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
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
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
--
*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
, 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
[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
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
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
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
[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
@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
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)
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