From C.C.Ballard@dl.ac.uk Wed Aug 31 14:28:59 2005 Date: Mon, 22 Aug 2005 09:57:17 +0100 From: Charles Ballard To: Mark Mayer Cc: ccp4@ccp4.ac.uk, garib@ysbl.york.ac.uk Subject: Re: [ccp4]: Alternative conformations Dear Mark, Garib will be able to give the definitive answer when he returns from his holidays. In the mean time, I believe that the "standard" pdb descriptions of alternative conformations should work, possibly augmented by LINK lines where different linking occurs (see refmac manual). THe gotchas include not having characters in the alternative location column of the ATOM line, occupancies not adding to 1.0, and not having CB in the alternative when refining with Hs. What follows is a simple case: ATOM 97 N ARG A 13 18.711 5.080 2.269 1.00 14.62 N ATOM 98 CA ARG A 13 17.412 5.362 2.848 1.00 14.52 C ATOM 99 C ARG A 13 16.763 6.370 1.915 1.00 14.13 C ATOM 100 O ARG A 13 16.941 7.585 2.047 1.00 13.77 O ATOM 101 CB AARG A 13 17.572 5.933 4.256 0.50 15.39 C ATOM 102 CG AARG A 13 16.395 5.691 5.173 0.50 17.28 C ATOM 103 CD AARG A 13 15.131 6.428 4.810 0.50 20.87 C ATOM 104 NE AARG A 13 14.518 7.035 5.997 0.50 22.90 N ATOM 105 CZ AARG A 13 13.902 6.369 6.973 0.50 23.77 C ATOM 106 NH1AARG A 13 13.388 7.041 7.999 0.50 23.25 N ATOM 107 NH2AARG A 13 13.785 5.042 6.939 0.50 25.69 N ATOM 108 CB BARG A 13 17.536 5.910 4.268 0.50 15.37 C ATOM 109 CG BARG A 13 16.222 5.899 5.037 0.50 16.95 C ATOM 110 CD BARG A 13 15.490 7.201 5.046 0.50 21.23 C ATOM 111 NE BARG A 13 16.085 8.163 5.965 0.50 23.02 N ATOM 112 CZ BARG A 13 15.707 8.366 7.226 0.50 23.56 C ATOM 113 NH1BARG A 13 16.328 9.296 7.937 0.50 23.41 N ATOM 114 NH2BARG A 13 14.732 7.654 7.790 0.50 23.86 N Charles Ballard CCP4 On Saturday, August 20, 2005, at 09:55 PM, Mark Mayer wrote: > Hello, > > I've dug around on web but cannot find out how to specify alternative > conformations in a PDB file and then use this for refinement in > refmac5. I'd really appreciate advice since my refinement is stalled > until I figure out how to do this. > > Thanks so much, > > mark > -- > Mark Mayer Ph.D. > LCMN NICHD NIH DHHS > Bldg 35, Room 3B 1002 MSC 3712 > 35 Lincoln Drive > Bethesda MD 20892 3712 > Phone: 301-496-9346 (office); 301-496-9347 (lab); FAX 301-496-2396 > Lab web site: http://mayerlab.nichd.nih.gov > > Send packages, Fedex and anything requiring a signature to: > > Bldg 35, Room 3B 1004 > 35 Lincoln Drive > Bethesda MD 20892 >