I don't know how much effort I would put into that, given how easy nucleic acid
sequencing has become.
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All Things Serve the Beam
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David J. Schuller
modern man in a post-modern world
MacCHESS, Cornell University
[email protected]
________________________________
From: CCP4 bulletin board <[email protected]> on behalf of Robbie Joosten
<[email protected]>
Sent: Friday, July 29, 2022 9:56 AM
To: [email protected] <[email protected]>
Subject: Re: [ccp4bb] Checking X-ray sequence (no more protein).
Hi Jon,
There are placeholders for ASP/ASN and GLU/GLN ambiguities: ASX and GLX
respectively. You can just use those. AFAICT there no such thing for VAL/THR
ambiguities. You could look for the most likely canadidata based on multiple
sequence alignments. Refinement of both alternatives can give hints in
B-factors and if you are lucky in difference density. But if hydrogen bonding
gives no hints, then the residues are also not in a place where the identity
really matters. You can give your best guess with a CAVEAT record or use the
name UNK to indicate that you do not know what the residue is. You would loose
the knowledge that it is either VAL or THR in that case.
Cheers,
Robbie
> -----Original Message-----
> From: CCP4 bulletin board <[email protected]> On Behalf Of Jon
> Cooper
> Sent: Friday, July 29, 2022 12:14
> To: [email protected]
> Subject: [ccp4bb] Checking X-ray sequence (no more protein).
>
> Hello, I am looking for suggestions of ways to check a 1.7 Angstrom X-ray
> sequence for a protein where it is impractical to do experimental sequencing,
> protein or DNA. The structure refines to publishable R/R-free and the main
> ambiguities seem to be Thr/Val, Asp/Asn and Glu/Gln where alternative H-
> bonding networks are possible. Running alpha-fold seems an interesting
> option? Any suggestions much appreciated.
>
> Cheers, Jon.C.
>
> Sent from ProtonMail mobile
>
>
>
>
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