Re: [ccp4bb] To Trim or Not to To Trim

I found the poll I wrote about earlier. This actually is way older than I had expected (2011). You can see the poll results (which was run by Ed Pozharski) and discussion at the time here in the CCP4BB archive: https://www.mail-archive.com/ccp4bb@jiscmail.ac.uk/msg20268.html In brief, the

Re: [ccp4bb] To Trim or Not to To Trim

Hello, yes, the trimming and occupancy tricks can be confusing and they can be a bit of a cheeky way to improve the model statistics. I prefer to build the whole side chain and if you can't see all or part of it, then that's just too bad, but I have erred. Best wishes, Jon Cooper.

Re: [ccp4bb] To Trim or Not to To Trim

We dealt with this in-depth during structural genomics days when we deposited over 1500 novel, high-quality, experimentally-phased structures into the PDB. Think it’s prudent to trim/truncate side chains without reliable density. Non-structural biologists using PDB structures without expert help

Re: [ccp4bb] To Trim or Not to To Trim

In fact, for non-SBs using the PDB, it is far likelier that they will recognize truncated side chains and thus seek help or know what to do themselves, compared to recognizing incorrectly modeled rotamers (as they won’t be checking electron density likely) and atoms with zero occupancy and

Re: [ccp4bb] To Trim or Not to To Trim

Hi Rhys, I am also all for leaving side chains and letting the B-factors deal with the weak/absent density. I don’t think there is a consensus, but I kind of remember that somebody did a poll a few years ago and if I remember correctly the main approaches were the one described above, or

Re: [ccp4bb] To Trim or Not to To Trim

I’d say no trimming to side chains for the following reason: There are non-structural biologists using PDB files and if atoms are missing they don’t know what to do. A better approach is where no side chain density allows support of placement, pick the most common rotamer and set the occupancy

Re: [ccp4bb] Structural alignment and classification

Try POSA and FATCAT from Godzik group for structural clusters/trees and multiple/flexible structure alignments: https://academic.oup.com/nar/article/48/W1/W60/5848494 https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4086100/ https://posa.godziklab.org/ https://fatcat.godziklab.org/ Best regards,

Re: [ccp4bb] Structural alignment and classification

Coot's ssm superposition does give the C-alpha rmsd, though, most easily seen if you run it from a terminal window? I guess it can't be miles different from a least-squares fit ;-? Best wishes, Jon Cooper. jon.b.coo...@protonmail.com Sent from Proton Mail mobile Original Message

[ccp4bb] To Trim or Not to To Trim

Hi All, I'm trying to crowdsource an opinion on how people deal with modelling side chains with poorly resolved electron or cryoEM density. My preference is to model the sidechain and allow the B-factors to go high in refinement to represent that the side chain is flexible. However, I'm aware

Re: [ccp4bb] Structural alignment and classification

On 06/03/2023 07:35, Armando Albert wrote: I want to align several structures we obtained from a fragment screening campaign and cluster them according to RMSD. To what end, may I ask? I would use LSQKAB, parse the log files for the RMSD and create an input file for R. (One cannot just do

[ccp4bb] Virtual Crash Course - Understanding PDBx/mmCIF | May 3rd | REGISTER NOW!

Use PDB data to their full extent: Understanding PDBx/mmCIF Wednesday, May 3rd 2023 | 1:00 PM EDT Registration: go.rutgers.edu/u3vpwjet * This RCSB Protein Data Bank (PDB) virtual course will be broadcast on Zoom. Please fill out the registration form to