[Chimera-users] Why is molmap changing the grid spacing and origin of simulated map

[Elaine Meng]

Hi Anes,
It may be a bug, but seems like you can avoid the problem by making sure that the map from "vop new" is shown at step 1 before using molmap.

In my tests, the "vop new" result was automatically shown at step 2 and then the molmap result had voxel size 2.  However, if I change the "vop new" map to step 1 before using molmap, the result of molmap has voxel size 1.

You could change the map to step 1 "manually" in the Volume Viewer, or use this command:

volume #1 step #1

Then at least in my tests, the molmap result will have voxel size 1.  When it has voxel size 2, it still has the same origin location, but the origin index (not the same thing) is different.  Origin index is explained here:
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/volumeviewer/volumeviewer.html#coordinates>

I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Sep 1, 2020, at 4:54 PM, Ouadou, Anes (MU-Student) <aomqc at mail.missouri.edu> wrote:
> 
> Hello,
> 
> I am using molmap to simulate cryo-em density maps from protein pdb file. I follow the two steps outlined in Chimera tutorial (http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/molmap.html#onGrid). 
> I first create an empty map with specific size, grid spacing, and origin. 
> vop new #1 size 116,96,152 gridspacing 1 origin -99.0,-39.0,-58.0
> Then simulate the pdb file on the empty map using the option the grid spacing 
> molmap #0 3 onGrid #1
> the resulting simulated map has grid spacing changed from 1A to 2A and the origin coordinates are also changed to half the values I provided. This does not happen with all cases. The following commands work perfectly and generate a simulated map with grid spacing of 1A
>  
> vop new #1 size 78,88,121 gridspacing 1 origin -32.73,-28.64,-63.42
> molmap #0 3 onGrid #1 
> 
> I can re-sample the map to obtain 1A grid spacing, but it adds extra work (I doing this to 100s of examples) and seems to affect the resolution of the simulated map.
> 
> Could you please adive me to why is this phenomenon is happening and how to solve it.
> 
> best regards 
> 
> Anes Ouadou    
> CS PhD Student    
> University of Missouri-Columbia
> aomqc at mail.missouri.edu    
> Mobile: (573 )-289-9073