Modelling of missing regions ussing Chimera
Dear Chimera's users! I need to model some missing segments ( In particular case I need to build missing N and C termi ) of my protein ussing Modeller's options. Could you tell me about possible solution of that issue ? On my win7 I have installed Chimera as well as Modeller v 9.10 suite. I've defined Modeller pathways in the Chimera's Model pool options but when I've selected option Prune seection to define region of interest I didnt obtain anythinf from both of Chimera or Modeller. On other hand the option Structure -> Modeller tools also not available for me. Does it means that I've installed modeller incorrectly ? Also I've used runmod.dat script with defined variables from which I obtained the below C:\Users\own\Desktop\worktemp>runmod.bat usage: mod9.10 script [...] Doest this means that all work fine ? By the way after executing of that script I could not launch modeller by means of mod9.10.exe from modeller folder. The error from modeller was C:\Program Files\Modeller\bin>mod9.10.exe FATAL ERROR: MODINSTALL9v10 environment variable not set: incomplete MODELLER in stallation Could you explain me whats I've done wrong and how I could fix this problem? Thanks for help Gleb
Hi Gleb, First you need to get a newer Chimera (version 1.7 daily build). You cannot build missing segments with the production release (1.6) and older versions of Chimera -- the "Model Loops" tool in those older versions only allows re-modeling segments that are already in the protein, not building missing segments. Daily build download: <http://www.cgl.ucsf.edu/chimera/download.html#daily> In Chimera 1.7 there have been many improvements in the Chimera-Modeller interface. You can build missing segments using the "Model/Refine Loops" tool (in menu under Tools... Structure Editing). For instructions, click the Help button on that tool or view its documentation here: <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/modeller.html#building> Another improvement is that you don't have do anything with a runmod.bat file on Windows, you only have to enter the location of the Modeller executable in the dialog (assuming you have installed Modeller correctly). Or, instead of your own installation you could just use our web service, which does not require you to install Modeller. I hope this helps Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Aug 4, 2012, at 4:44 AM, Gleb Novicov wrote:
Dear Chimera's users! I need to model some missing segments ( In particular case I need to build missing N and C termi ) of my protein ussing Modeller's options. Could you tell me about possible solution of that issue ?
On my win7 I have installed Chimera as well as Modeller v 9.10 suite.
I've defined Modeller pathways in the Chimera's Model pool options but when I've selected option Prune seection to define region of interest I didnt obtain anythinf from both of Chimera or Modeller. On other hand the option Structure -> Modeller tools also not available for me. Does it means that I've installed modeller incorrectly ?
Also I've used runmod.dat script with defined variables from which I obtained the below
C:\Users\own\Desktop\worktemp>runmod.bat usage: mod9.10 script [...]
Doest this means that all work fine ?
By the way after executing of that script I could not launch modeller by means of mod9.10.exe from modeller folder. The error from modeller was
C:\Program Files\Modeller\bin>mod9.10.exe FATAL ERROR: MODINSTALL9v10 environment variable not set: incomplete MODELLER in stallation
Could you explain me whats I've done wrong and how I could fix this problem?
Thanks for help
Gleb _______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Dear Elaine! Thank you for your advises. Your new Modeller's module in new Chimera release works perfect. Could you tell me how I could define path to the modeller local installation ? I have installed Modeller on my Linux debian OS in the default locations. As I understood in that case Modeller is the part of the python modules. It's been installed both in the usr/lib/ and usr/include/ dirrs. Where the executable file is? Thanks again, Gleb 2012/8/7 Elaine Meng <meng@cgl.ucsf.edu>
Hi Gleb, First you need to get a newer Chimera (version 1.7 daily build). You cannot build missing segments with the production release (1.6) and older versions of Chimera -- the "Model Loops" tool in those older versions only allows re-modeling segments that are already in the protein, not building missing segments. Daily build download: <http://www.cgl.ucsf.edu/chimera/download.html#daily>
In Chimera 1.7 there have been many improvements in the Chimera-Modeller interface. You can build missing segments using the "Model/Refine Loops" tool (in menu under Tools... Structure Editing). For instructions, click the Help button on that tool or view its documentation here: < http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/mod...
