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<p class="x_MsoNormal">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.</p>
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<div id="x_divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" color="#000000" style="font-size:11pt"><b>From:</b> Elaine Meng <meng@cgl.ucsf.edu><br>
<b>Sent:</b> Tuesday, July 16, 2019 12:40:07 PM<br>
<b>To:</b> Ryan Harlich<br>
<b>Cc:</b> chimera-users@cgl.ucsf.edu BB<br>
<b>Subject:</b> Re: [Chimera-users] Finding dimensions of density map</font>
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<div class="PlainText">Hi Ryan,<br>
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.<br>
<br>
Click Help on dialogs when you are using them and you get an error, before asking on the list.<br>
Best,<br>
Elaine<br>
<br>
> On Jul 16, 2019, at 11:55 AM, Ryan Harlich <ryanharlich@hotmail.com> wrote:<br>
> <br>
> Hi Elaine,<br>
> <br>
> 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.<br>
> <br>
> Best,<br>
> Ryan Harlich<br>
> <br>
> Sent from Mail for Windows 10<br>
> <br>
> From: Elaine Meng <meng@cgl.ucsf.edu><br>
> Sent: Thursday, July 11, 2019 12:49:19 PM<br>
> To: Ryan Harlich<br>
> Cc: chimera-users@cgl.ucsf.edu<br>
> Subject: Re: [Chimera-users] Finding dimensions of density map<br>
> <br>
> Hi Ryan,<br>
> 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.<br>
> <br>
> <<a href="https://nam02.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.rbvi.ucsf.edu%2Fchimera%2Fdocs%2FContributedSoftware%2Fvolumeviewer%2Fframevolumeviewer.html&data=02%7C01%7C%7C942088a546f1469916f408d70a25690e%7C84df9e7fe9f640afb435aaaaaaaaaaaa%7C1%7C0%7C636989028123002384&sdata=mBl1i29nupLseHehVLHIZXq6s9bOIbolpz7vN3O06Pg%3D&reserved=0">https://nam02.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.rbvi.ucsf.edu%2Fchimera%2Fdocs%2FContributedSoftware%2Fvolumeviewer%2Fframevolumeviewer.html&data=02%7C01%7C%7C942088a546f1469916f408d70a25690e%7C84df9e7fe9f640afb435aaaaaaaaaaaa%7C1%7C0%7C636989028123002384&sdata=mBl1i29nupLseHehVLHIZXq6s9bOIbolpz7vN3O06Pg%3D&reserved=0</a>><br>
> <<a href="https://nam02.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.rbvi.ucsf.edu%2Fchimera%2Fdocs%2FContributedSoftware%2Fvolumeviewer%2Fvolumeviewer.html%23coordinates&data=02%7C01%7C%7C942088a546f1469916f408d70a25690e%7C84df9e7fe9f640afb435aaaaaaaaaaaa%7C1%7C0%7C636989028123002384&sdata=KjazTdLtJitxTNVADDbu2guA6DoBP%2BuZG7Wxgrc7G%2B4%3D&reserved=0">https://nam02.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.rbvi.ucsf.edu%2Fchimera%2Fdocs%2FContributedSoftware%2Fvolumeviewer%2Fvolumeviewer.html%23coordinates&data=02%7C01%7C%7C942088a546f1469916f408d70a25690e%7C84df9e7fe9f640afb435aaaaaaaaaaaa%7C1%7C0%7C636989028123002384&sdata=KjazTdLtJitxTNVADDbu2guA6DoBP%2BuZG7Wxgrc7G%2B4%3D&reserved=0</a>><br>
> <br>
> 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:<br>
> <br>
> meshmol #4 1<br>
> <br>
> <<a href="https://nam02.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.rbvi.ucsf.edu%2Fchimera%2Fdocs%2FUsersGuide%2Fmidas%2Fmeshmol.html&data=02%7C01%7C%7C942088a546f1469916f408d70a25690e%7C84df9e7fe9f640afb435aaaaaaaaaaaa%7C1%7C0%7C636989028123002384&sdata=EdHtA6SACMhpm7nj5lyXWZPa3J77BNOoKEG8QjLVLqc%3D&reserved=0">https://nam02.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.rbvi.ucsf.edu%2Fchimera%2Fdocs%2FUsersGuide%2Fmidas%2Fmeshmol.html&data=02%7C01%7C%7C942088a546f1469916f408d70a25690e%7C84df9e7fe9f640afb435aaaaaaaaaaaa%7C1%7C0%7C636989028123002384&sdata=EdHtA6SACMhpm7nj5lyXWZPa3J77BNOoKEG8QjLVLqc%3D&reserved=0</a>><br>
> <br>
> then,<br>
> … Ctrl-click on one corner of box to select atom, press up arrow one time to promote to whole box<br>
> ...use “write” command or File… Save PDB with their respective option to save only the selected part<br>
> <br>
> I hope this helps,<br>
> Chimera ;-)<br>
> -----<br>
> Elaine C. Meng, Ph.D.<br>
> UCSF Chimera(X) team<br>
> Department of Pharmaceutical Chemistry<br>
> University of California, San Francisco<br>
> <br>
> > On Jul 11, 2019, at 10:57 AM, Ryan Harlich <ryanharlich@hotmail.com> wrote:<br>
> > <br>
> > Hi Chimera,<br>
> > <br>
> > 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?<br>
> > <br>
> > Best,<br>
> > Ryan Harlich<br>
> <br>
> _______________________________________________<br>
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