Installing TEXTALTM

Brief Index

System Requirements

Minimum

Preferred

Unpacking and Installing

Linux (RPM Method)

The TEXTALTM distribution consists of two RPM packages,
textal_data-1.0-1.i386.rpm
The database and support files
textal-1.0-1.i386.rh9.rpm
The executable code and scripts
These packages will install TEXTALTM and all associated files under /usr/local/textal. To install, login as root and insert the TEXTALTM cd. Double click on the textal_data-1.0 RPM first to install the data directory. Once complete, double click on the appropriate textal-1.0 RPM to install the executables. If you're using another version of Red hat Linux, use the appropriate RPM (i.e. textal-1.0-1.i386.rh8.rpm for Red hat 8.0).

Alternatively, you can use the command-line version of RPM to install TEXTALTM. Execute the following commands as root: 

	rpm -i textal_data-1.0-1.i386.rpm
	rpm -i textal-1.0-1.i386.rh9.rpm

Note: tclx is required only for the GUI interface to TEXTALTM. It is possible to bypass the dependency check by adding the "--nodeps" flags to the rpm command, i.e. 

	rpm -i --nodeps textal-1.0-1.i386.rh9.rpm
It's recommended that you try installing first without the --nodeps find any additional dependencies you may have, then install them prior to installing TEXTALTM with the --nodeps flag.


Linux, IRIX, and OS/X (tar files)

Note: These instructions assume you are using the GNU version of tar
The TEXTALTM distribution consists of two tar compressed tar files,
textal_data-1.0.tar.bz2
The database and support files
textal-1.0.vers.tar.bz2
The executable code and scripts
Note: vers will depend on which architecture/OS you are installing on. For example, it'll be rh9 for Red hat 9.0, or osx for MacOS X.

These packages will install TEXTALTM and all associated files in a directory called textal. TEXTALTM expects this to be installed in /usr/local.

To install, execute the following commands as root: 

	cd /usr/local
	tar xvj PATH_TO_TEXTAL_TAR_FILES/textal_data-1.0.tar.bz2
	tar xvj PATH_TO_TEXTAL_TAR_FILES/textal-1.0.rh9.tar.bz2
Where PATH_TO_TEXTAL_TAR_FILES is the pathway to where you have the TEXTALTM tar files stored.


Setting up the User's Environment

Users should source either txenv.sh for bourne shell and bash shells, or txenv.csh for c-shell and tcsh, prior to running TEXTALTM. These files are installed in /usr/local/textal by default. To tell which shell you are using, type: 
	echo $SHELL


Using TEXTALTM with Blast and PHd (optional)

If you wish to use BLAST and PHd with TEXTALTM, you may need to edit the environment setup scripts for TEXTALTM, txenv.sh and txenv.csh. TEXTALTM is smart enough to find BLAST and PHd if they are installed in "standard" locations (such as /usr/local/bin) or can be found in the user's $PATH. To edit the scripts for BLAST and PHd, change the PHD_PATH and BLAST_PATH variables.


Setting up the License File

Simply copy the license file your received into /usr/local/textal/data/textal.lic, or copy and paste the contents into an existing textal.lic file if you have multiple licenses.


Non-root Installations

TextalTM can be installed in places other than /usr/local/textal and by users other than root. To do so, use the aforementioned TAR method. Simply untar TextalTM into a directory so you have everything inside a directory called textal. Then put your license codes into textal/data/textal.lic.

You will then need to edit the textal/txenv.sh and textal/txenv.csh files to set the environment for TextalTM to run. You will need to change the TEXTAL_DIST variable to point to where you have your textal directory installed. You may also want to review the section above on using PHd and blast with textal...

Configuring TEXTALTM

TEXTALTM sports many options that can be configured via a series of configuration files called Texrc files. The actual file may be called either .texrc or Texrc depending on where TEXTALTM is searching for it. Central to understanding how to create and use Texrc files is understanding how TEXTALTM uses environment variables. See Understanding TEXTALTM Environment Variables for more information. More detailed information about constructing Texrc files and how TEXTALTM uses them can be found in the Creating and Using Texrc Files section.

The site-wide Texrc file lives in the TEXTA_DATA directory. You will most likely need to edit a couple of options depending on your machine's resources. The most important ones are the size of the density map cache (mapcache_size) and the size of the PDB cache (pdbcache_size). The larger they are, the more memory will be consumed, but the faster TEXTALTM will execute. A map cache size of 200 will use approximately 250MB of RAM. A pdb cache size of 200 will use approximately 60MB of RAM.

Other options you may want to change include:

ncpus
Number of cpus used in parallel code (IRIX-only). Will override the MP_SET_NUMTHREADS variable. Must be an integral divisor of 30.

verbosity
Controls the level of logging (and debugging) output from TEXTALTM. Higher numbers means more copious output.

topk
Larger values means TEXTALTM will search through more hits to find the best matching side-chain. The larger it is, in principal, the better the results will be at the expense of execution speed. You generally will not want to change this.

xmaps_dir
This points to where the electron density maps are stored. For performance reasons, you may want to convert the maps to a binary format and change this to point to that location.

Testing Your Installation

Now that you have installed TEXTALTM, some quick tests are probably in order... First, be sure to source the appropriate txenv.sh file prior to trying any of these tests! On your CD should be an example data tar file called czra_test.tar.bz2 (you can also download this from the TEXTALTM web site). CD to a directory you can write to and unbundle the tar file, 
	tar xjvf czra_test.tar.bz2

This creates a directory called czra_test. Now execute the following commands, 
	cd czra_test
	neotex.sh czra

This may take some time to run to completion. If it fails, look at the start of the output and make sure you see a line that says "Textal license validated!". If you do not, then there is some problem with your license. Check the following: If all of these criteria are satisfied, or you saw the "Textal license validated!" message but TEXTALTM, then contact the TEXTALTM support team for assistance.

When TEXTALTM finishes running, you can either compare the output by loading the manually refined structure from czra.pdb along with the TEXTALTM model in czra-textal.pdb in a graphics program. Alternatively, you can compare the two files by executing the following commands (assuming you're using bash as your shell), 

	evaluate czra 2>/dev/null | kondense.pl
and check to see if your CA RMSD is a reasonable value (around 1.0 Angstroms).

Uninstalling TEXTALTM

RPM Method

To uninstall TEXTALTM, execute the following command: 
	rpm -e textal-1.0
To also remove the data files, use: 
	rpm -e textal_data-1.0

TAR Method

Assuming you have installed TEXTALTM in /usr/local/textal, you can delete the executables by removing everything but the data directory, or remove the whole kit-n-caboodle by typing in: 
	rm -r /usr/local/textal