[ccp4bb] alternative conformation refinement by phenix

Hi all, I am refining a DNA-protein complex structure by phenix. My protein is a nuclease and the DNA bound to protein is a mixture of the substrate and product. Partial DNA was cleavaged by the protein and others is keep a un-cleavaged strand. I am trying to rerine this mixture with phenix.

[ccp4bb] selective protection of C-terminal carboxylate

Dear all, is anyone aware of a way to selectively protect the carboxylate at a protein C-terminus, while leaving unaffected those of Asp and Glu side chains? Thanks a lot in advance, have a nice weekend, ciao, s -- Sebastiano Pasqualato, PhD Crystallography Unit Department of Experimental

Re: [ccp4bb] alternative conformation refinement by phenix

On Fri, 2012-05-25 at 19:01 +0800, LISA wrote: try to refine this structure by phenix but failed. Not that I have an answer to your question, but you have to describe what you mean by failed. Maybe you should try refmac. Will also make your inquiry better suited for this forum (although it's

Re: [ccp4bb] alternative conformation refinement by phenix

Hi Lisa, I am not an phenix expert and, as Ed mentioned, from the message that refinement failed it is hard to figure out what or how it failed. Nevertheless, here are a few suggestions. -do your alternate conformations make consistent sets? E.g. do the AADE and AGUA both belong to the linked

[ccp4bb] zero mosaicity

I should do more digging, but I hope maybe there is a simple explanation and someone has seen this before. On some datasets (collected at SSRL) I get SCALA reporting average mosaicity of 0.0. This probably happens at the integration stage, and for this whole set of datasets *always* happens when

Re: [ccp4bb] selective protection of C-terminal carboxylate

If you express the protein as an intein fusion you can make a C-terminal thioester, which you can then modify quite specifically with various reagents . Pat On 25 May 2012, at 10:00 AM, Sebastiano Pasqualato wrote: Dear all, is anyone aware of a way to selectively protect the carboxylate at

Re: [ccp4bb] zero mosaicity

Hi Ed, If you use XDS for integration then all of the reflections are full (they are summed by the program during the integration), so there are no partials from which to determine an estimate of the mosaic spread in Scala. Mosflm 0 mosaic spread is a different issue, but has been much improved

[ccp4bb] PDB deposition of internally truncated protein

Dear All, I need to deposit in the PDB the co-ordinates of a protein with an internal truncation. If I do this in the normal way with consecutive numbering according to the actual polypeptide sequence in the crystal, the residue numbers after the truncation will not correspond to the

Re: [ccp4bb] zero mosaicity

Hi Ed, the mosaicity is always zero after xds, because the processing is different as Graeme mentioned. If the cell refinement is unstable and mosaicity becomes zero, I estimate the mosaicity from a few pictures and write my own value in the mosaicity estimation window of the gui. Than one

Re: [ccp4bb] zero mosaicity

Thanks - indeed I was simply unaware that the mosaicity is always reported as zero when using (auto)xds. So I guess since only two datasets also behave badly in mosflm, and both have bad multiple latticitis, my questions are answered. Thanks, Ed. On Fri, 2012-05-25 at 16:31 +0100, Graeme

Re: [ccp4bb] PDB deposition of internally truncated protein

Dear Stephen, On Fri, 2012-05-25 at 17:42 +0200, Stephen Cusack wrote: Dear All, I need to deposit in the PDB the co-ordinates of a protein with an internal truncation. If I do this in the normal way with consecutive numbering according to the actual polypeptide sequence in the

Re: [ccp4bb] PDB deposition of internally truncated protein

Hi Stephen, I think that while the PDB may accept the new numbering that you provide with your truncated structure (I'm not sure about that though), it'll be quite annoying for somebody who'd like to compare your structure with that of the untruncated one. Besides, from what I've seen and

Re: [ccp4bb] zero mosaicity

SCALA doesn't do anything with the mosaicity, it just reports what was passed from the integration program. On 25 May 2012, at 17:12, Ed Pozharski wrote: I should do more digging, but I hope maybe there is a simple explanation and someone has seen this before. On some datasets (collected at

Re: [ccp4bb] alternative conformation refinement by phenix

Hi LISA, if you send me more details I might be able to address your questions (as Phenix developer). Though a better place to post your Phenix related questions is a Phenix mailing list, not CCP4bb. P.S. Ugh, I find Ed's reply totally.. how to say it softer using my non-native-English...

[ccp4bb] question about a dataset with pseudotranslational symmetry

Dear All, Recently I collected a data set to about 3.1 angstrom. Using Xtriage program, I found a pseudo translational symmetry on the c-axis. I noticed that overall diffraction intensity is weak for this dataset. I wonder if there are flaws in the crystal and I have difficulty to solve the