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

Elaine Meng meng at cgl.ucsf.edu
Thu May 26 08:56:16 PDT 2016

Dear Ardan,
There is an “edgePadding” option in “molmap” but it is relative to the bounding box of the atoms, so you would not necessarily get a cube or easily obtain a specific set of dimensions.

Instead, after using molmap, maybe you could use “vop resample” on the molmap result to make another map resampled on the grid of the comparison map.

It would not be centered, however, unless you had already centered the atoms or their resulting molmap relative to the comparison map.

I hope this helps,
Elaine C. Meng, Ph.D. 
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On May 26, 2016, at 12:43 AM, Ardan Patwardhan <ardan at ebi.ac.uk> wrote:
> 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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