Chimera memory management

Hi, I am currently working on few datasets that exceeds the given memory limit for chimera. The log file indicates: MemoryError: can't allocate memory for array How can I increase the memory for chimera? Any suggestion regarding chimera´s memory management would be appreciated. Thanks a lot, Mike -- Lust, ein paar Euro nebenbei zu verdienen? Ohne Kosten, ohne Risiko! Satte Provisionen für GMX Partner: http://www.gmx.net/de/go/partner

Hi Mike, Are you running out of memory loading molecular models (PDB files) or volume data? If volume data, what file format? How much memory does your machine have? What operating system are you running (Windows, Mac, Linux)? I guess from your error message you are reading volume data. Chimera will by default read in the entire volume. If you look at the file size you can see how big that is. In versions of Chimera older than 1.2143 (June 25, 2005) two copies of the volume were in memory when reading the file. The more recent versions only put one copy in memory. If the file is simply too big to read the whole thing in then you can change some settings in the Volume Viewer dialog and read in only part of the data set. For some file formats this will not help because the whole data set is read in even if only a piece of the data is requested (eg. DSN6, Delphi, XPLOR). Other formats will read only the part of the data you request (eg. MRC / CCP4). In Chimera 1.2184 or newer use menu entry Tools / Volume Data / Volume Viewer and then use volume dialog menu entry Features / Data Display Options This shows a setting in the volume dialog that says "Show data when opened if smaller than 256 Mvoxels". Change the 256 to a smaller number so that your file does not get immediately read when opened, or click off the switch so no volume data will be read immediately on opening. Then open your volume data with Chimera menu entry File / Open.... The data will not be shown. Use volume dialog menu entry Features / Region bounds You will see in the volume dialog a line like Region min max step x 0 255 1 y 0 255 1 z 0 255 1 In this example the data set is 256 by 256 by 256. To display just a 128 ^ 3 subblock starting at index 0,0,0 I would change these numbers to: Region min max step x 0 127 1 y 0 127 1 z 0 127 1 Then press the volume dialog Show button. These features are described in the Chimera User's Guide under the Tools section, under Volume Viewer. You can press the Help button on the volume dialog to see that documentation. Tom
participants (2)
-
lutetium@gmx.net
-
Thomas Goddard