Difference between revisions of "3DNA"
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== 3DNA == | == 3DNA == | ||
| − | 3DNA provides a perl script which produces Calladine-Drew style block representations based on the standard reference frame for nucleic acids, the produced files are in raster image, and are also procesed by molscript. Therefore to produce the following representations you will need to install: | + | 3DNA provides a perl script (<b>blocview</b>) which produces Calladine-Drew style block representations based on the standard reference frame for nucleic acids, the produced files are in raster image, and are also procesed by molscript. Therefore to produce the following representations you will need to install: |
- 3DNA V1.5 [http://rutchem.rutgers.edu/~xiangjun/3DNA] | - 3DNA V1.5 [http://rutchem.rutgers.edu/~xiangjun/3DNA] | ||
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- Molscript [http://www.avatar.se/molscript/download.html] | - Molscript [http://www.avatar.se/molscript/download.html] | ||
| − | Once you have the previous software installed and the path to their binaries correctly configured you | + | Once you have the previous software installed and the path to their binaries correctly configured you can get the block representation for any nucleic acid. The next example shows how to do it for tRNA (PDB:ID 1ehz) |
<pre> | <pre> | ||
| − | blocview -o | + | pdb_get.py 1ehz |
| + | blocview -o 1ehz.pdb | ||
| + | </pre> | ||
| + | |||
| + | The pdb_get python script comes from Dr. Robert Campbell's website http://pldserver1.biochem.queensu.ca/~rlc/work/scripts/pdb_get.py [http://pldserver1.biochem.queensu.ca/~rlc/work/scripts/pdb_get.py] | ||
| + | |||
| + | Once blocview is run it will generate various r3d files which can be combined with the original pdb files to produce the following image: | ||
| + | |||
| + | [[Image:Example.jpg]] | ||
| + | |||
| + | To generate the previous image the following script was used: | ||
| + | trna.pml | ||
| + | |||
| + | <pre> | ||
| + | |||
| + | </pre> | ||
| + | |||
| + | |||
| + | An automatically generated pymol ray traced image can also be obtained by running <b>blocview</b> on version 2.0 or 3DNA directly in the following way: | ||
| + | |||
| + | <pre> | ||
| + | blocview -o -t=100 1ehz.pdb | ||
</pre> | </pre> | ||
Revision as of 19:57, 6 March 2008
3DNA
3DNA provides a perl script (blocview) which produces Calladine-Drew style block representations based on the standard reference frame for nucleic acids, the produced files are in raster image, and are also procesed by molscript. Therefore to produce the following representations you will need to install:
- 3DNA V1.5 [1]
- 3DNA V2.0 [2]
- Raster 3D [3]
- Molscript [4]
Once you have the previous software installed and the path to their binaries correctly configured you can get the block representation for any nucleic acid. The next example shows how to do it for tRNA (PDB:ID 1ehz)
pdb_get.py 1ehz blocview -o 1ehz.pdb
The pdb_get python script comes from Dr. Robert Campbell's website http://pldserver1.biochem.queensu.ca/~rlc/work/scripts/pdb_get.py [5]
Once blocview is run it will generate various r3d files which can be combined with the original pdb files to produce the following image:
To generate the previous image the following script was used: trna.pml
An automatically generated pymol ray traced image can also be obtained by running blocview on version 2.0 or 3DNA directly in the following way:
blocview -o -t=100 1ehz.pdb