Re: [ccp4bb] UPPSALA: ERROR --- Serious FRCSYM error

- 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: UPPSALA: ERROR --- Serious FRCSYM error
From: Hailiang Zhang zhangh1 {- at -} UMBC {- dot -} EDU
Date: 2010-05-25

Next message:
Subject: Re: Alignment software
From: Roger Dodd roger {- dot -} dodd {- at -} GMAIL {- dot -} COM
Date: 2010-05-25

Subject: Re: UPPSALA: ERROR --- Serious FRCSYM error
From: "Edward A {- dot -} Berry" BerryE {- at -} UPSTATE {- dot -} EDU
Date: 2010-05-25

Hailiang Zhang wrote:
> Hi,
>
> When I run UPPSALA rsfit, there are lots of "ERROR --- Serious FRCSYM
> error". These atoms/residues are generally around the protein surface, so
> I guess the reason is the mask were out of the unit cell. Is there any way
> to avoid this?
>
I've seen that error in averaging/expanding. As you suggest it
seems to be the voxel is on the edge, and one more layer
beyond the exact asymmetric unit needs to be added.
In my case it could be fixed with ccp4 mapmask,
something like

(for GRID 280 340 456)
#2.MAPMASK:
mapmask MAPIN temp.map MAPOUT chg1.map << END-extend
xyzlim 0 280 0 340 0 114
END-extend

here this is exactly one asymmetric unit (P212121)-
If you still get fracsym's add one layer to each dimension until
it behaves?
Ed

CCP4bb navigation

CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

Previous message:
Subject: UPPSALA: ERROR --- Serious FRCSYM error
From: Hailiang Zhang zhangh1 {- at -} UMBC {- dot -} EDU
Date: 2010-05-25

Next message:
Subject: Re: Alignment software
From: Roger Dodd roger {- dot -} dodd {- at -} GMAIL {- dot -} COM
Date: 2010-05-25