[Chimera-users] Cage maker

Tom Goddard goddard at sonic.net
Tue Jun 2 16:32:42 PDT 2015

The Cage Builder cage is just atoms and bonds, so you can use the Chimera molmap command to make a density map from the atoms, for example,

	molmap #1 10

to make a density map from cage model #1 with resolution 10.  Then you can save the map with the Volume Viewer dialog menu File / Save Map As… or with the volume command in MRC format.  There is no save option for spi (Spider) or pif map formats.  The molmap command also only uses the atoms not the bonds, so you cage map won’t look exactly like the cage itself.


> On Jun 1, 2015, at 9:30 AM, Anindito Sen  wrote:
> Dear All,
> Is it possible to generate a synthetic 3d density map of hexagons and/ pentagons using the Cage building  option with file extension like mrc or spi or pif ( the usuals). If so, how to save it in such a format ? 
> Thanks
> Andy
> Sent from my iPad
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