Re: FW: [ccp4bb]: pseudo symmetry?

[Ana Gonzalez <ana@SMB.SLAC.STANFORD.EDU>]

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On Fri, 28 Apr 2000, david lawson wrote:

dl >Anyway, the maps look quite nice, but the refinement is a bit disappointing
dl >: Rfac=25%, Rfree=28% (they were 19 and 22 in the small R3 cell). Also the
dl >overall FOM in REFMAC is 0.51 (it was 0.84). Could this be because the
dl >alternate layers of strong and weak reflections make it difficult to scale
dl >Fobs to Fcalc in REFMAC? 

I recently had a very similar problem: P21 crystal,with a 2 fold NCS axis
almost parallel to b. The maps looked very good (these were also high
resolution data) , but the r-factor got stuck just below 30% (r-free
around 32%). Later on we collected a native data set, which happened to
crystallize in the smaller cell (no NCS) and the previous model refined
easily to about  15% without doing anything to the protein chain.  I
always had the strong  feeling that it was the weak "in between" 
reflections which were to blame for the high r-factor in the case of the
former data set.

dl >The data have been processed with DENZO/SCALEPACK,
dl >maybe the situation could be improved using MOSFLM/SCALA. 

We used MOSFLM/SCALA, so if the problem is indeed the same, my answer
would be "no" :-)

dl >Unfortunately we
dl >can't get MOSFLM to correctly autoindex in the large cell as the spot
dl >picking routine struggles to find the weaker spots - it just gives us the
dl >small cell. Is there a way to convert a DENZO autoindexing soultion into
dl >MOSFLM format so that we can proceed with this approach??

There is a "denzo2mosflm" jiffy which reads the .x file from denzo and
outputs a mosflm matrix file. Alternatively you can try to coax mosflm
into taking the weak spots by playing the spot acceptance criteria. That
worked for me.

Ana