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Re: [ccp4bb] monomer library in refmac5 |
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CCP4bb navigationCCP4bb <-- 2007 <-- March 2007 <-- 01 March 2007Subject: Re: monomer library in refmac5 From: zhu5 {- at -} PURDUE {- dot -} EDU Date: 2007-03-01 acetyl-D-glucosamine, even the description says it is N-acetyl-D- glucose. After I pulled out the structure from the cif file, I found it is actually the structure I am looking for but with a wrong name. So I guess if you can correct the name in this monomer, everything will be fine. Thanks. Jianghai On Mar 1, 2007, at 9:19 AM, Garib Murshudov wrote: > Dear Jianghai > > I will add it to library but meanwhile you can create your own > sugar and use it in refinement as external library (if you use > script it is done using libin > is a field in the ccp4i for user library) > > Garib > > On 1 Mar 2007, at 14:07, Jianghai Zhu wrote: > >> Dear Garib, >> >> NBG is 1-N-acetly-beta-D-glucosamine. However, the sugar >> connected to a glycosylation site is actually 2-N-acetyl-D- >> glucoamine, which is normally referred as N-acetyl-D-glucoamine >> (NAG). The N is connected to C2, not C1, and C1 is actually >> connected to ND2 of ASN to form a glycosylation bond. You can get >> the high-res structure from HIC-UP and compare them. I would >> strongly suggest to add NAG to the monomer library since it is >> probably the most common sugar you can find at a glycosylation site. >> >> I think I know why refmac5 didn't take my library. Because of the >> glycosylation bond between ASN ND2 and NAG C1, and the bonds >> between NAG C1 and NAG O6 (if there are more than 1 NAG), the O1 >> of NAG is always missing. So the sugar in the structure is always >> incomplete comparing to the provided library and refmac5 will try >> to pull the description from its own monomer library even the >> "make check none" keyword is provided. My questions is how I can >> get refmac5 to use my library in this situation. I even tried to >> use another unique name for N-acetyl-D-glucosamine and it didn't >> work since the sugar structure is always not complete and refmac5 >> always pulled out the description for N-acetyl-D-glucose from the >> monomer library. >> >> If I have to wait until you add NAG to the monomer library, could >> you please do it asap? Thank you very much. >> >> Jianghai >> >> >> >> On Mar 1, 2007, at 8:06 AM, Garib Murshudov wrote: >> >>> Have you looked at NBG it seems to be N-acetyl-beta-D-glucosamine >>> >>> Garib >>> >>> On 28 Feb 2007, at 23:13, Jianghai Zhu wrote: >>> >>>> Dear Dr. Murshudov, >>>> >>>> I have some N-acetyl-glucosamine (NAG) in my structure. When I >>>> searched the monomer library in CCP4 6.0.2, I found out that NAG >>>> is actually N-acetyl-glucose, which is much less common, I >>>> believe. I downloaded the high-resolution structure of N-acetyl- >>>> glucosamine from HIC-UP and used sketcher to generate a cif >>>> library. I named the sugar NAG. I read this new cif file into >>>> refmac5 (5.3) and used "make check none" in the refinement. I >>>> thought my library would overwrite the NAG in the monomer >>>> library in CCP4, but refmac5 still use the NAG it found from >>>> the monomer library. Is there anyway to make sure refmac5 will >>>> use my library even there is another one in the monomer library >>>> with the same name? >>>> >>>> Ethan Merritt told me that N-acetyl-glucosamine was in the >>>> monomer library a few versions back. But I could not find it >>>> anywhere. >>>> >>>> Thanks. >>>> >>>> Jianghai >>>> >>>> >>> >> >> > CCP4bb navigationCCP4bb <-- 2007 <-- March 2007 <-- 01 March 2007 |
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