Quick navigation: Home   |    Site Map   ||    References   |    Biography   ||    Copyright   |    Other copyright   |    Contact us   |    Advert   |   
 

Re: [ccp4bb] Fix for MIFit8 compatibility issue with CCP4 6.1.1
- Protein crystallography

Main steps:

   - Protein purification
   - Crystallisation

Special:

   - Programs for crystallography
   - X-ray detectors

Basic tutorials:

   - Chemistry
   - Protein
   - Peptide
   - Amino Acids

Xtal community:

   - CCP4BB

CCP4bb navigation

CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999
Previous message:
Subject: Fix for MIFit8 compatibility issue with CCP4 6.1.1
From: John Badger jbadger1 {- at -} SAN {- dot -} RR {- dot -} COM
Date: 2009-04-01		Next message:
Subject: Re: NCBHT: severe warning
From: Marius Schmidt marius {- dot -} schmidt {- at -} PH {- dot -} TUM {- dot -} DE
Date: 2009-04-01


Subject: Re: Fix for MIFit8 compatibility issue with CCP4 6.1.1
From: Donnie Berkholz dberkholz {- at -} GENTOO {- dot -} ORG
Date: 2009-04-01

On 21:12 Wed 01 Apr , John Badger wrote:
> We are examining alternatives for water-picking that workable in the
> context of automated refinement and are not aware of any other
> incompatibilities at this time.

No doubt you're already aware of findwaters, which comes with coot and
looks like it can be run in an automated fashion:

Usage: /usr/bin/findwaters-real --pdbin pdb-in-filename --hklin mtz-filename --f f_col_label --phi phi_col_label --pdbout waters-filename --sigma sigma-level --flood --chop
--mapin ccp4-map-name can be used instead of --hklin --f --phi
where pdbin is the protein (typically)
and pdbout is file for the waters.
The default sigma level is 2.0
Use --chop to remove waters below given sigma-level
In this case, pdbout is the modified input coordinates
Use ---flood to fill everything with waters (not just water peaks)


--
Thanks,
Donnie

Donnie Berkholz
P. Andrew Karplus lab
Oregon State University

CCP4bb navigation

CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999
Previous message:
Subject: Fix for MIFit8 compatibility issue with CCP4 6.1.1
From: John Badger jbadger1 {- at -} SAN {- dot -} RR {- dot -} COM
Date: 2009-04-01		Next message:
Subject: Re: NCBHT: severe warning
From: Marius Schmidt marius {- dot -} schmidt {- at -} PH {- dot -} TUM {- dot -} DE
Date: 2009-04-01
ProteinCrystallography.org: Copyright 2006-2010 by Quid United Ltd