which file is the Modeller executable on linux?
Forwarding to chimera-users@cgl.ucsf.edu <mailto: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: <https://www.rbvi.ucsf.edu/chimerax/docs/user/tools/modeller.html> <https://www.rbvi.ucsf.edu/chimerax/docs/user/tools/modeller.html> Also, there is a different address chimerax-users@cgl.ucsf.edu <mailto: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
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 <mailto: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: <https://www.rbvi.ucsf.edu/chimerax/docs/user/tools/modeller.html> <https://www.rbvi.ucsf.edu/chimerax/docs/user/tools/modeller.html>
Also, there is a different address chimerax-users@cgl.ucsf.edu <mailto: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
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participants (2)
-
Elaine Meng -
Eric Pettersen