Indeed, update 54 from Mar 29 seems to have messed up several monomer definitions and/or their handling in coot (the version distributed with ccp4):
- GLU and ASP contain lines referencing GLN and ASN, respectively, preventing coot from finding any chi angles.
- For GLN, chi angles appear twice in the coot torsion dialog.
- Many amino acid definitions now contain main chain torsion angles, which are erroneously listed as chi in coot.
The coot version available from Paul Emsleys website comes with its own version of the monomer library, which seems to work fine.
Best
Oliver
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PD Dr. Oliver H. Weiergräber
Institute of Complex Systems
ICS-6: Structural Biochemistry
Tel.: +49 2461 61-2028
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From: CCP4 bulletin board [[log in to unmask]] on behalf of Eleanor Dodson [[log in to unmask]]
Sent: Thursday, April 26, 2018 11:49 AM
To: [log in to unmask]
Subject: Re: [ccp4bb] Coot 'Edit Chi Angles' on Mac misbehaving
Oops - oh dear - GLN labels should NOT appear in a list devoted to GLU!!
Well spotted..
Eleanor
On 26 April 2018 at 10:34, Chris Richardson <[log in to unmask]<mailto:[log in to unmask]>> wrote:
Many thanks for explaining where it is going awry.
Looking at GLU.cif in the monomer library that is part of the CCP4 distribution, it contains the following lines:
GLN chi1 N CA CB CG 180.000 15.000 3
GLN chi2 CA CB CG CD 180.000 15.000 3
GLN chi3 CB CG CD OE1 0.000 30.000 2
In the monomer library you link, it has:
GLU chi1 N CA CB CG 180.000 15.000 3
GLU chi2 CA CB CG CD 180.000 15.000 3
GLU chi3 CB CG CD OE2 0.000 30.000 2
Which makes more sense.
Thanks again,
Chris
________________________________________
From: CCP4 bulletin board <[log in to unmask]<mailto:[log in to unmask]>> on behalf of Huw Jenkins <[log in to unmask]<mailto:[log in to unmask]>>
Sent: 26 April 2018 09:47
To: [log in to unmask]<mailto:[log in to unmask]>
Subject: Re: [ccp4bb] Coot 'Edit Chi Angles' on Mac misbehaving
> On 26 Apr 2018, at 09:19, Chris Richardson <[log in to unmask]<mailto:[log in to unmask]>> wrote:
>
> I've just compiled Coot on the same Mac using Fink, and the dialogue for this version of Coot shows CA <--> CB, CB <--> CG, and CG <--> CD angles for the same residue.
From a quick look at the Fink coot.info<http://coot.info> it appears to get the monomer library from here:
http://www2.mrc-lmb.cam.ac.uk/groups/murshudov/content/refmac/Dictionary/refmac_dictionary_v5.41.tar.gz
Setting $CLIBD_MON to point to this and the 'Edit Chi Angles' dialogue for CCP4 distributed Coot 0.8.9.1 shows CA <--> CB, CB <--> CG and CG <--> CD of Glu 14 A from the RNase tutorial model.
Huw
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