Re: [ccp4bb] CCP4 Cloud structure determination help

Hi Marco Is the N terminal part present in the correct place if you show symmetry in COOT? If so you can just save the symmetry coordinates and merge it in to the chain it is supposed to belong to. Best wishes Matthew. From: CCP4 bulletin board on behalf of B

Re: [ccp4bb] Reduces the RSRZ outliers in the wwPDB validation report

Hi This may be totally out of date, but in the past the PDB used Refmac to calculate the validation maps, and this caused RSZ problems for certain structures refined with phenix (certain resolution ranges use of TLS If I remember rightly). I think the RSZ outlier score can also be affected by

Re: [ccp4bb] Pipetting Robot

We have a Dragonfly in Manchester, the software makes designing screens/gradients really easy but ours at least only makes plates one at a time. You also need the "MX one" mixer to mix your plate to avoid tedious pipetting. Best wishes Matthew. From: CCP4 bullet

Re: [ccp4bb] cryoEM molecular replacement

Hi Gloria I didn’t see this mentioned (perhaps I missed it). But if you are struggling to get your initial docking solution, do check that your hand is correct. If your map is good enough you can possibly get it by building small trial sections (alpha helices can be good), for more challengin

Re: [ccp4bb] O-linked glycans

Thanks for everyone's Helpful replies, it seems like the "make link in Acedrg" tool is exactly what I was looking for. ____ From: Matthew Snee Sent: 13 November 2024 11:35 To: CCP4BB@JISCMAIL.AC.UK Subject: O-linked glycans Hi All This is a rela

[ccp4bb] O-linked glycans

header to turn it into a residue that COOT will recognise as a non-standard amino acid. Is this the "correct" way with respect to what the PDB expects these days? Best wishes Matthew. Matthew Snee, PhD Post-doctoral Research Associate The Baldock Lab | Michael Smith Build

Re: [ccp4bb] circular peptide structure refinement

Hi All To prevent Phenix removing link records, you can use Readyset to create a parameters file based on LINK records, and feed it to the refinement program, otherwhise they are deleted. Best wishes Matthew. From: CCP4 bulletin board on behalf of Nicholas Cla

[ccp4bb] COOT RSR

Hi all I had a bit of trouble getting used to the new COOT real space refine... it took me an embarrassingly long time to work out that there is nothing wrong with the fitting/restraints.. it just doesn't seem to allow clashes with parts of the model that aren't in the selected RSR zone even wh

Re: [ccp4bb] convert loop into a sheet

Is it not just a case of adding "beta sheet restraints" in the real-space refine options menu? If it goes back to a loop during refinement then that may mean that the atomic positions don't meet the requirements? Get Outlook for Android F

Re: [ccp4bb] External: Re: [ccp4bb] AlphaFold: more thinking and less pipetting (?)

It seems immensely powerful, but my impression is it shows just how much information can be extrapolated from the PDB if a technique that can make use of "deep similarity" can be employed. Obviously alphafold2 can make use of relationships that arent limited to direct homology, but if there is

[ccp4bb] Protein expression (codon bias)

Hi all I'm designing genes for expression in M. smegmatis (safe host for Mtb proteins), but its not possible (or advisable due to the GC content) to optimise for mycobacterial expression. Would anyone with experience be able to tell me if its fine to stick with the E. coli codon optimisation,

[ccp4bb] Ideas for improving refinement with anisotopic data.

Hi everyone. I have an x ray structure that I am finishing up, and there are a few ambiguous regions where the peptide is poorly resolved. The data is highly anisotrophic, and requires truncation to around 2.4A to achieve acceptable merging stats, although there is data in the "good" direction