3DNA Forum

Questions and answers => General discussions (Q&As) => Topic started by: acolasanti on October 08, 2013, 01:02:27 pm

Title: Individual Model images in x3dna_ensemble block_image
Post by: acolasanti on October 08, 2013, 01:02:27 pm: Hello,

I am using the x3dna_ensemble program to process NMR and multi model structures. When I use block_image I get as output a pdb and r3d of the entire ensemble, is it possible to get r3d output for each model using this method?

Thank you

Andrew
Title: Re: Individual Model images in x3dna_ensemble block_image
Post by: acolasanti on October 08, 2013, 02:09:40 pm: Also,

What is the difference between the following

x3dna_ensemble reorient -r "b" -e in.pdb -o out_reorient_b.pdb

which uses the best principal axis of base atoms from the rotate_mol command

and
x3dna_ensemble reorient -v -e in.pdb -o out_reorient_e.pdb

which uses the the "best view" from the reorient command. If I open the images together they are very similar.

Thanks

Andrew
Title: Re: Individual Model images in x3dna_ensemble block_image
Post by: xiangjun on October 08, 2013, 08:52:17 pm: Hi Andrew,

Quote
I am using the x3dna_ensemble program to process NMR and multi model structures. When I use block_image I get as output a pdb and r3d of the entire ensemble, is it possible to get r3d output for each model using this method?
The resultant .pdb and .r3d files are as expected -- x3dna_ensemble works on an ensemble. To get separate .r3d, you can use the ex_str/blocview command pair for each model explicitly.

Regarding the difference between the following two runs:
Quote
x3dna_ensemble reorient -r "b" -e in.pdb -o out_reorient_b.pdb
x3dna_ensemble reorient -v -e in.pdb -o out_reorient_e.pdb
See below for help message from x3dna_ensemble reorient -h. Basically, the option "-v (--bestview)" is a short-hand form for "-r 'cb' -k".

Code: [Select]
~ [516] x3dna_ensemble reorient -h ------------------------------------------------------------------------ Reorient models of a MODEL/ENDMDL delineated ensemble of NMR structures or MD trajectories based on user specified base-pair reference frame or rotation matrix. Coordinate transformation is perform by 'frame_mol' or 'rotate_mol'. Useful for 'local' structural alignment. The transformed ensemble can be converted to an image using 'x3dna_ensemble block_image' and visualized with Jmol or PyMOL. Usage: x3dna_ensemble reorient options Examples: x3dna_ensemble reorient -f 'm -6' -b bpfile.dat -e 2kei.pdb # reorient each model using the reference frame of bp #6 # with minor groove facing the viewer (-m) # options to -f must be quoted, where dash is optional # generate 'model_list.dat', 'ensemble_example_trx.pdb' x3dna_ensemble reorient -f '8,9' -b bpfile.dat -e 2kei.pdb # reorient each model using the middle reference frame # between base-pairs #8 and #9 x3dna_ensemble reorient -v -e 2kei.pdb -o extended_view.pdb # transform the ensemble to its most extended view and # keep the original relative orientation. Options: ------------------------------------------------------------------------ --bpfile, -b <s>: Name of file containing base-pairing info --outfile, -o <s>: Output file (default: ensemble_example_trx.pdb) --single, -s: Single-stranded DNA/RNA --ensemble, -e <s>: Ensemble delineated with MODEL/ENDMDL pairs --models, -m <s>: File containing an explicit list of model numbers --pattern, -p <s>: Pattern of model files to process (e.g., *.pdb) --list, -l <s>: File containing an explicit list of models --rotate, -r <s>: Options to be transfered to rotate_mol (quoted) --frame, -f <s>: Options to be transfered to frame_mol (quoted) --keep, -k: Keep the original relative orientation --bestview, -v: Set to the most extended view; keep orientation --help, -h: Show this message
HTH,

Xiang-Jun
Title: Re: Individual Model images in x3dna_ensemble block_image
Post by: acolasanti on October 14, 2013, 10:54:10 am: Thank you, the description of the -v option being shorthand for other options helped.

As far as ensemble output being as expected, I understand that. I guess a feature request would be a command line opting to produce an r3d file for each model without the need to use ex_str to break the models into individual files and then blockview on each structure to generate the image, for now I will wrap those commands in a script.

Thanks for your help.

Andrew
Title: Re: Individual Model images in x3dna_ensemble block_image
Post by: xiangjun on October 15, 2013, 05:46:07 pm: A more logical option would be that you make your script available in the Users' contributions section. Other users then may benefit from your effort.

Xiang-Jun