Hi, Suppose I want to find the distance between all atoms of residue-A and residue-B & write the distances to a file. Is it possible to do so in a meaningful way? -- Prathvi Singh, Research Fellow, Department of Biological Sciences & Bioengineering, Indian Institute of Technology, Kanpur-208016
Hi Prathvi, You can get all-by-all distances written to a file or the Reply Log by using Find Clashes/Contacts or the clashes command, by defining residue-A as the first set of atoms, residue-B as the second set of atoms, and and using a large negative cutoff value that will just get everything. For example, if it's residue 10 in chain A of model 0 versus residue 50 in chain B of model 1, the command to send info to the Log could be something like findclash #0:10.A test #1:50.B overlap -1000 log true (and/or use the saveFile option to save to file) Find Clashes/Contacts tool <https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/findclash/findclash.html> findclash command and its options <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/findclash.html> ChimeraX (our newer program) also has a tool and command to do this same thing, if you're interested. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Nov 8, 2021, at 3:39 AM, Prathvi Singh via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:
Hi, Suppose I want to find the distance between all atoms of residue-A and residue-B & write the distances to a file. Is it possible to do so in a meaningful way?
Thanks Elaine for the help. I checked out ChimeraX & it is definitely much more user-friendly. The presence of the reply log at the right side really helps keep track of the actions one is performing and THANKS A LOT for the undo feature. I really miss it in Chimera. Still, I wonder if there is a way or a plugin to incorporate the "undo" command in chimera... On Mon, Nov 8, 2021 at 9:35 PM Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hi Prathvi, You can get all-by-all distances written to a file or the Reply Log by using Find Clashes/Contacts or the clashes command, by defining residue-A as the first set of atoms, residue-B as the second set of atoms, and and using a large negative cutoff value that will just get everything. For example, if it's residue 10 in chain A of model 0 versus residue 50 in chain B of model 1, the command to send info to the Log could be something like
findclash #0:10.A test #1:50.B overlap -1000 log true
(and/or use the saveFile option to save to file)
Find Clashes/Contacts tool < https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/findclash/findcla...
findclash command and its options <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/findclash.html>
ChimeraX (our newer program) also has a tool and command to do this same thing, if you're interested.
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Nov 8, 2021, at 3:39 AM, Prathvi Singh via Chimera-users < chimera-users@cgl.ucsf.edu> wrote:
Hi, Suppose I want to find the distance between all atoms of residue-A and residue-B & write the distances to a file. Is it possible to do so in a meaningful way?
-- Prathvi Singh, Research Fellow, Department of Biological Sciences & Bioengineering, Indian Institute of Technology, Kanpur-208016
Sorry, no. It is actually quite difficult to implement undo, or so I'm told (I'm not the one doing it). Chimera has an "Undo Move" tool but that's pretty much it, and we are not actively developing Chimera to add features any more. <https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/undomove/undomove.html> Our development focus is now on ChimeraX. The ChimeraX undo doesn't include everything, but we tried to include many common actions. Glad you like it! ChimeraX undo: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/undo.html> ChimeraX short list of advantages over Chimera: <https://rbvi.ucsf.edu/chimerax/docs/user/advantages.html> Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Nov 8, 2021, at 5:41 PM, Prathvi Singh via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:
Thanks Elaine for the help. I checked out ChimeraX & it is definitely much more user-friendly. The presence of the reply log at the right side really helps keep track of the actions one is performing and THANKS A LOT for the undo feature. I really miss it in Chimera. Still, I wonder if there is a way or a plugin to incorporate the "undo" command in chimera...
On Mon, Nov 8, 2021 at 9:35 PM Elaine Meng <meng@cgl.ucsf.edu> wrote: Hi Prathvi, You can get all-by-all distances written to a file or the Reply Log by using Find Clashes/Contacts or the clashes command, by defining residue-A as the first set of atoms, residue-B as the second set of atoms, and and using a large negative cutoff value that will just get everything. For example, if it's residue 10 in chain A of model 0 versus residue 50 in chain B of model 1, the command to send info to the Log could be something like
findclash #0:10.A test #1:50.B overlap -1000 log true
(and/or use the saveFile option to save to file)
Find Clashes/Contacts tool <https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/findclash/findclash.html>
findclash command and its options <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/findclash.html>
ChimeraX (our newer program) also has a tool and command to do this same thing, if you're interested.
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Nov 8, 2021, at 3:39 AM, Prathvi Singh via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:
Hi, Suppose I want to find the distance between all atoms of residue-A and residue-B & write the distances to a file. Is it possible to do so in a meaningful way?
-- Prathvi Singh, Research Fellow, Department of Biological Sciences & Bioengineering, Indian Institute of Technology, Kanpur-208016 _______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
I got it. Thanks Elaine. On Tue, Nov 9, 2021 at 7:21 AM Elaine Meng <meng@cgl.ucsf.edu> wrote:
Sorry, no. It is actually quite difficult to implement undo, or so I'm told (I'm not the one doing it). Chimera has an "Undo Move" tool but that's pretty much it, and we are not actively developing Chimera to add features any more. < https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/undomove/undomove...
Our development focus is now on ChimeraX. The ChimeraX undo doesn't include everything, but we tried to include many common actions. Glad you like it!
ChimeraX undo: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/undo.html>
ChimeraX short list of advantages over Chimera: <https://rbvi.ucsf.edu/chimerax/docs/user/advantages.html>
Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Nov 8, 2021, at 5:41 PM, Prathvi Singh via Chimera-users < chimera-users@cgl.ucsf.edu> wrote:
Thanks Elaine for the help. I checked out ChimeraX & it is definitely much more user-friendly. The presence of the reply log at the right side really helps keep track of the actions one is performing and THANKS A LOT for the undo feature. I really miss it in Chimera. Still, I wonder if there is a way or a plugin to incorporate the "undo" command in chimera...
On Mon, Nov 8, 2021 at 9:35 PM Elaine Meng <meng@cgl.ucsf.edu> wrote: Hi Prathvi, You can get all-by-all distances written to a file or the Reply Log by using Find Clashes/Contacts or the clashes command, by defining residue-A as the first set of atoms, residue-B as the second set of atoms, and and using a large negative cutoff value that will just get everything. For example, if it's residue 10 in chain A of model 0 versus residue 50 in chain B of model 1, the command to send info to the Log could be something like
findclash #0:10.A test #1:50.B overlap -1000 log true
(and/or use the saveFile option to save to file)
Find Clashes/Contacts tool < https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/findclash/findcla...
findclash command and its options <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/findclash.html>
ChimeraX (our newer program) also has a tool and command to do this same thing, if you're interested.
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Nov 8, 2021, at 3:39 AM, Prathvi Singh via Chimera-users < chimera-users@cgl.ucsf.edu> wrote:
Hi, Suppose I want to find the distance between all atoms of residue-A and residue-B & write the distances to a file. Is it possible to do so in a meaningful way?
-- Prathvi Singh, Research Fellow, Department of Biological Sciences & Bioengineering, Indian Institute of Technology, Kanpur-208016 _______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
-- Prathvi Singh, Research Fellow, Department of Biological Sciences & Bioengineering, Indian Institute of Technology, Kanpur-208016
participants (2)
-
Elaine Meng -
Prathvi Singh