CCPALC: not enough memory

From: Ingo P. Korndoerfer
Date: 6 September 2011 09:56
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

----------
From: Kevin Cowtan
Can you send the command script, and mapdump output for any input maps? Also, if you are entering a PDB file, the cell, spacegroup, and an idea of range of X, Y, and Z values?

----------
From: Kevin Cowtan
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

----------
From: Garib N Murshudov

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).

Garib N Murshudov
Structural Studies Division

MRC Laboratory of Molecular Biology

Hills Road 

Cambridge 

CB2 0QH UK
Web http://www.mrc-lmb.cam.ac.uk