Re: [ccp4bb] validating ligand density

2013-03-14 Thread Robbie Joosten
From: sreera...@yahoo.co.in Subject: Re: [ccp4bb] validating ligand density To: CCP4BB@JISCMAIL.AC.UK Thank you very much to all those who suggested a way out for our situation. We have so far refined the occupancies on phenix and the ligand shows an uniform occupancy of 0.8 post the refinement

Re: [ccp4bb] validating ligand density

2013-03-12 Thread Robbie Joosten
Of R.Srinivasan Sent: Monday, March 11, 2013 23:03 To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] validating ligand density Hello all, We co-crystallized an inactive variant of our enzyme in the presence of substrate and have determined the structure at 1.85A. Now

Re: [ccp4bb] validating ligand density

2013-03-12 Thread Herman . Schreuder
Of R.Srinivasan Sent: Monday, March 11, 2013 11:03 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] validating ligand density Hello all, We co-crystallized an inactive variant of our enzyme in the presence of substrate

Re: [ccp4bb] validating ligand density

2013-03-12 Thread Eleanor Dodson
-- *From:* CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] *On Behalf Of * R.Srinivasan *Sent:* Monday, March 11, 2013 11:03 PM *To:* CCP4BB@JISCMAIL.AC.UK *Subject:* [ccp4bb] validating ligand density Hello all, We co-crystallized an inactive

Re: [ccp4bb] validating ligand density

2013-03-12 Thread Bernhard Rupp
, the book is good reading. Best, BR -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Robbie Joosten Sent: Tuesday, March 12, 2013 10:03 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] validating ligand density Dear Srinivasan, Although

Re: [ccp4bb] validating ligand density

2013-03-12 Thread Jacob Keller
[mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Robbie Joosten Sent: Tuesday, March 12, 2013 10:03 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] validating ligand density Dear Srinivasan, Although the Twilight program can only look at deposited PDB entries, the tips about ligand validation

Re: [ccp4bb] validating ligand density

2013-03-12 Thread Herman . Schreuder
Sent: Tuesday, March 12, 2013 3:44 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] validating ligand density One final quote that is not in the twilight paper summarizes it nicely: The scientist must be the judge

Re: [ccp4bb] validating ligand density

2013-03-12 Thread Jacob Keller
bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] *On Behalf Of *Jacob Keller *Sent:* Tuesday, March 12, 2013 3:44 PM *To:* CCP4BB@JISCMAIL.AC.UK *Subject:* Re: [ccp4bb] validating ligand density One final quote that is not in the twilight paper summarizes it nicely: The scientist must

[ccp4bb] FW: [ccp4bb] validating ligand density

2013-03-12 Thread Herman . Schreuder
To: Schreuder, Herman RD/DE Cc: CCP4BB@jiscmail.ac.uk Subject: Re: [ccp4bb] validating ligand density Dear Jacob, You are overinterpreting, the statement is about judging, not proving a hypothesis. I am sure Mr. Edwards judged his

Re: [ccp4bb] [ccp4bb] validating ligand density

2013-03-12 Thread Bosch, Juergen
[mailto:j-kell...@fsm.northwestern.edu] Sent: Tuesday, March 12, 2013 4:14 PM To: Schreuder, Herman RD/DE Cc: CCP4BB@jiscmail.ac.ukmailto:CCP4BB@jiscmail.ac.uk Subject: Re: [ccp4bb] validating ligand density Dear Jacob, You are overinterpreting, the statement is about judging, not proving a hypothesis

Re: [ccp4bb] validating ligand density

2013-03-12 Thread R.Srinivasan
@JISCMAIL.AC.UK Sent: Tuesday, 12 March 2013 4:32 PM Subject: Re: [ccp4bb] [ccp4bb] validating ligand density Going back to the initial question. I would recommend looking at AFITT http://www.eyesopen.com/afitt   Works like a dream (in certain cases). Jürgen P.S. I wish I had some stocks from

[ccp4bb] validating ligand density

2013-03-11 Thread R.Srinivasan
Hello all,     We co-crystallized an inactive variant of our enzyme in the presence of substrate and have determined the structure at 1.85A.     Now, we want to validate the fitting of the ligand into the electron density. We tried validating using the difference map (2Fo-Fc)