modeller_usage

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modeller_usage@salilab.org

July 2011

11 participants
22 discussions

Re: [modeller_usage] FATAL ERROR: MODINSTALL9v9 environment variable not set: incomplete MODELLER installation on Ubuntu 10.4
by R K Belew 03 Jul '11

03 Jul '11

(i'm trying to tack on to the thread closest to my experience) i've successfully installed mod9.9 on MacOS, but want to have less-mediated Python access, and so am re-installing on Ubuntu. i grabbed modeller_9.9-1_i386.deb, invoked dpkg as recommended: > sudo env KEY_MODELLER=<myCode> dpkg -i modeller_9.9-1_i386.deb and the install seemed to work fine. but then going to .../examples/ and trying to run_tests: > monk:/usr/share/doc/modeller-9.9/examples> ./run_tests > Entering directory: all-steps > #!/bin/sh -v > mod9.9 search.py > Could not find platform independent libraries <prefix> > Could not find platform dependent libraries <exec_prefix> > Consider setting $PYTHONHOME to <prefix>[:<exec_prefix>] > 'import site' failed; use -v for traceback > ... (similar errors for all other scripts) going thru the archives, you (Ben) say things like: "it needs certain environment variables set first, which python or mod9.9 take care of. " "... You don't actually need to set *any* of the environment variables you have above" regarding previous releases, and so i don't want to mess until i have to! i can also go back to the generic Unix version, but thought you must want Ubuntu's .deb option also working? thanks for your great work, rik

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Regarding Modeller model building script
by Ashish Runthala 01 Jul '11

01 Jul '11

Dear Modellers & Respected Sir Benn, If i am correct Modeller uses distance restraints from multiple templates based on alignment, Tell me the way to use one complete template during modeling and chunks from others. I tried doing that but GDT score decreased when i aligned chunks to one complete template alignment. The aligned chunks were covering target region which was unaligned by one selected complete template span. So HOW TO GENERATE FOLD BASED ALIGNMENT WHICH IMPROVES GDT SCORES BY INCREASING CONSIDERATION WEIGHT OF A SINGLE TEMPLATE AS COMPARED TO OTHERS IN MODELLING. Thanks Ashish Ashish Runthala, Lecturer, Structural Biology Cell, Biological Sciences Group, BITS, Pilani Rajasthan, INDIA

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