[Chimera-users] Question on pdb to mrc

Hunkeler, Moritz Moritz_Hunkeler at DFCI.HARVARD.EDU
Fri Jan 14 09:15:57 PST 2022


the reference for cryoSPARC needs to be in a cubic box of X x X x X voxels (X must match the dimensions of the extracted particles and the voxel size should be = pixel size of the particles). After running molmap, the resulting map in chimera is not in a cubic box (but rather in what I assume is the smallest possible box without cutting through the generated density). The easiest ways of getting the reference into the right box (box size & voxel size):

- Resample onto a map that has the right dimensions (maybe from an ab initio run from the same particle set): 'vop resample #x onGrid #y'. (where #x is the map from molmap and #y the map from ab initio). There is a small loss in quality, but you'll anyways low-pass filter the map before using it in refinement.

Alternatively, you could use relion_image_handler to place the density into a cubic box and then change the voxel size.


On 1/14/22, 11:50, "Chimera-users on behalf of Elaine Meng via Chimera-users" <chimera-users-bounces at cgl.ucsf.edu on behalf of chimera-users at cgl.ucsf.edu> wrote:

            External Email - Use Caution        

    > On Jan 13, 2022, at 6:54 PM, Guan, Lan <Lan.Guan at ttuhsc.edu> wrote:
    > Dear Elaine,
    > I try to generate a reference model from crystal structure pdb file for cryo-EM particle alignment.
    > I can get the map by “molmap #1 6”; #1 = my pdb file id; 6 = resolution I want to get in the output model.
    > After imported into cryosparc, I can not use it. Error “ Cubic volumes only”.  My question is how to change this Molmap output into a cubic volumes in Chimera?
    > I would appreciate for your input.
    > Lan

    Hi Lan,
    (CC'ing chimera-users at cgl.ucsf.edu  which is the address recommended for asking questions since others may have better answers)

    I don't know what cryosparc means by "cubic volumes only".  My only guess is that maybe you did not save the molmap map correctly.  The molmap command should make a new model which is the map, and then you can save the map with the Volume Viewer tool's File menu, or with the "volume" command.

    Saving data:

    Volume Viewer menu (File... Save map as...)

    volume command saving options

    Or, maybe cryosparc does not read any of the map formats that Chimera can write (listed in the link above).

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

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