[Chimera-users] multiple volumes' orientation in space

Elaine Meng meng at cgl.ucsf.edu
Mon Apr 22 15:49:53 PDT 2013

Hi Yunji Wu,
I would instead just open the whole PDB structure in Chimera and then use the "molmap" command to generate maps for the respective chains. The maps will retain the relationships of the atomic coordinates.  For example, commands for a simpler case:

open 1zik
molmap :.a&protein 8
molmap :.b&protein 8

The second part of the molmap command specifies which atoms.  In the examples, I specified chain A protein (thus excluding water and anything else that might have the same chain ID) and chain B protein to create two maps.  You can control the coloring of each map in the Volume Viewer dialog, which automatically appears when the maps are created.  The "8" in the examples is resolution, basically how much to smear out atoms when creating the map; you could use some different value depending on how much detail or bumpiness you want.  See the "molmap" documentation for details and additional command options:

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 Apr 20, 2013, at 12:56 PM, Yunji Wu wrote:

> Dear all -- 
> I am a total newb to Chimera, and I have an issue which I feel like can be easily resolved with your help. 
> I am trying to make a 'structure-based schematic' with the purpose of clarifying the locations of the domains of a complicated crystal structure. There are 12 domains in this structure that I want to represent as 'blobs', and they are oriented in space in a very confusing way, especially if represented as the standard ribbons or cartoons. 
> I used pdb2mrc (in EMAN2) to create 25Å maps from my .pdb files for (with the command e2pdb2mrc.py -R 25 H.pdb K.mrc). These show up fine individually in Chimera, but the separate maps are not oriented properly in space. It looks like the map volume files have no instructions about where to be in space relative to the coordinate files that generated them. If I take a single .pdb file with all 4 chains and generate a single .mrc file, I obviously get something that has the chains correctly oriented. 
> This is less useful and satisfying, since I'd like to make separate chains into separate map volumes so I can color them separately (for example: chains H,K,L,M as H.pdb, K.pdb, L.pdb, M.pdb into H.mrc, K.mrc, L.mrc, M.mrc). When these 4 volumes are plotted in Chimera, they appear to be semi-randomly piled in the middle of the viewing field, with no correlation to the original pdb coordinates (attached screenshot of volumes from 4 chains, calculated from 4 individual pdb files). Is this just a result of a preset in Chimera that I am not aware of that needs to be adjusted? If I plot the original pdb file with the 4 chains from which these volumes were generated, there is no spatial correlation between the structure and the volumes. 
> <Screen shot 2013-04-20 at 12.27.59 PM.png>
> In trying to solve this, I know that "Fit to Map" will allow the coordinates to be fit into the map volume, but I cannot seem to fit the separately map to the individual chains, which would be a longer way around the issue. Is there some way to do this, or to just create maps that are oriented properly in space relative to each other? 
> Thank you so much for your help,
> Yunji Wu

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