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Re: [ccp4bb] Sketcher and stereochemistry |
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CCP4bb navigationCCP4bb <-- 2007 <-- March 2007 <-- 19 March 2007Subject: Re: Sketcher and stereochemistry From: Garib Murshudov garib {- at -} YSBL {- dot -} YORK {- dot -} AC {- dot -} UK Date: 2007-03-19 strings. You can of course put atoms by their priorities then you will have correspondence to R/S assignments. However you do not have to do it. In many case I find it useful to put chirality 'both' and then refine against this dictionary. This way you can handle severla stereoisomers (configurations) with the same dictionary. Regards Garib On 20 Mar 2007, at 00:49, Vu Thai wrote: > thanks for the link. I had already seen it and was using it to > assign my > chirality. I guess I should clarify my question. In sketcher, > does one > input the highest priority neighbor first, then the second, and > finally the > third? The sketcher GUI has three columns list: B/3, F/4, & 1/5. > Do these > columns have any significance? > > Vu > > On Mon, 19 Mar 2007 15:35:43 -0700, Dale Tronrud > > wrote: > >> Garib has documentation on his website that I presume matches >> what is >> required by sketcher. It can be found at >> >> http://www.ysbl.york.ac.uk/~garib/refmac/docs/theory/chiral.html >> >> (I did a Google of "ccp4 chiral" to find it.) >> >> Dale Tronrud >> >> Vu Thai wrote: >>> Hi All, >>> >>> I was wondering how to properly define the stereochemistry for a >>> new ligand >>> in sketcher. In the sketcher interface there are three columns >>> after the >>> stereochem sign option. I would assume that the order in which >>> you enter >>> the chiral neighbors would effect the sign that you choose for your >>> stereochemistry. Does any one know how sketcher reads these >>> three columns >>> to determine the stereochemsitry? >>> >>> Thanks in advance for your help. >>> Cheers, >>> Vu > > CCP4bb navigationCCP4bb <-- 2007 <-- March 2007 <-- 19 March 2007 |
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