[Chimera-users] Question on pdb to mrc

[Hunkeler, Moritz]

Hi,

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.


Best,
Moritz




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:
    <https://secure-web.cisco.com/1KJjTOB77GWUzY9zlH7PpX2YLGhys6wx2jmGdM7D5Us17SXRMg1GbcAd6V3CaCCBXtkgM-viJv8e1YzaZJfTDI8NXqylfQXYc_wOlCm9NLaTKFJmi4K0hq2rqQu4Ei520WdYr1V55zO6vdby1tbSca87F7XQenjdzegmxE3KK4iXHZAzPh_whMMvOpuGDb0F1apP67hYSkVnAs8kyB7znynVdSbGFB58wNloEdBkRvmAY9ajNQn8VmQbRunfhbnRFry3kZ0vbXGkDLQjLzGXN6ykaxF3FcuXNC93K91qCNN4P3tBybBYFQrYVf8UzuZdZr_YeA1AWys1McKm7S8Kd7w/https%3A%2F%2Fwww.rbvi.ucsf.edu%2Fchimera%2Fdocs%2FUsersGuide%2Fsavemodel.html>

    Volume Viewer menu (File... Save map as...)
    <https://secure-web.cisco.com/195-UqlXEMFgrzMzBW4pMP1_mR4i3JzB5ylhYEs4cvaWxFsHVjTndTlE_Zjjb5MaKY9Z1zkemjJCFMI0xwzjn_El34y5WIyK35Bin72nYdXE1Fy_tLm0Ozd3OQf8nhvBl9-CqALd0dQ1wQQwOA5y_KaVzbdwVgQgJGEjp3SRriu9iFAhiVSR91ilwiG-5gpnwEOGyQhe5axo44YclTZrU6YlQFdJZ1r6yo2jwQt4YJDC9_agqdWlwqH1WvfCNY4q_J2Cw1Yeq_kBeXF0Pd0wPCDemwXPhV3jY-_GtzV9JYGNeGay2SIg3ZIlwScPvwDSUKtRxyd436QFsxDTM4J0Ryw/https%3A%2F%2Fwww.rbvi.ucsf.edu%2Fchimera%2Fdocs%2FContributedSoftware%2Fvolumeviewer%2Fvolumeviewer.html%23organization>

    volume command saving options
    <https://secure-web.cisco.com/1y0YoGmG4T1KD2SazJJjmZtxSGfFHz-zELLPHf_Jc_0ZDTR6OWNmUnAP9FSZMaskbHF0t_d5peQgEl7LNMqjNgdDaf78fDyjmJIsY89x4dGh0SChc7geQtgO6nudgnUkH74878wZh6XZicrSZ_2IAuQUQn_n_NG5PdoQcFH1Bgh6YapjjpJjxmXg01MXoorMEOFDGWPfAxixIIx6RmGAQg7dsLo_kUOzeUrG2uhjxwC7czHqsuGsT8ww_uOCezIZMt4Mvt6jURWW6iHc90TxFBuzYdCnOrazCV2W8Rs7KH1jvZxX30-6gS_0OlrgZOFEZ-DEuME-nTLBsazXmckc8FA/https%3A%2F%2Fwww.rbvi.ucsf.edu%2Fchimera%2Fdocs%2FUsersGuide%2Fmidas%2Fvolume.html%23output>

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



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