Hi Marilyn, I have been struggling with carbohydrates in the pre Glyco module era, which was *not nice*. However, the following strategy works reasonably well:
1) Get the XYP monomer with the "get monomer" command. 2) Move the XYP manually in its electron density. This can be very approximate 3) Do a real space refinement of the XYP monomer alone. This should work should give a decent fit of the monomer 4) Delete one of the oxygens of the future linkage and use the "make link" command (extensions-modeling-make link) to link your monomer to the carbohydrate tree. For buster, I had some restraints files to link carbohydrates, I do not have any experience with phenix refine. With some luck, just a covalent link with reasonably well-defined sugars would be sufficient. Changing the stereochemistry of a standard carbohydrate link file may also do the trick. Good luck! Herman Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von Yoder, Marilyn Gesendet: Donnerstag, 5. Juli 2018 16:01 An: CCP4BB@JISCMAIL.AC.UK Betreff: [EXTERNAL] [ccp4bb] COOT: adding xylose to a plant glycosylation chain Hello, I'm having problems adding XYP (beta-xylose) to my glycosylation chain in a plant protein. I have a 1.87 Angstrom map, 4 molecules in the asymmetric unit. I have two primary N-glycosylation sites, per protein. I am not using NCS for refinement or model building. The density for the NAG-(FUC)-NAG is very clear at both sites of all molecules in the a.u. The BMA (beta mannose after the 2nd NAG) is clear at one of the glycosylation sites. At this glycosylation site, I see good density for a MAN at the C3 and C6 sites of BMA. I can see good density for a xylose at the C2 - it is really quite clear. Using COOT, and the Glyco module, set to Hybrid (Plant), I have been able to add all the NAGs, MANs, and FUCs with a press of a mouse button. It is a *very nice* function of COOT. But..... I can't get the XYP added correctly. I select the "add an XYP-BMA XYP", and it pops the XYP where I want it, but then it rapidly wiggles away. It is as if it is actively finding an area of no density (I am not exaggerating). Selecting 'Refine Tree' does not resolve the problem. I've tried manually moving the xylose close enough, but this is not working well. It just refines away in Phenix Refine. For refinement, I used ReadySet to generate the restraints (apparently the XYP-BMA XYP does not have restraints in the standard library - is that correct?) This is a big enough problem, I am hoping I am just doing something 'big' that is wrong. I'm assuming (perhaps) it is a library problem. I would appreciate any suggestions. Software details: On Windows, WinCoot 0.8.9 On Mac, Phenix version 1.13-29998-000 (Coot is version 0.8.9) I model build in WinCoot, refine with Phenix on the Mac Regards, Marilyn ___________________________________________________________ Marilyn Yoder | 816-235-1986 | SCB 526 | Division of Cell Biology & Biophysics, University of Missouri-Kansas City ________________________________ To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1<https://urldefense.proofpoint.com/v2/url?u=https-3A__www.jiscmail.ac.uk_cgi-2Dbin_webadmin-3FSUBED1-3DCCP4BB-26A-3D1&d=DwMFAg&c=Dbf9zoswcQ-CRvvI7VX5j3HvibIuT3ZiarcKl5qtMPo&r=HK-CY_tL8CLLA93vdywyu3qI70R4H8oHzZyRHMQu1AQ&m=RHHMDLf2fwi7dZ4a8QlLAthByGA6anigLDutJl2kNEc&s=_Asy6uo23Y90cq7kVyr8vdELWgK8qH3eZCA75PrDFpQ&e=> ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
