Re: [ccp4bb] staff scientist Keck Center for Molecular Structure

Apologies for the typographical error in the start date... From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of Kantardjieff, Katherine Sent: Wednesday, November 07, 2007 5:06 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] staff scientist Keck Cente

Re: [ccp4bb] torsion restraints and phi/psi

I wrote: Isn't it the case that vdw interactions are turned off between atoms in a residue, and perhaps with the residues before and after? No it is not the case, at least in refmac5 and SHELLXL. Thanks to those who clarified this. Jim Naismith's earlier post, which I had not seen, suggests a b

[ccp4bb] Research Associate and Post doctoral positions

Several Research Associate (team leader) and Post-doctoral positions in structural biology are available in the Chromatin biology and Epigenetic group at the Structural Genomics Consortium, University of Toronto. My group aims to characterize chromatin proteins involved in histone code "readi

[ccp4bb] staff scientist Keck Center for Molecular Structure

INSTRUCTIONAL SUPPORT TECH III, STAFF SCIENTIST, W. M. KECK FOUNDATION CENTER FOR MOLECULAR STRUCURE The College of Natural Sciences and Mathematics and Department of Chemistry and Biochemistry seek applications for the position of Staff Scientist, W.M. Keck Foundation Center for Molecular Stru

Re: [ccp4bb] refined vs 'others'

> Of course, you cannot reproduce the output. The question was actually different. Minor differences in numbers are not the problem. The absence of 'others' in the restraint table is inconsistent with the statement at the end of the table that riding hydrogens were used. BR -Original M

Re: [ccp4bb] refined vs 'others'

Hi, I reran that (same refmac version) but I cannot reproduce the output. Of course, you cannot reproduce the output. This is most likely because the H atoms were used internally in all calculations but they were not deposited in PDB (like in most of cases). So, to reproduce the numbers

Re: [ccp4bb] refined vs 'others'

All right, one more peculiar question on the subject: If that is true - that > "others" in case means the bonds to the hydrogens added in riding positions during refinement then how comes that in example 2veh the restraint listing does not have 'others' but still says that hydrogens were added?

[ccp4bb] Research Associate (team leader) and Post doctoral positions

Several Research Associate (team leader) and Post-doctoral positions in structural biology are available in the Chromatin biology and Epigenetic group at the Structural Genomics Consortium, University of Toronto. My group aims to characterize chromatin proteins involved in histone code "readi

Re: [ccp4bb] torsion restraints and phi/psi

SHELXL does not provide torsion angle restraints. As far as I can tell, the normal procedure using REFMAC and PHENIX.REFINE is to refine with torsion angle restraints applied to side-chains but not to the psi and phi angles (all three programs have ways of keeping peptide units approximately pl

Re: [ccp4bb] torsion restraints and phi/psi

I could not say about other program but in refmac there are intra residue vdw repulsions if atoms are at least two bonds are apart. If atoms are only two bonds apart then vdw distance is reduced and it can be controlled. I do agree that at lower resolution you should use as much info as you

Re: [ccp4bb] torsion restraints and phi/psi

Bernhard Rupp wrote: Dear All, I wonder about the exact use of torsion restrains and the effect on phi/psi/w validation. a) does refmac restrain phipsi at all (except vdw repulsion which does not bias them otherwise)? Isn't it the case that vdw interactions are turned off between ato

Re: [ccp4bb] elusive DNA density

While working with a low-affinity, nonspecific DNA binding protein, I ran into this problem dishearteningly often. In several cases, even when running washed crystals out on a gel had told me that they contained both DNA and protein (32P-labeling for DNA, Coomassie for protein), I was unable to

Re: [ccp4bb] torsion restraints and phi/psi

If memory serves correctly Ramachandran based his plot on VDW. Therefore all programs which use VDW will tend to put residues in the right place. Certainly in phenix.refine adding H's to one of my problematic structures (twinning) not only improved the clash score but pushed a further 4% into th

Re: [ccp4bb] elusive DNA density

All statistics aside, I never believe a molecular replacement solution until it produces an Fo-Fc map with peaks for something that should have been there but wasn't in the model. If you know roughly where the DNA should bind, you could try making a solvent mask that includes that region (pl

[ccp4bb] torsion restraints and phi/psi

Dear All, I wonder about the exact use of torsion restrains and the effect on phi/psi/w validation. I think in refmac, omega is restrained with a 1-4 dihedral or planarity, cis when the proper LINK statement is invoked - no questions there. In literature I find remarks like 'usually not restrain

Re: [ccp4bb] elusive DNA density

-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Hi; You might also consider if it is likely that you have statistical disorder, causing a blur in the DNA. This could be the case if your binding is not specific, in which case it is possible that DNA is shifted by a couple of bases (or if your