[Chimera-users] Question on pdb to mrc

Tom Goddard goddard at sonic.net
Fri Jan 14 14:10:37 PST 2022 

Hi Lan,

Here is another way to get the cube shaped map for a PDB from Chimera saved on the desktop as cube.mrc:

	open 7b9u
	molmap #0 6 gridSpacing 1.23 edgePad 20
	volume #0 region 0,4,3,74,78,77 save ~/Desktop/cube.mrc

I set the grid size to 1.23 Angstroms in the molmap command and the resolution to 6 Angstroms.  This gave a map of size 75 by 83 by 81 grid points because molmap just adds some padding to the bounds of the molecule and it of course is not cube shaped.  I told it in the molmap command to add 20 Angstroms of padding.  Then I simply cropped the resulting map to be 75 by 75 by 75 grid points with the volume command and saved the result to an MRC file.  The region option specifies xmin,ymin,zmin,xmax,ymax,zmax grid indices (starting at 0), so I just trimmed the y and z axes (from both ends symmetrically) so they had only 75 grid points.

	Tom


> On Jan 14, 2022, at 11:47 AM, Guan, Lan via Chimera-users <chimera-users at cgl.ucsf.edu> wrote:
> 
> 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 <mailto: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.
>> 
>> 
>> 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$ <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$> >
>> 
>>   Volume Viewer menu (File... Save map as...)
>>   <https://urldefense.com/v3/__https://secure-web.cisco.com/195-UqlXEMFgrzMzBW4pMP1_mR4i3JzB5ylhYEs4cvaWxFsHVjTndTlE_Zjjb5MaKY9Z1zkemjJCFMI0xwzjn_El34y5WIyK35Bin72nYdXE1Fy_tLm0Ozd3OQf8nhvBl9-CqALd0dQ1wQQwOA5y_KaVzbdwVgQgJGEjp3SRriu9iFAhiVSR91ilwiG-5gpnwEOGyQhe5axo44YclTZrU6YlQFdJZ1r6yo2jwQt4YJDC9_agqdWlwqH1WvfCNY4q_J2Cw1Yeq_kBeXF0Pd0wPCDemwXPhV3jY-_GtzV9JYGNeGay2SIg3ZIlwScPvwDSUKtRxyd436QFsxDTM4J0Ryw/https*3A*2F*2Fwww.rbvi.ucsf.edu*2Fchimera*2Fdocs*2FContributedSoftware*2Fvolumeviewer*2Fvolumeviewer.html*23organization__;JSUlJSUlJSUl!!PZU9J6Y!K_VLgCBEcgMcDvnIbj2PkLnCllVTUQ61fyLtfdEli6Om9VJz6Gi3TY8mRn1DvQ08ww$ <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$> >
>> 
>>   volume command saving options
>>   <https://urldefense.com/v3/__https://secure-web.cisco.com/1y0YoGmG4T1KD2SazJJjmZtxSGfFHz-zELLPHf_Jc_0ZDTR6OWNmUnAP9FSZMaskbHF0t_d5peQgEl7LNMqjNgdDaf78fDyjmJIsY89x4dGh0SChc7geQtgO6nudgnUkH74878wZh6XZicrSZ_2IAuQUQn_n_NG5PdoQcFH1Bgh6YapjjpJjxmXg01MXoorMEOFDGWPfAxixIIx6RmGAQg7dsLo_kUOzeUrG2uhjxwC7czHqsuGsT8ww_uOCezIZMt4Mvt6jURWW6iHc90TxFBuzYdCnOrazCV2W8Rs7KH1jvZxX30-6gS_0OlrgZOFEZ-DEuME-nTLBsazXmckc8FA/https*3A*2F*2Fwww.rbvi.ucsf.edu*2Fchimera*2Fdocs*2FUsersGuide*2Fmidas*2Fvolume.html*23output__;JSUlJSUlJSUl!!PZU9J6Y!K_VLgCBEcgMcDvnIbj2PkLnCllVTUQ61fyLtfdEli6Om9VJz6Gi3TY8mRn07LXKh3Q$ <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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