Hello, Thinking that more is better I ended up with Delphi potential maps on a rather large grid which I would like to visualize with chimera (gsize=213) Chimera seems to think the grid is to large. Is there an easy way to have chimera accept bigger grids (speed is not really an issue)? Alternatively, what is the largest grid that chimera can accept? Thanks for your help. Klaas Decanniere
Hi Klaas, The size of the Delphi potential map Chimera can display is only limited by the size of your computer memory. If you open a large map it does not get shown immediately if the map is larger than 1 Mvoxels (~100^3). This is controlled by an option under the Volume Viewer options pane "Show data when opened if smaller than XXX Mvoxels". If you open a large data set, you need to press the Show button at the bottom of the Volume Viewer dialog to display it. This is intended to allow you to adjust the bounds to show a subregion and avoid loading the whole map. This setting can be changed to specify a larger volume limit, or always show the data immediately when opened. When you press Show to display the large map, it will show a subsampled version, for example skipping every other plane along each axis. This is indicated in the "Step" menu near the top of the Volume Viewer dialog. The automatic subsampling happens because of another Volume Viewer / Options setting "Adjust step to show at most XXX MVoxels". The default setting is to subsample for data sets larger than 2 MVoxels. You can change the step to not do subsampling using the Step menu (set it to "1 1 1"). You can turn off the automatic subsampling option or increase the volume size limit. Delphi grid values are 4 byte floats, so a 213^3 map will take about 38 Mb (213^3 * 4), plus some additional memory will be used to make a surface representation. I've worked with 256^3 maps with no problem. Probably the practical limit is around 512^3 for a machine with a gigabyte of memory. Tom
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Klaas Decanniere -
Thomas Goddard