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On the whole I agree that in dealing with problems at low resolution and/or high R-factor, CNS has its advantages, but my list of plus points would be rather shorter than yours - basically just the torsion angle dynamics / simulated annealing option. In our experience Refmac's radius of convergence is generally better than that of CNS, at least when using conventional co-ordinate based refinement. This seems to be in part related to CNS's tight default stereochemistry which I see as a minus point in the context of initial refinement - as others have pointed out tight restraints are _not_ what you want in the initial stages, they really slow things down and can mean that you don't reach the minimum in finite time. Isn't Refmac's minimisation more aggressive at least in part because it's not slowed down by over-tight restraints (at least if you set the weight correctly)? I'm not sure what you mean by 'ability to use harmonic restraints' - aren't geometric restraints harmonic in all refinement programs? Atomic B-factor refinement in Refmac can be turned off easily with the REFI BREF OVER option, and I can't think of any circumstances where I would want to refine only B factors (after all they're pretty meaningless if the atoms are not in the right positions!). -- Ian > -----Original Message----- > From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On > Behalf Of Anthony Duff > Sent: 06 December 2005 22:33 > To: [email protected]; Qun Wan > Subject: Re: [ccp4bb]: question about alternate residues > > In my opinion... > > CNS seems superior for low resolution structures (resolution > worse than 3A) and early refinement (R worse than 30%). Reasons: > > * good radius of convergence, > * tight default stereochemistry, > * very easy to use with a simple model > * simulated annealing > * ability to refine part only of the model > * ability to use harmonic restraints, > * ability to not refine B-factors, > * ability to only refine B-factors > > Otherwise REFMAC is superior: > > * more aggressive minimisation algorithm. > * very easy to use alternate conformers > * Ongoing development > * excellent community support for when things get tricky > (ccp4bb) > > I suggest that the best transition point is where you need to > model alternate conformers. Once you have your first > alternate conformer, abandon CNS and use REFMAC from that > point forward. > > > Anthony > > > At 08:57 AM 7/12/2005, you wrote: > > > *** For details on how to be removed from this list > visit the *** > *** CCP4 home page http://www.ccp4.ac.uk > <http://www.ccp4.ac.uk /> *** > > > Dear all, > My model (total 354 residues) has 13 residues which > have alternate conformations. when I generate the alternate > conformation with alternate.inp in CNS, the program does not > give me the AC conformers because the atom selection only > allows for 265 letter. However, all these residue selection > will more than 264 strings. Does any one know how to the > alternates in CNS? > > > DEFINE>{========================== atom selection > ===========================} > DEFINE> > DEFINE>{* select atoms to have multiple conformations *} > %COPYST-ERR: ST2MAX too small. Check input file. > Offending string:"{===>} atom_select=((segid > A and residue 12) or (segid A and residue 169) or (segid A > and residue 175) or (segid A and residue 172) or (segid A and > residue 37) or (segid A and residue 222) or (segid A and > residue 126) or (segid A and residue 51) or (segid A and re " > with length= 265 > Max allowed length of string= 264 > > ---------------------------------------------------------------------- > Anthony Duff > Postdoctoral Fellow > School of Molecular and Microbial Biosciences Biochemistry > Building, G08 University of Sydney, NSW 2006 Australia > Phone. 61-2-9351-3907 Fax. 61-2-9351-4726 > ---------------------------------------------------------------------- > > Disclaimer This communication is confidential and may contain privileged information intended solely for the named addressee(s). It may not be used or disclosed except for the purpose for which it has been sent. 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