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Author Topic: Individual Model images in x3dna_ensemble block_image  (Read 8154 times)

Offline acolasanti

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Individual Model images in x3dna_ensemble block_image
« 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

Offline acolasanti

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Re: Individual Model images in x3dna_ensemble block_image
« Reply #1 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



Offline xiangjun

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Re: Individual Model images in x3dna_ensemble block_image
« Reply #2 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

Offline acolasanti

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Re: Individual Model images in x3dna_ensemble block_image
« Reply #3 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

Offline xiangjun

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Re: Individual Model images in x3dna_ensemble block_image
« Reply #4 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

 

Created and maintained by Dr. Xiang-Jun Lu [律祥俊] (xiangjun@x3dna.org)
The Bussemaker Laboratory at the Department of Biological Sciences, Columbia University.