Re: [ccp4bb] A babyish question on coot

[Josiah Obiero]

Try alternate rotamers first, and then choose the closest to the 
'right' electron density, before you do 'real space refine'
Regards,
Josiah.

Hi,

I use coot almost around the clock. One thing troubles me is that:
when clicking on 'real space refine zone', coot seems only care about 
the 
'real space'(Electron density), sometimes it will bring the model to 
the density no matter whether the density was already  claimed by other 
model atoms or not, resulting in clash and unreasonable geometry. How 
can 
I avoid this?

Sorry for an old crystallographer to ask so babyish question. But your 
help can save me lots of time.
Thanks
Yanming

[ccp4bb] R32 data

[Josiah Obiero]

Dear all,

I have set of data (~2.7A). After indexing, HKL2000 suggests a 
rhombohedral space group or C centered monoclinic space group. I tried 
molecular replacement with R32 ( 109.55 109.55 155.28 90.00 90.00 
120.00) and C2 (121.092   109.31581.53790.00097.874
90.000) (both have good merging statistics), but did not get any 
solution. I also tried P1 ( 81.55381.52781.52384.202
84.13284.156) but did get any solution ( wt structure is known and 
the only difference with the wt structure is that the new structure is 
complexed with a smaller protein). I expect that there'll be some 
domain movement so searched for individual domains in phaser.

The self rotation function in P1 showed both two fold and three fold 
peaks but they were both off the centre. The data does not appear to be 
twinned. I am curious to know if it is normal for cell dimensions to 
drastically vary from one space group to another. I am running out of 
ideas, could I be dealing with a wrong space group or pseudosymetry?

Any suggestions would be appreciated.

Thanks.

Josiah.

[ccp4bb] Rosettadock/Robetta server Interface analysis

[Josiah Obiero]

Hi all,I am trying to compare the binding affinities of two small proteins to a bigger receptor protein by interface analyis (computational interface alanine scanning by Rosettadock/Robetta server). I was wondering:1.  If it possible to use DDGs of the individual amino acid residues to predict binding affinities2. If there is another method of predicting binding affinities in silicoThanks,Regards,Josiah.

[ccp4bb] Gap volume calculation

[Josiah Obiero]

Hello all,I am trying to calculate the gap volume of a protein-protein complex interface using SURFNET but I cannot locate the download files from: ftp.biochem.ucl.ac.uk . Is there any other program I can try?Thanks.Josiah.