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
