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@cgl.ucsf.edu on behalf of chimera-users@cgl.ucsf.edu> wrote: External Email - Use Caution > On Jan 13, 2022, at 6:54 PM, Guan, Lan <Lan.Guan@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@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/1KJjTOB77GWUzY9zlH7PpX2YLGhys6wx2jmGdM7D5Us17SX...> Volume Viewer menu (File... Save map as...) <https://secure-web.cisco.com/195-UqlXEMFgrzMzBW4pMP1_mR4i3JzB5ylhYEs4cvaWxFs...> volume command saving options <https://secure-web.cisco.com/1y0YoGmG4T1KD2SazJJjmZtxSGfFHz-zELLPHf_Jc_0ZDTR...> 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 _______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: https://secure-web.cisco.com/1eZ9aLpAeG93V-SSigPjVMUDDVhudZ3Mtn3qSex9jcJh14b... The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at http://www.massgeneralbrigham.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.