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
- 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
Dear Careina,
Keep in mind that MolPrrobity does not see symmetry (unlike RefDens or
WHAT_CHECK). This means that the clashes that may come from having the wrong
spacegroup are not detected.
Good luck,
Robbie Joosten
Date: Tue, 18 Jan 2011 10:52:48 +0100
From: mjvanra...@cnb.csic.es
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
Dear All,
We are seeking to recruit a postdoctoral researcher to study
multi-protein complexes involved in eukaryotic transcriptional
regulation by X-ray crystallography and biochemistry. The successful
candidate will join the Christoph Müller group at the Structural and
Computational
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 of
On Jan 17, 2011, at 11:46 AM, James Holton wrote:
I am willing to bet that the earliest no method entries (particularly the
ones that lack a REMark 200 record) were probably MIR, since that was the
obvious method to solve a structure for some time. Modern NULL entries
seem to be mostly
Dear Colleagues,
This is a reminder that the on-line applications are being accepted for
the 4th annual CCP4 summer school From data collection to structure
refinement and beyond, which will take place early June, 2011 at the
APS near Chicago.
There is no registration fee for the school.
