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

Ouadou, Anes (MU-Student) aomqc at mail.missouri.edu
Tue Sep 1 16:54:16 PDT 2020


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
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