Hi Thomas,

There is a Chimera extension that produces an MRC density map from a PDB file. It is part of the Analysis of Intermediate Resolution Structures (AIRS) toolkit that is distributed with the EM single article reconstruction package EMAN1.

http://ncmi.bcm.tmc.edu/software/AIRS http://blake.bcm.tmc.edu/eman

If you install EMAN and configure Chimera to find the EMAN / Chimera extensions as described here

http://ncmi.bcm.tmc.edu/software/AIRS/doc_html

then there will be a Chimera menu entry Tools / AIRS / PDB to MRC. It allows you to specify a resolution and number of angstroms per pixel for the map.

This is a good bit of work to setup and I plan on including the ability to make a density map from a PDB model directly in Chimera distributions in the future. It will use a Gaussian for each atom. I'll add this to my list of requested Chimera features.

http://www.cgl.ucsf.edu/chimera/plans.html

Thanks for the suggestion.

Tom

Hi Laura, Chimera's PDB support was written with macromolecules in mind and adheres as closely as possible to the PDB standard. This means that it outputs amino and nucleic acid atoms within a residue in the same order that the PDB uses, regardless of original input order. Not much thought was given to the order of "other" residue atoms, and they basically come out in random order -- which is obviously bad in your case. I'm going to open a bug report on this, with you on the recipient so that you will know when the behavior is fixed. Until then, the only way to preserve ordering is to output in some other format, e.g. Mol2, which may or may not be acceptable for what you're doing.

--Eric

Eric Pettersen UCSF Computer Graphics Lab pett@cgl.ucsf.edu http://www.cgl.ucsf.edu