Hi,
The drop in LLG for the 5th monomer could fit with your observation that it didn't look good in the e.d. map.
There two things I can suggest (based on a similar experience with 6 mols. in the a.u.)
1) I would definitely try other possible s.g.'s (very easy in Phaser).
2) You might want to check the log file and see why other monomers weren't picked up. Is it because of packing problems ? It is possible that your model has extra loops that don't match your current protein and that the sequence alignment may show. In this case you could just chop them out and use the chopped model.
If you have SAD/MAD data the 4 monomers Phaser found could be sufficient to bootstrap phasing.
Cheers,
Boaz
----- Original Message -----
From: Jiamu Du <[log in to unmask]>
Date: Monday, August 17, 2009 8:22
Subject: Re: [ccp4bb] Questions about Phaser
To: [log in to unmask]
> Dear Yuan,
> If the first solution is right by looking at the density. Then
> you can
> search the others by fixing the the first solution. This will
> accelarateyour searching accuraty. Or you can first try to do
> some limited model
> building to the first solution and then use the refined model as
> template to
> search.
> Best wishes.
>
> On Mon, Aug 17, 2009 at 11:42 AM, Yuan Cheng
> <[log in to unmask]> wrote:
>
> > Hey,
> > I am trying to use phaser to solve a protein structure.
> There is predicted
> > to be 8 mol/asu based on Matthew coefficient analysis.I am
> using a protein
> > that shares about 35% identity with my protein as a search
> model. Phaser
> > found the first five solutions and then failed to find the
> 6th. The LLG and
> > Z-score are as following. The possible loop in the chainsawed
> model has been
> > truncated.
> >
> > "SOLU SET
> > RFZ=5.2 TFZ=7.1 PAK=0 LLG=44
> > RFZ=5.3 TFZ=13.8 PAK=0 LLG=169
> > RFZ=4.3 TFZ=69.6 PAK=0 LLG=1209
> > RFZ=4.6 TFZ=60.6 PAK=0 LLG=2200
> > RFZ=4.3 TFZ=5.7 PAK=0 LLG=2163
> >
> > I used coot to check the difference map made with
> the model including the
> > above five solutions.The first four solutions fit the density
> very well
> > (didn't see many positive or negative densities). The 5th
> solution didn't
> > fit the density at all. I saw many empty density in the map,
> indicating I
> > still need to find more solutions.The space group I am using
> is P3 2 1.
> > Could this be caused by a wrong space group?
> > Could anyone give me some suggestions about this? Thanks
> a lot!
> >
> > Yuan
> >
>
>
>
> --
> Jiamu Du, Ph.D.
> State Key Laboratory of Molecular Biology
> Institute of Biochemistry and Cell Biology
> Shanghai Institutes for Biological Sciences
> Chinese Academy of Sciences
> 320 Yue-Yang Road
> Shanghai 200031
> P. R. China
> Tel: +86-21-5492-1117
> E-mail: [log in to unmask]
>
Boaz Shaanan, Ph.D.
Dept. of Life Sciences
Ben-Gurion University of the Negev
Beer-Sheva 84105
Israel
Phone: 972-8-647-2220 ; Fax: 646-1710
Skype: boaz.shaanan