Dear Chimera users, I have an EM map and pdb coordinates. I am trying to show density fit of some of my sidechain. I want to display a particular sidechain fitting into the density. I was trying to use zonesel feature: zonesel #0 (reference pdb):2 (residue #2) 3 (cutoff 3A) #1 (EM map) show sel But somehow it did not show the EM density of residue #2, rather the entire map. I am wondering what I did wrong? Best, Yangqi Sent from Mail for Windows 10
Hi Yangqi, To show the density near some atoms, use the zone option in Volume Viewer. Choose "Features… Zone" from the Volume Viewer menu to show the zone options in the dialog, and then with the atoms selected, click Zone to apply the chosen radius value. <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/volumeviewer/volum...> Or, you can do the same thing with the “sop zone” command, maybe something like: sop zone #1 #0:2 3 There are other possible options, see: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/sop.html#zone> The reason you couldn’t do it with “zonesel" is that you can’t select only part of the map; it always selects the whole thing. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jan 7, 2019, at 6:40 PM, BuddySphinx <yangqi.gu@yale.edu> wrote:
Dear Chimera users, I have an EM map and pdb coordinates. I am trying to show density fit of some of my sidechain. I want to display a particular sidechain fitting into the density. I was trying to use zonesel feature: zonesel #0 (reference pdb):2 (residue #2) 3 (cutoff 3A) #1 (EM map) show sel But somehow it did not show the EM density of residue #2, rather the entire map. I am wondering what I did wrong? Best, Yangqi
It worked beautifully! Thank you very much! Best, Yangqi Sent from Mail for Windows 10 From: Elaine Meng Sent: Tuesday, January 8, 2019 10:45 AM To: BuddySphinx Cc: chimera-users Subject: Re: [Chimera-users] Select density of particular sidechains Hi Yangqi, To show the density near some atoms, use the zone option in Volume Viewer. Choose "Features… Zone" from the Volume Viewer menu to show the zone options in the dialog, and then with the atoms selected, click Zone to apply the chosen radius value. <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/volumeviewer/volum...> Or, you can do the same thing with the “sop zone” command, maybe something like: sop zone #1 #0:2 3 There are other possible options, see: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/sop.html#zone> The reason you couldn’t do it with “zonesel" is that you can’t select only part of the map; it always selects the whole thing. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jan 7, 2019, at 6:40 PM, BuddySphinx <yangqi.gu@yale.edu> wrote:
Dear Chimera users, I have an EM map and pdb coordinates. I am trying to show density fit of some of my sidechain. I want to display a particular sidechain fitting into the density. I was trying to use zonesel feature: zonesel #0 (reference pdb):2 (residue #2) 3 (cutoff 3A) #1 (EM map) show sel But somehow it did not show the EM density of residue #2, rather the entire map. I am wondering what I did wrong? Best, Yangqi
participants (2)
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BuddySphinx -
Elaine Meng