Hi Careina,
Are you using riding hydrogens during refinement? The default in Refmac is to use hydrogens only if
present in the input file - change this setting under the "Refinement Parameters" to
"generate all hydrogens". This significantly helps with clashes.
Also, did you check the quality
If your dataextends to 2A resolution I suggest you run Arp-Warp or
Buccaneer to rebuild the structure. At that resolution the automated
building programd can usually fix errors.
At the end use this option to get the new build back to overlap the original
csymmatch -pdbin-ref MR.pdb -pdbin arp-
bject: [ccp4bb] So many clashes
Dear CCP4 bulletin board
I am trying to solve structure with molecular-replacement. I have got good
solution using Phaser. The refined structure fits well to electron density and
appears reasonable in terms of geometry, ramachandran, rotamers etc. The
prob
sic.es
> Subject: Re: [ccp4bb] So many clashes
> To: CCP4BB@JISCMAIL.AC.UK
>
> - look at the clashes one by one and fix them, using your biochemical
> knowledge and common sense
> - make sure there are no mistakes in the protein sequence used (resequence if
> necessary
- look at the clashes one by one and fix them, using your biochemical knowledge
and common sense
- make sure there are no mistakes in the protein sequence used (resequence if
necessary), a few amino acids may be different from what you expect and,
combined with local ambiguous density, lead to c
Dear CCP4 bulletin board
I am trying to solve structure with molecular-replacement. I have got good
solution using Phaser. The refined structure fits well to electron density and
appears reasonable in terms of geometry, ramachandran, rotamers etc. The
problem I experience is that there are ver
