Here I was thinking I had the latest version of coot, but I didn't! I downloaded 0.8.9 and everything is working now. Thanks!
Erik ________________________________ From: Paul Emsley <[email protected]> Sent: Friday, March 9, 2018 12:57:19 PM To: Erik Klontz Cc: [email protected] Subject: Re: [ccp4bb] Building carbohydrates in coot using glyco module CAUTION: This message originated from a non UMB, UMSOM, FPI, or UMMS email system. Whether the sender is known or not known, hover over any links before clicking and use caution opening attachments. On 09/03/2018 17:29, Erik Klontz wrote: > > > I have solved a few Fc crystal structures, and am having trouble building the > full length glycans onto them. > I've been using the coot "glyco" module which I really like, Glad to hear it. > but I don't see any options for adding B(1-2) > NAG. I'm using the latest version of coot on windows. I guess that 0.8.9's Glyco module has not been ported to Python. Coot-0.8.9's Glyco module is an improvement over previous version. I am planning a (small?) modification for 0.8.9.1. > I've seen screenshots from other people's modules that > show this (and many other linkages) as options. Is this only available on > linux or is there something I need > to do to access the full module? To be clear, it's not a Linux vs everything problem, it's a guile vs non-guile problem. Personally, I'd try to install a coot on the Ubuntu Linux subsystem that comes with Windows these days. > > > Alternatively, is there an easier way of doing this? I've tried building the > glycans using GLYCAM, but I > can't figure out any way of linking them to the asparagine so the Asn-glycan > bond parameters are reasonable. If you put it in the "right place" (less than 2.2A between the C1 and ND2) and if the glycan is in the same chain as your protein, then coot will make the linkage for you in refinement. You can also do a Extensions -> Modelling -> Make Link, which adds a link record to the exported coordinates files, so that other programs know that there is a link there. Paul.
