[Chimera-users] Creating maps from models for map/model FSC calculations

Ardan Patwardhan ardan at ebi.ac.uk
Thu May 26 00:43:31 PDT 2016

Dear all

We are using Chimera to align PDB models to maps, then creating maps from the models using the following command (as an example):
molmap #0 5 gridSpacing 1.3

This should create a map with the voxel spacing of 1.3A and a gaussian atom spread function with the width related to 5A resolution (https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/molmap.html).

Our problem is
a) the map that is created can have an arbitrary size - we need it to be cubic and have the same (known) dimensions as the second map against which it will be compared
b) we have tried padding it in other programs like bsoft but then we sometimes run into problems of centring the model.

I was wondering if there was a way to get a centred map of a certain size from a model directly from Chimera?
Perhaps there are certain parameters that can be used in molmap?

You thoughts and advice on this issue are much appreciated!

Many thanks and best wishes

Ardan Patwardhan
Coordinator - cellular structure & PDBe production
Protein Data Bank in Europe (PDBe)
European Bioinformatics Institute (EMBL-EBI) European Molecular Biology Laboratory
Wellcome Trust Genome Campus
Hinxton, Cambridge CB10 1SD
Tel: +44 1223 492649

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