Another improvement is that you don't have do anything with a runmod.bat file on Windows, you only have to enter the location of the Modeller executable in the dialog (assuming you have installed Modeller correctly). Or, instead of your own installation you could just use our web service, which does not require you to install Modeller.
I hope this helps Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco
On Aug 4, 2012, at 4:44 AM, Gleb Novicov wrote:
Dear Chimera's users! I need to model some missing segments ( In particular case I need to build missing N and C termi ) of my protein ussing Modeller's options. Could you tell me about possible solution of that issue ?
On my win7 I have installed Chimera as well as Modeller v 9.10 suite.
I've defined Modeller pathways in the Chimera's Model pool options but when I've selected option Prune seection to define region of interest I didnt obtain anythinf from both of Chimera or Modeller. On other hand the option Structure -> Modeller tools also not available for me. Does it means that I've installed modeller incorrectly ?
Also I've used runmod.dat script with defined variables from which I obtained the below
C:\Users\own\Desktop\worktemp>runmod.bat usage: mod9.10 script [...]
Doest this means that all work fine ?
By the way after executing of that script I could not launch modeller by means of mod9.10.exe from modeller folder. The error from modeller was
C:\Program Files\Modeller\bin>mod9.10.exe FATAL ERROR: MODINSTALL9v10 environment variable not set: incomplete MODELLER in stallation
Could you explain me whats I've done wrong and how I could fix this problem?
Thanks for help
Gleb _______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Hi Gleb! I'm glad it worked well for you. In the Chimera-Modeller dialog, you can browse to set the location. However, it sounds like the real question is where to find the executable on your Linux system, and I don't know the answer to that part. On my Mac, it is /usr/bin/mod9.10 (which actually points to /Library/modeller-9.10/bin/mod9.10 ) ... is there a something like that under /usr/bin/ or /usr/lib/ on your machine? Maybe the Modeller website has the answer... <http://salilab.org/modeller/release.html> ...or maybe somebody who has used Modeller on Linux can comment. Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Aug 7, 2012, at 1:15 AM, Gleb Novicov wrote:
Dear Elaine! Thank you for your advises. Your new Modeller's module in new Chimera release works perfect.
Could you tell me how I could define path to the modeller local installation ? I have installed Modeller on my Linux debian OS in the default locations. As I understood in that case Modeller is the part of the python modules. It's been installed both in the usr/lib/ and usr/include/ dirrs. Where the executable file is? Thanks again, Gleb
On 08/07/2012 01:15 AM, Gleb Novicov wrote:
I have installed Modeller on my Linux debian OS in the default locations. As I understood in that case Modeller is the part of the python modules. It's been installed both in the usr/lib/ and usr/include/ dirrs. Where the executable file is?
If by "default locations" you mean you installed the Debian package (.deb file) then the Modeller 'mod9.10' script will be in /usr/bin/. But the preferred way to run Modeller is just to run python, since it is a Python module. Ben -- ben@salilab.org http://salilab.org/~ben/ "It is a capital mistake to theorize before one has data." - Sir Arthur Conan Doyle
On Aug 8, 2012, at 11:57 AM, Ben Webb wrote:
On 08/07/2012 01:15 AM, Gleb Novicov wrote:
I have installed Modeller on my Linux debian OS in the default locations. As I understood in that case Modeller is the part of the python modules. It's been installed both in the usr/lib/ and usr/include/ dirrs. Where the executable file is?
If by "default locations" you mean you installed the Debian package (.deb file) then the Modeller 'mod9.10' script will be in /usr/bin/. But the preferred way to run Modeller is just to run python, since it is a Python module.
Chimera, when executing Modeller locally rather than via web service, does run the Modeller executable/script rather than invoke it via Python. Perhaps it should/could use Python instead, but Chimera would still need to be informed of the Python executable location, so this problem wouldn't really be eliminated! --Eric
participants (4)
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Ben Webb -
Elaine Meng -
Eric Pettersen -
Gleb Novicov