Hi Yassin,
If you installed Modeller normally, then the Modeller executable is just the path to the Python interpreter that you installed Modeller into, because Chimera is going to provide a Python script as an argument when running the executable.  You do not have to provide a custom script location unless you want to totally override how Chimera runs Modeller (the custom script becomes the argument to the executable instead).  You can see the contents of the script that Chimera normally provides with the "Get Current Modeller Script" button on Chimera's Modeller dialog.

--Eric

Eric Pettersen
UCSF Computer Graphics Lab
 

On Oct 29, 2024, at 4:19 PM, Elaine Meng via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:

Forwarding to chimera-users@cgl.ucsf.edu so that somebody who knows the answer can respond. I don't know since I'm not on linux and do not use a local installation, sorry.  That is the recommended address for asking questions about Chimera.

Note that we do not actively develop Chimera any more.  ChimeraX is recmomended instead -- it has essentially the same capabilities to interface with Modeller (local or web service) for loop modeling and for comparative modeling.  The comparative modeling tool in ChimeraX is better than in Chimera, because it allows modeling multimers whereas the Chimera tool only allows modeling a single protein chain.

Here are the help pages for the two ChimeraX tools, Model Loops and Modeller Comparative:

Also, there is a different address chimerax-users@cgl.ucsf.edu for asking questions about ChimeraX.

Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Resource for Biocomputing, Visualization, and Informatics
Department of Pharmaceutical Chemistry
University of California, San Francisco

From: Modeller Caretaker <modeller-care@salilab.org>
Subject: Re:
Date: October 29, 2024 at 3:58:41 PM PDT
To: Yassin Ahmed <yassin.ahmed2200m@copharm.uobaghdad.edu.iq>

On 10/29/24 8:12 AM, Yassin Ahmed wrote:
Please l have download and installed modeller in my Linux system ,
now I want to run modeller locally by Chimera
Please where can I find the "Modeller executable file location" and also where can I find the "custom Modeller script file location" ? ,,,,
Because there are many files named modeller and mod in installation folder,so I am confused. Please guide me

Hi Yassin, I'm not 100% sure what the Chimera developers mean by "Modeller executable file" so I've cc'd Elaine from the Chimera team, but assuming you're running the latest version of Modeller, they probably mean the mod10.6 script. Where that is depends on how you installed Modeller. If you used the RPM, it is /usr/bin/mod10.6.

In most cases you would not need to change the Modeller script file, instead using that generated by Chimera, so you can leave that box blank, I think.

Ben Webb, Modeller Caretaker

_______________________________________________
Chimera-users mailing list -- chimera-users@cgl.ucsf.edu
To unsubscribe send an email to chimera-users-leave@cgl.ucsf.edu
Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimera-users@cgl.ucsf.edu/