[ccp4bb] looking for proteins with no homologues in pdb

For testing purposes, we want to solve structures of proteins that are not in the PDB and have no significant sequence homologues in the PDB (i.e. a blast of the pdb will get no significant hits). Does anyone happen know a good way to find such proteins efficiently? Having an interesting

Re: [ccp4bb] How can I refine the occupancy with Refmac?

Certainly Elenaor.  Here are a few: # typical lysozyme % refmac_occupancy_setup.com 193l.pdb occupancy refine occupancy group id 1 chain A residue 1 alt A occupancy group id 2 chain A residue 1 alt B occupancy group id 3 chain A residue 59 alt A occupancy group id 4 chain A residue 59 alt B

Re: [ccp4bb] How can I refine the occupancy with Refmac?

James - could you send me a few examples to add to the documentation? Lockdown means I cant easily access my own examples - all trapped on the lab desktop.. Eleanor On Mon, 7 Jun 2021 at 17:18, James Holton wrote: > I wrote a script for auto-generating occupancy refinement relationships > for

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Re: [ccp4bb] How can I refine the occupancy with Refmac?

I wrote a script for auto-generating occupancy refinement relationships for refmac. It is perhaps not as sophisticated as what phenix does internally, but it gets common things right, like if you have a 2-headed side chains or partial-occupancy metals.

[ccp4bb] self-inhibitory fragments from a protein

Dear CCP4bb, I have a partly specific question, relating to multidomain enzymes. We have a nice hi-res structure of an enzyme, which comprises domain A (non-catalytic) and domain B (enzymatic) Through the magic of unstimulated in-tray proteolysis, there are one and a half copies in the ASU,

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Re: [ccp4bb] H-bond modelling

There are tools such as hbplus https://www.ebi.ac.uk/thornton-srv/software/HBPLUS/ that will calculate predicted hydrogen bonds (including ligands, you just need to define their chemistry) throughout a structure. These tools usually go beyond simple distance considerations and analyze further

Re: [ccp4bb] How can I refine the occupancy with Refmac?

In GUI2 the Advanced box allows you to do that eg RESO 10 3 say if you wanted to restrict resolution.. Eleanor On Mon, 7 Jun 2021 at 11:35, Marina Gárdonyi < marina@pharmazie.uni-marburg.de> wrote: > Hi, > > I didn't know that I can also enter keywords without a file! That is a > good note,

Re: [ccp4bb] How can I refine the occupancy with Refmac?

Hi, I didn't know that I can also enter keywords without a file! That is a good note, thank you!! Best regards, Marina Zitat von Jon Cooper : Hello, the keywords can be entered in refmac gui (in one of the dropdown things), so you don't need a file, as such, but it's useful to keep a

Re: [ccp4bb] H-bond modelling

On Mon, 2021-06-07 at 01:35 +0530, vivek sharma wrote: > > How does one validate if 2 atoms (non-hydrogen) which are close enough, > actually participate in H-bonding? > I have a recent data that i am currently working on, the NH2 of ARG is at > 2.61A from ligand's oxygen atom (refer to >

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