[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.
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/molmap.html#options>

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.
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/vop.html#resample>

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
----------
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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