The help button is greyed out. Meshmol is an mrc and you said I could save it as a pdb. I don’t think this is possible. I did what you said. Sent from Mail<https://go.microsoft.com/fwlink/?LinkId=550986> for Windows 10 ________________________________ From: Elaine Meng <meng@cgl.ucsf.edu> Sent: Tuesday, July 16, 2019 12:40:07 PM To: Ryan Harlich Cc: chimera-users@cgl.ucsf.edu BB Subject: Re: [Chimera-users] Finding dimensions of density map Hi Ryan, You did not say what you did. If using the save PDB dialog, you have to choose the model in the dialog as well as the selected-only option if you’ve used the mouse to select only the box part of the model in the window. Click Help on dialogs when you are using them and you get an error, before asking on the list. Best, Elaine
On Jul 16, 2019, at 11:55 AM, Ryan Harlich <ryanharlich@hotmail.com> wrote:
Hi Elaine,
I decided to give the meshmol a try but cannot save. Get error “No models chosen to save” and I have mesh density.mrc (#1) selected.
Best, Ryan Harlich
Sent from Mail for Windows 10
From: Elaine Meng <meng@cgl.ucsf.edu> Sent: Thursday, July 11, 2019 12:49:19 PM To: Ryan Harlich Cc: chimera-users@cgl.ucsf.edu Subject: Re: [Chimera-users] Finding dimensions of density map
Hi Ryan, The “Coordinates” section of Volume Viewer (open from its Features menu) gives values used to convert between the dataset grid and Cartesian coordinates. You’d have to back-calculate from the origin index and voxel size.
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Another approach might be to show the volume outline box and then use the “meshmol” command to make it into a (pseudo)atomic model. That will also make the volume isosurface triangles into atoms, but you can select just the box part and write selected-only as a PDB file. E.g. if the volume model is #4, command:
meshmol #4 1
then, … Ctrl-click on one corner of box to select atom, press up arrow one time to promote to whole box ...use “write” command or File… Save PDB with their respective option to save only the selected part
I hope this helps, Chimera ;-) ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jul 11, 2019, at 10:57 AM, Ryan Harlich <ryanharlich@hotmail.com> wrote:
Hi Chimera,
I want to plot 8 voxels (atoms) in a pdb such that they are the slightly greater than the greatest bounding box of two mrc density maps. In order to do that I need the dimensions of both mrc density maps or there eight greatest corners. How would I go about doing this; that is, getting the 8 corners of the mrc density maps? Is there a command to help this process?
Best, Ryan Harlich
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