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<https://x3dna.org/highlights/two-slightly-different-definitions-of-sugar-pucker> x3dna.org Homepage of the 3DNA suite of software programs for the analysis, rebuilding and visualization of 3-dimensional nucleic acid structures Kenneth A. Satyshur, M.S., Ph.D. Senior Scientist, Depts. Bacteriology, Bio Molecular Chemistry, Neuroscience, Oncology, Carbone Cancer Center, and the School of Pharmacy University of Wisconsin-Madison Madison, Wisconsin, 53706 608-215-5207 ________________________________ From: Bernhard Rupp <[email protected]> Sent: Thursday, May 9, 2019 9:14:07 AM To: Kenneth Satyshur; [email protected] Subject: RE: 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 prefer the fuzzball image, some sort of a ‘volume of possible presence’…. I think this is becoming more and more important but still a long way to go…. Thanks! Best, BR From: Mailing list for users of COOT Crystallographic Software <[email protected]> On Behalf Of Kenneth Satyshur Sent: Thursday, May 9, 2019 15:07 To: [email protected] Subject: Re: Carbohydrate torsion Put structure in modeling program like Maestro or Sybyl, twist, minimize, save, generate restraints, refine. Get Outlook for Android<https://aka.ms/ghei36> ________________________________ From: Mailing list for users of COOT Crystallographic Software <[email protected]<mailto:[email protected]>> on behalf of Paul Emsley <[email protected]<mailto:[email protected]>> Sent: Thursday, May 9, 2019 7:21:01 AM To: [email protected]<mailto:[email protected]> Subject: Re: 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 from that description it seems better to me to do a glyco tree regularization. It seems ‘general torsion’ works only on bona fide amino acid torsions and not in a strict ‘general’ sense? That shouldn't be the case. "Torsion general" least sophisticated way of moving atoms by manipulation of torsion angles. FWIW, I'd prefer, if possible, to use Chi Angle manipulation or Multi-residue torsion. I don't use WinCoot, so I don't know the status of these tools. How can I do such arbitrary torsions in wincoot? For now, I can do it in ICM. Fighting talk :-) Paul. ________________________________ To unsubscribe from the COOT list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=COOT&A=1 ________________________________ To unsubscribe from the COOT list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=COOT&A=1 ######################################################################## To unsubscribe from the COOT list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=COOT&A=1
