[Chimera-users] Question on pdb to mrc

Fri Jan 14 11:47:09 PST 2022

Hi Moritz,

Thank you very much for your clear explanation. I will test it.
Best,
Lan 

> On Jan 14, 2022, at 11:15 AM, Hunkeler, Moritz <Moritz_Hunkeler at DFCI.HARVARD.EDU> wrote:
> 
> CAUTION: This email originated from outside of TTUHSC. Do not click links or open attachments unless you recognize the sender and know the content is safe.
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> 
> 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://urldefense.com/v3/__https://secure-web.cisco.com/1KJjTOB77GWUzY9zlH7PpX2YLGhys6wx2jmGdM7D5Us17SXRMg1GbcAd6V3CaCCBXtkgM-viJv8e1YzaZJfTDI8NXqylfQXYc_wOlCm9NLaTKFJmi4K0hq2rqQu4Ei520WdYr1V55zO6vdby1tbSca87F7XQenjdzegmxE3KK4iXHZAzPh_whMMvOpuGDb0F1apP67hYSkVnAs8kyB7znynVdSbGFB58wNloEdBkRvmAY9ajNQn8VmQbRunfhbnRFry3kZ0vbXGkDLQjLzGXN6ykaxF3FcuXNC93K91qCNN4P3tBybBYFQrYVf8UzuZdZr_YeA1AWys1McKm7S8Kd7w/https*3A*2F*2Fwww.rbvi.ucsf.edu*2Fchimera*2Fdocs*2FUsersGuide*2Fsavemodel.html__;JSUlJSUlJQ!!PZU9J6Y!K_VLgCBEcgMcDvnIbj2PkLnCllVTUQ61fyLtfdEli6Om9VJz6Gi3TY8mRn31jxhtmQ$ >
> 
>    Volume Viewer menu (File... Save map as...)
>    <https://urldefense.com/v3/__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__;JSUlJSUlJSUl!!PZU9J6Y!K_VLgCBEcgMcDvnIbj2PkLnCllVTUQ61fyLtfdEli6Om9VJz6Gi3TY8mRn1DvQ08ww$ >
> 
>    volume command saving options
>    <https://urldefense.com/v3/__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__;JSUlJSUlJSUl!!PZU9J6Y!K_VLgCBEcgMcDvnIbj2PkLnCllVTUQ61fyLtfdEli6Om9VJz6Gi3TY8mRn07LXKh3Q$ >
> 
>    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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