On Tue, 2021-07-13 at 23:59 -0700, Seth Harris wrote: > > I have some good resolution (~1.3 A) data with glycosylation that can pretty > clear describe the expected N-linked tree > of Asn-NAG-NAG-BMA with two MAN off the end and a FUC at the base NAG (plus > something on the other side of the base > NAG that also looks like a sugar??). But the main issue I have is that the > rather impressive and lovely glycosylation > tools in Coot that I think I've used before to build this are (at least now > in Coot 0.9.5) doing well on the first > NAG-FUC-NAG combo and then the coot module correctly suggests the B1,4 BMA > attachment which at first is placed nearby > at density and then is refined or moved way out, with the heavy dashed > connector that should be a regular bond length > seemingly forced to be 2 to 3x too long. No type of sphere or real space > refinement brings it back, it always flips > itself through any kind of gymnastics it can to keep it too far away, despite > really terrific density that would be > good with a regular bond distance. I haven't put any LINK or such in the PDB > yet, these are just being built by COOT > itself and I can't see any waters or sym mates that would push it away in > this manner. > > I tried carrying on through with some alpha 1,3 MANnose and alpha 1,6 MANnose > additions to that in case I could > correct it all after a rough build, but the same problems occur here, with > janky and irretrievable placements in the > end. Meanwhile the first 3 sugars are pretty perfectly placed. Did something > go different with the mannose that I'm > doing wrong? > > Am I allowed to attach a screenshot? I'll try to here...The second NAG out is > nicely in density at the bottom center, > the beta 1,4 BMA is the first one seemingly ignoring density and pushed out > on that dashed line with the other MAN > also way off... >
Hi Seth, Just to make sure that there's something wrong with your Coot, can you try to build the glycosylation in 2qc1? Thanks, Paul. ######################################################################## To unsubscribe from the COOT list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=COOT&A=1 This message was issued to members of www.jiscmail.ac.uk/COOT, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
