Hi Prathvi, Both of these things are much easier/better in ChimeraX, since it has commands to do them. We are recommending everybody use ChimeraX if possible (if it has the features that they need). In Chimera, the Reply Log has buttons to Clear and to Save, but there are no commands for those functions. If there were commands, it would be mentioned in the Reply Log help. <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/reply.html> For saving only (not clearing), there are instructions of how to do it in python at the bottom of this page: <https://www.rbvi.ucsf.edu/chimera/docs/ProgrammersGuide/basicPrimer.html> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco

On Jun 27, 2023, at 4:21 AM, Prathvi Singh via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:

Hi Elaine, Is there a way to clear the Reply Log using the command line? Is there a way to write the contents of the Reply log to a text file?

-- Prathvi Singh, Research Fellow, Department of Biological Sciences & Bioengineering, Indian Institute of Technology, Kanpur-208016

Hi Prathvi, Normally one would *not* include any residue numbers in a mmaker command. You only need model numbers (not chain IDs either, except if you want to make sure that specific chains match specific other chains when each model has more than one chain). Also it is completely useless to include the @ca in a mmaker command because mmaker always only uses @ca for proteins anyway. See the mmaker help for whichever program you are using (Chimera or ChimeraX). Your description does not make sense for Chimera. You must be using ChimeraX. The specifications are different for Chimera and ChimeraX, only ChimeraX uses "/" for chains. In either program, you would simply omit the chain part of the specification if there is no chain ID. To avoid confusing others, make sure to email chimerax-users if you are asking about ChimeraX usage, and chimera-users for Chimera. Thanks! Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco

On Jun 28, 2023, at 1:47 AM, Prathvi Singh via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:

Thank you so much for the info Elaine! I just have one more question. Is it possible to run the "mmaker" command without inputting chain IDs of the residues to be superimposed? I am asking this because I have a few PDB files whose residues lack chain ID information (I know this because when I hover my mouse over one of these residues, it shows something like: "/? PRO 190") I tried the command: mmaker #0/?:162-172@CA to #1/?:162-172@CA But it shows the error: No molecules/chains to match specified

On Tue, Jun 27, 2023 at 9:46 PM Elaine Meng <meng@cgl.ucsf.edu> wrote: Hi Prathvi, Both of these things are much easier/better in ChimeraX, since it has commands to do them. We are recommending everybody use ChimeraX if possible (if it has the features that they need).

In Chimera, the Reply Log has buttons to Clear and to Save, but there are no commands for those functions. If there were commands, it would be mentioned in the Reply Log help. <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/reply.html>

For saving only (not clearing), there are instructions of how to do it in python at the bottom of this page: <https://www.rbvi.ucsf.edu/chimera/docs/ProgrammersGuide/basicPrimer.html>

I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco

...

On Jun 27, 2023, at 4:21 AM, Prathvi Singh via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:

Hi Elaine, Is there a way to clear the Reply Log using the command line? Is there a way to write the contents of the Reply log to a text file?

-- Prathvi Singh, Research Fellow, Department of Biological Sciences & Bioengineering, Indian Institute of Technology, Kanpur-208016

-- Prathvi Singh, Research Fellow, Department of Biological Sciences & Bioengineering, Indian Institute of Technology, Kanpur-208016 _______________________________________________ Chimera-users mailing list -- chimera-users@cgl.ucsf.edu: To unsubscribe send an email to chimera-users-leave@cgl.ucsf.edu Manage subscription: