Re: [COOT] Carbohydrate torsion

Here is a good website for ring pucker of sugars, as investigated by Sundaralingam et.al. https://x3dna.org/highlights/two-slightly-different-definitions-of-sugar-pucker 3DNA Homepage -- Nucleic Acid Structures x3

Re: [COOT] Carbohydrate torsion

Just a note to remember: This is a modelling job - no density and if a refined glycan tree conformation would be what is really there, we also would see them in structures one would guess.. I envision this more to see whether the glycans are in the way (and to what degree I can bend them away). I

Re: [COOT] Carbohydrate torsion

Rinse, and repeat. Get Outlook for Android From: Kenneth Satyshur Sent: Thursday, May 9, 2019 8:06:45 AM To: Paul Emsley; COOT@JISCMAIL.AC.UK Subject: Re: Carbohydrate torsion Put structure in modeling program like Maestro or Sybyl, twist,

Re: [COOT] Carbohydrate torsion

Put structure in modeling program like Maestro or Sybyl, twist, minimize, save, generate restraints, refine. Get Outlook for Android From: Mailing list for users of COOT Crystallographic Software on behalf of Paul Emsley Sent: Thursday,

Re: [COOT] Carbohydrate torsion

On 08/05/2019 12:17, Bernhard Rupp wrote: > > Dear Fellow Cootsters, > >   > > I am trying to use the flexibility of glycans as validation of a > docking model (no density available) > > by torsioning the glycans into conformations where they do not > interfere/clash with the models. > OK, but fro

[COOT] Carbohydrate torsion

Dear Fellow Cootsters, I am trying to use the flexibility of glycans as validation of a docking model (no density available) by torsioning the glycans into conformations where they do not interfere/clash with the models. It seems 'general torsion' works only on bona fide amino acid torsio