oleg Kovalevskiy - UKRI STFC 

Dear Christoph,

Unfortunately there is no command line option to install any earlier version; 
Windows installer provides only latest CCP4 version.

All the best,
Oleg Kovalevskiy and Andrey Lebedev

-- 
Dr Oleg Kovalevskiy
CCP4 team
Science and Technology Facilities Council
Rutherford Appleton Laboratory
Harwell Campus
Didcot
OX11 0QX

On 13/12/2019, 13:54, "CCP4 bulletin board on behalf of Christoph Parthier" 
 wrote:

Hi,

In context of an unattended installation/update of CCP4 for Windows 7/10 
  in a computer pool environment, is it possible to install CCP4 (from 
scratch) via update manager (ccp4um) command line option to an earlier 
version than the latest (e.g. 7.0.072 instead of 7.0.078)? If yes, what 
would be the apropriate command line parameter(s)?

Or would this rather be a job for the CCP4 package manager (ccp4pm)? 
What would be the respective command line paramters?

Any other suggestion to do this task unattended (batch file)?

Thanks,
Christoph



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