Try using phenix, which is the successor to CNS. phenix.refine foo.mtz bar.pdb
and Bob's your uncle. http://www.phenix-online.org/ jean wrote: > Thank you all for your suggestions. Unfortunately I am still stuck with > the > segmentation fault problem. > > > > The swap partition is mounted fine. > > Setting max_chains to a lower number does nothing. > > There's nothing wrong with my selection criteria (0 atoms were selected as > rigid groups, 36 for annealing) > > > > I tried systematically deleting parts of the pdb input file, then > rerunning > generate.inp and then anneal.inp. That worked fine for my ligand alone > (as > I understand it, given the right toppar inputs, CNS should be able to run > torsion dynamics on my ligand - am I right?), but the protein component > caused failure again. I can't spot a problem by looking so I'm at a bit > of > a loss. > > > > Any more ideas? > > > > Sincerely > > Jean > > > > _____ > > From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of jean > Sent: 11 May 2007 12:45 > To: CCP4BB@JISCMAIL.AC.UK > Subject: [ccp4bb] CNS problem: anneal.inp segmentation fault > > > > Hi all > > > > Apologies for the non-ccp4 question - hopefully some of you who use CNS > can > help me - I have a problem with anneal.inp in CNS: > > > > When I run the anneal script for my structure containing novel ligand, the > program fails before the start of the torsion dynamics with no error > message > - except SEGMENTATION FAULT at the bash commandline. > > > > With "quiet" output, the last lines in the output file are: > > > > ASSFIL: file /usr/local/CNS/cns_solve_1.1/libraries/toppar/torsionmdmods > opened. > > MESSage=NORM > > EVALUATE: symbol $MESSAGE_OLD_TMOD set to "NORM" (string) > > ECHO=FALSe {OFF} > > EVALUATE: symbol $ECHO_OLD_TMOD set to FALSE (logical) > > NEXTCD: condition evaluated as false > > Program version= 1.1 File version= 1.1 > > SELRPN: 0 atoms have been selected out of 4883 > > > > so the torsionmods routine (and everything before it) ran fine but the > torsion dynamics never started. > > > > My pdb, mtf, top and par files all work fine for minimization so I don't > think there's anything wrong with them. > > > > I have been using CNSv1.1 on this Linux machine for some time so it's not > a > compile problem. > > > > I can run the same routine on the same PC, from the same script, with the > same protein but with a different ligand and there's no fault. > > > > Can anyone suggest a solution? I've tried just about everything short of > running the whole script manually from the command line! > > > > Sincerely > > Jean Watermeyer > > > > > >
