Hi Paul, That's a good control and yes, the coot glyco module works beautifully on 2qc1; as well my own structure/maps when loaded alongside. This led me to find that it was only happening in my project directory and using some scripts I have that pre-load a working environment as coot is opened...and among those 'pre-loads' it was finding an old .cif restraints file which included a definition for BMA -- and was thus overwriting the atom definitions for that sugar which was naturally throwing off the builder. Once removed (that erroneous .cif I had), it's back to its incredible self, the Glyco module.Thanks for helping track that down, and more so for the terrific glycosylation builder (in fact this is an old structure I came back to years later only now that the tools improved enough to build these without going insane!).
Cheers, Seth On Thu, Jul 15, 2021 at 1:10 AM Paul Emsley <pems...@mrc-lmb.cam.ac.uk> wrote: > 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/ > ######################################################################## 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/
