I have seen these type of cases. They cause problem. They may come from O, from cns or other programs. Origins may even not be known. My solution was that if an atom has coordinates 9998.000 or more then consider them absent (i.e. set occupancies 0).
On 6 Sep 2011, at 14:30, Kevin Cowtan wrote: > OK, here's the solution (also to BB in case anyone else has this problem). > > The PDB file appears to come from CNS. > > The coordinate file contains the following atoms: > > ATOM 2244 CG LEU A 452 9999.0009999.0009999.000 1.00 0.00 A > ATOM 2245 CD1 LEU A 452 9999.0009999.0009999.000 1.00 0.00 A > ATOM 2246 CD2 LEU A 452 9999.0009999.0009999.000 1.00 0.00 A > > These coordinates are no doubt dummy values of some sort. But, interpreted as > coordinates, they are so far from the rest of the model that attempting to > build a mask around them and the rest of the model would take a vast file. > > The PDB file header contains the following lines generated by CNS: > > REMARK unknown coordinates for atom: A LEU 452 CG > REMARK unknown coordinates for atom: A LEU 452 CD1 > REMARK unknown coordinates for atom: A LEU 452 CD2 > > That suggests to me that the problem may have been with the file input to > CNS. You'd have to look at your input file to work out exactly what is going > on. In the meantime, deleting these atoms or autofitting the sidechain in > coot ought to fix it. > > Hope that solves it, > Kevin > > On 09/06/2011 09:56 AM, Ingo P. Korndoerfer wrote: >> hello, >> >> it seems i am recently getting the above error quite a lot in mapmask. i >> have searched for a solution, but only found the problem mentioned a >> few times with no precise solution indicated. >> >> would there be a way to find out HOW MUCH memory mapmask is hoping for ? >> >> i do have 2 Gb of memory and 3 Gb of swap, and "limit" says >> >> cputime unlimited >> filesize unlimited >> datasize unlimited >> stacksize 8192 kbytes >> coredumpsize 0 kbytes >> memoryuse unlimited >> vmemoryuse unlimited >> descriptors 1024 >> memorylocked 64 kbytes >> maxproc unlimited >> >> mapmask itself dies in the middle of running and without error message >> to its log file. >> >> thanks >> >> ingo Garib N Murshudov Structural Studies Division MRC Laboratory of Molecular Biology Hills Road Cambridge CB2 0QH UK Email: ga...@mrc-lmb.cam.ac.uk Web http://www.mrc-lmb.cam.ac.uk
