The usual way in the classic xplor language is with the constraints fix statement:
constraints fix (segid B) end is all that's necessary. --JK On Jul 27, 2006, at 10:30 PM, wzhang14 wrote: > Dear John: > > Thank you very much! > The "NCS" term is no zeo now. while I have another related > question: Since the > reference structure need to be fixed for the NCS restraint, I used > harm to > restraint all the atoms of segB. while I had a feeling that it may > not be the > correct way. Could you give some suggestion on that? > Thanks a lot! > > Wei > >> ===== Original Message From John Kuszewski <[email protected]> ===== >> Hi Wei, >> >> Did your script include those curly braces? That's one way to define >> a comment in the >> classic xplor language. >> >> In addition, your atom selections probably don't select what you >> intended. If you were trying >> to select the backbone heavyatoms of all those residues, you need to >> have parentheses >> around the entire "resid or resid" section. That is, something like >> >> (segid A and (resid 3:7 or resid 12:33 or resid 46:54 ...) and (name >> ca or name c or name n)) >> >> The selections you gave will select all atoms from residues 3-7, >> 12-33, etc., and only the backbone >> atoms from residues 86-103. >> >> Please let us know if these changes don't solve the problem! >> >> --JK >> >> On Jul 27, 2006, at 7:01 PM, wzhang14 wrote: >> >>> Dear all: >>> >>> I am trying to use the 'NCS' restraint during my structure >>> refinement. I have >>> read charles's reply to Haydyn on the similiar question. so I built >>> the >>> topology as a dimer and generate the coordinates (pdb) as dimer too >>> and >>> provided segid A snd B , respectively. To refine only segid A, I >>> added segid >>> A to all the restraint files such as dihedral and sani. But the >>> output NCS >>> energy term was always zero. >>> I have been struggling for quit a while, any suggestion will be >>> highly >>> appreciated! >>> >>> Please refer to the ncs restrait part of my script below: >>> >>> >>> >>> { ncs restraints >>> initialize >>> group >>> equi ( segid A and (resid 3:7 or resid 12:33 or resid 46:54 >>> or resid >>> 68:72 >>> or resid 77:79 or resid 86:103 and ( name c or name n or >>> name ca))) >>> equi ( segid B and (resid 3:7 or resid 12:33 or resid 46:54 >>> or resid >>> 68:72 >>> or resid 77:79 or resid 86:103 and ( name c or name n or >>> name ca))) >>> weight=300. >>> end >>> >>> ? >>> end >>> } >>> >>> flags include ncs enid >>> >>> >>> Wei Zhang >>> BCMB >>> University of Tennessee >>> >>> >>> _______________________________________________ >>> Xplor-nih mailing list >>> [email protected] >>> http://dcb.cit.nih.gov/mailman/listinfo/xplor-nih >
