[ccp4bb] high temperature factors

Hello, We have a structure that consists of two molecules per asymmetric unit, each molecule is a hexamer. We solved the structure with molecular replacement, R=22%, Rfree=27%. One hexamer has temp. factors (with bdomain.inp of cns) around 50A2. The other has temp factors >60A2 with two subunits

[ccp4bb] Stretching Modelled B-DNA - Programs

Dear CCP4bbers, My original query was; "I am trying to find a program that enables the user to vary the pitch of the generated output model of dsDNA. I have found several programs that generate a dsDNA .pdb file given an input sequence (random in my case), and a web server that allows 'curvature'

Re: [ccp4bb] oxidised cys

Hi Stefano, How certain are you that this link is truly what you think it is? If I understand what you're saying - you want to create a (thioperoxythio) link - this chemistry should be hideously unstable. Can you explain this using disorder, or perhaps the residual density is a symmetry artifact?

[ccp4bb] SAD question

Hi, I have some questions regarding SAD. Can one use Scaleit to initially analyze anomolous data when doing SAD (ie to get the scaleit.summary statistics)? How does one properly prepare the flags and mtz file for SAD (ie what program to convert the sca file to mtz and properly; I am coming fr

[ccp4bb] Stretching Modelled B-DNA

Dear CCP4bbers, I am trying to find a program that enables the user to vary the pitch of the generated output model of dsDNA. I have found several programs that generate a dsDNA .pdb file given an input sequence (random in my case), and a web server that allows 'curvature' analysis of the outpu

Re: [ccp4bb] Post facto fix to R-free selection

Probably easiest to start again with the correct FreeR You can perturnb the strucures pdbset xyzin MR.pdb xyzout- MRshaken.pdb NOISE 0.3 That moves everything a bit. Or if you do enough cyles the FreeR should increase steadily to a sensible value then level off Easiest to use the GUI and cl

[ccp4bb] Post facto fix to R-free selection

BS"D Dear All, Someone has come to ask my opinion about some inhibitor-protein complexes they have refined, isomorphous with a known native structure (P21212). After a short look at the statistics, I became suspicious about the R-free selection for the new complexes. Indeed, the pers

Re: [ccp4bb] Summary - Valid to stop Refmac after TLS refinement?

I see that Dale and I are in pretty well complete agreement on this subject (even though I honestly hadn't read Dale's response when I sent mine!) - I think we now have a definitive explanation, so hopefully this will be the last time that this question comes up, or if not at least we now have a

Re: [ccp4bb] antibody refinement in REFMAC with Kabat numbering

John Pak wrote: Hi all. I'm currently refining an Fab structure. All was going reasonably well until I renumbered the PDB according to the Kabat numbering convention. After which, REFMAC does not refine the inserted residues properly (ie. residues 82A, 82B, 100A, 100B, 100C, etc.). It refi

[ccp4bb] oxidised cys

Dear all in my structure I think I can see an oxidised Cys in cys-SO. Refining cys-SO I observe a residual density between the oxigen of one oxidised cys and the one of the other molecule in AU. I'd like to try to refine it as cys-SO-OS-cys. I didn't find an example of it in the pdb database. C