Netiquette · Download · News · Gallery · G-quadruplexes · DSSR-Jmol · DSSR-PyMOL · Video Overview · DSSR v2.5.1 (DSSR Manual) · Homepage
I have a suggestion on a new feature for multi-model NMR files, some sort of alignment command to align on each model's reference frame. I performed this by hand as an example using the following
- Split the multi-model file into individual pdb files, 1 for each model
- for each model...
- find_pair on the structure
- rotate_mol using the ref_frame.dat file from find_pair
The pairing is consistent in all of the models but we have to run find_pair on each structure in order to get the reference frame data.
True, analyze can provide the ref_frame.dat. I looked into using nmr_strs which runs analyze on each structure but it overwrites the ref_frame.dat file on each model. You may be able to modify nmr_strs to take rotate_mol as an input, but a standalone ruby script would also work, whatever you think is best.
Before I can get something for an "official" release of 3DNA v2.1 with this new feature included, I will try to come up with a Ruby script this week for you to try out.
Now to a specific point related to the procedure your outlined:QuoteI have a suggestion on a new feature for multi-model NMR files, some sort of alignment command to align on each model's reference frame. I performed this by hand as an example using the following
- Split the multi-model file into individual pdb files, 1 for each model
- for each model...
- find_pair on the structure
- rotate_mol using the ref_frame.dat file from find_pair
The pairing is consistent in all of the models but we have to run find_pair on each structure in order to get the reference frame data.
As with the MD simulation analysis script ('x3dna_md.rb'), it would be best for a user to specify the base pairing information. Thus the program 'find_pair' does not need to be run with each model. This would ensure consistency in all the models. Instead, the model-specific 'ref_frame.dat' can be generated with 'analyze'.
------------------------------------------------------------------------
Usage:
ensemble_reorient options
Examples:
ensemble_reorient --frame-opt='-m -6' -b bpfile.dat -e 2kei.pdb
# reorient each model using the reference frame of base-pair #6
# with minor groove facing the viewer (-m)
# note the use the double dash (--) style with equal sign, and
# the options to be transfered to frame_mol must be quoted
# generate 'model_list.dat', and 'ensemble_example_trx.pdb'
ensemble_reorient -f '\-m -6' -b bpfile.dat -m model_list.dat -o reoriented.pdb
# Same transformation as above, but using an explicit list of
# models, and the transformed ensemble in 'reoriented.pdb'
# diff ensemble_example_trx.pdb reoriented.pdb
ensemble_reorient -f '\-8,9' -b bpfile.dat -e 2kei.pdb
# reorient each model using the middle reference frame between
# base-pairs #8 & #9. Again, note the quote and back slash
Options:
------------------------------------------------------------------------
--bpfile, -b <s>: File containing base-pairing info (as generated from find_pair,
and EDITED as appropriate)
--outfile, -o <s>: Output parameters file name (default: ensemble_example_trx.pdb)
--frame-opt, -f <s>: Options to transfer to frame_mol (quoted)
--ensemble, -e <s>: Model ensemble delineated with MODEL/ENDMDL
--models, -m <s>: File with explicit listing of model numbers
--help, -h: Show this message
Funded by the NIH R24GM153869 grant on X3DNA-DSSR, an NIGMS National Resource for Structural Bioinformatics of Nucleic Acids
Created and maintained by Dr. Xiang-Jun Lu, Department of Biological Sciences, Columbia University