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Author Topic: web access  (Read 10559 times)

Offline ghzheng

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web access
« on: December 11, 2008, 07:23:45 pm »
Hi Xiangjun,

As you may remember, we have accessing problem to the X3DNA through the web, namely the apache user doesn't have the permission to read X3DNA parameter files due to the environment set-up.

It was solved by a temporary solution: setting up the X3DNA environment in the command line, e.g.,

env  X3DNA=/usr/local/X3DNA_2.0  /usr/local/X3DNA_2.0/bin/find_pair 1KX3.pdb

However, this method doesn't work when I tried to run the blocview command, since it calls molscript and raster3d, which also have environment or permission problems. So the best way would be setting a local account that can be directed by the apache.

Our computer staff was assisting on this, but he didn't figure out how to configure the server to run through the PHP web as a particular local user. The other day, you memtioned that there is a way to running through the web as a local user. Can you suggest several ways to do so? I will discuss with the computer staff.



Offline xiangjun

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Re: web access
« Reply #1 on: December 12, 2008, 09:46:15 pm »
Hi Guohui,

It certainly should not be that hard. The system administrator should be able to set up the X3DNA environment variable and add $X3DNA/bin directory to command line search path, so the 'apache' process, or all users, can access them.

This is clearly an IT issue where Wilma should be able to play a crucial here. In the lab I am working, there is a (part-time) system-admin to solve such issues.

While the problem persists, you could focus on the rebuilding and analysis parts to get them done in a more decent form. As for 'blocview', the system needs to have MolScript, Raster3D, and ImageMagick installed, and properly configured for system-wide access. You could (through Wilma, perhaps) check with the NDB/PDB people -- they use 'blocview' for all the nucleic-acid containing structures.

Have a good weekend.



Created and maintained by Dr. Xiang-Jun Lu [律祥俊] (
The Bussemaker Laboratory at the Department of Biological Sciences, Columbia University.