Modeller9.10 on Centos 6.2
I've installed Modeller9.10 on my Centos 62. linux station. I had an earlier version working under Centos 5.x. Now I find that if I set an alias I call mod9v10 to point to modeller9.10_x86_64-intel8 in analogy to the alias I successfully set to its analog previously, I get the messages about not finding libraries described on the modeller web pages. Furthermore, I get an error indicating that my .ali file can't be found & I've triple-checked to make sure I've entered the name correctly.
There is no modpy.sh in the directory to which the web pages point. Instead, there is a file modpy.sh.in. Regardless of whether I use the copy of this script in its installed location, or whether I copy it to my cwd, it cannot find the equivalent of foo.py unless I give the full path to foo.py. When I specify the full path, I get error messages such as "from: command not found" & a crash, indicative of a massive failure to access python.
If I try to use the script mod9.10, whether in its original location or a copy in cwd, it fails to find the ali file, whether or not I enter its full path.
The inputs I am using are all derived from successful modeller runs, albeit an earlier version running under an earlier Centos, so I did not expect these results. But what really makes me want to tear my hair out is this: a previous modeller manual included a short python code to extract a sequence from a PDB file. I've called it pdb2ali.py. If I type the command: mod9v10 pdb2ali.py, I get the error messages about failing to find platform dep/indep files, but I have output! There is no problem finding the input pdb file in cwd.
Please help me debug this! Thanks in advance!
Irene
On 3/6/12 1:31 PM, Irene Newhouse wrote: > I've installed Modeller9.10 on my Centos 62. linux station. I had an > earlier version working under Centos 5.x. Now I find that if I set an > alias I call mod9v10 to point to modeller9.10_x86_64-intel8 in > analogy to the alias I successfully set to its analog previously
There's no need to do that - there's already a script called mod9.10 which does basically that, which ships as part of Modeller. But we generally recommend to use Python instead if you can.
> Furthermore, I get an error indicating that my > .ali file can't be found& I've triple-checked to make sure I've > entered the name correctly.
Are you sure it's complaining about the .ali file and not something else? Or maybe you're running in the wrong directory.
> There is no modpy.sh in the directory to which the web pages point.
If you installed the RPM, there is no modpy.sh because it isn't necessary. You can just run your regular system Python, e.g. "python foo.py".
> it cannot find the equivalent of foo.py unless I give the full path to foo.py
If you're trying to run "foo.py" in the current directory by just typing "foo.py", that typically won't work on a Unix system since the current directory isn't usually in your path. Try "./foo.py" instead.
> When I specify the full path, I get error > messages such as "from: command not found"& a crash, indicative of > a massive failure to access python.
This sounds like you have tried to run the Python script as a shell script. Either prefix it with "python", as above, or add "#!/usr/bin/python" to the first line of your Python script to tell the system to use Python to run it.
Ben Webb, Modeller Caretaker
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Irene Newhouse -
Modeller Caretaker