I have never met a computational chemist who did not "notice" when a
side chain is modeled as more than one conformer.
-James Holton
MAD Scientist
On 3/31/2023 8:31 AM, Olga Moroz wrote:
Hi everyone,
I always thought it is better to truncate so that biologists looking
at the structures are not misled?
Not sure it the best aproach though...
Olga
On 10 Mar 2023, at 02:45, Bernhard Lechtenberg
<0000968307750321-dmarc-requ...@jiscmail.ac.uk> wrote:
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 trimming the
side-chains.
Bernhard
*Bernhard C. Lechtenberg*PhD
NHMRC Emerging Leadership Fellow
Laboratory Head
Ubiquitin Signalling Division
elechtenber...@wehi.edu.au <mailto:lechtenber...@wehi.edu.au>
T +61 3 9345 2217
*From:*CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> on behalf of Rhys
Grinter <000022087c81e8c6-dmarc-requ...@jiscmail.ac.uk>
*Date:*Friday, 10 March 2023 at 12:26 pm
*To:*CCP4BB@JISCMAIL.AC.UK <CCP4BB@JISCMAIL.AC.UK>
*Subject:*[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 that some people truncate sidechains if density is
not present to justify modelling. I've also seen models where the
sidechain is modelled but with zero occupancy if density isn't present.
Is there a consensus and justifying arguments for why one approach is
better?
Cheers,
Rhys
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