superimpose original structure with rebuilt structure

[mfb]

How do I superimpose a rebuilt structure with the original structure?

I have a pdb file for a short helix bot_hlx.pdb. The following commands were executed

find_pair bot_hlx.pdb stdout | analyze
cp bot_hlx.pdb bot_hlx.xse.pdb
grep HETATM bot_hlx.out >> bot_hlx.xse.pdb
rebuild -atomic bp_step.par bot_hlx.3dna.pdb
frame_mol -1 ref_frames.dat bot_hlx.xse.pdb bot_hlx2.xse.pdb

Here are segments of resulting files
head bot_hlx.xse.pdb bot_hlx2.xse.pdb
==> bot_hlx.xse.pdb <==
REMARK   1                     PDB file generated by ptraj (set  7576)
ATOM      1  P     G     1      19.913   8.210 -35.750  0.00  0.00
ATOM      2  O1P   G     1      19.867   9.473 -36.510  0.00  0.00
ATOM      3  O2P   G     1      19.402   8.238 -34.388  0.00  0.00

==> bot_hlx2.xse.pdb <==
REMARK    3DNA v2.0 [June 8, 2008] (by Dr. Xiang-Jun Lu; 3dna.lu@gmail.com)
ATOM      1  C1'   G A   1      -2.847   5.369  -0.801
ATOM      2  N9    G A   1      -1.650   4.570  -0.553
ATOM      3  C8    G A   1      -0.371   5.033  -0.356

As you see bot_hlx2.xse.pdb  and  bot_hlx.3dna.pdb are still in different orientations.

Thanks for your help.

Mike

[xiangjun]

Dear Mike,

There is some subtlety to "superimpose original structure with [3DNA] rebuilt structure". Your example serves to illustrate how to do it properly. In your original post:

Code: [Select]

find_pair bot_hlx.pdb stdout | analyze
cp bot_hlx.pdb bot_hlx.xse.pdb
grep HETATM bot_hlx.out >> bot_hlx.xse.pdb
rebuild -atomic bp_step.par bot_hlx.3dna.pdb
frame_mol -1 ref_frames.dat bot_hlx.xse.pdb bot_hlx2.xse.pdbYou do not need to bother with the "cp ..." and "grep ..." steps. Instead, you can achieve what you want simply as below:

Code: [Select]

find_pair bot_hlx.pdb stdout | analyze
frame_mol -1 ref_frames.dat bot_hlx.pdb bot_hlx_frame1.pdb
rebuild -atomic bp_step.par bot_hlx.3dna.pdbThen compare "bot_hlx_frame1.pdb" and "bot_hlx.3dna.pdb"; the coordinates for the base atoms would be very close. Have a try and report back how it goes. It would help if you have attached the example file "bot_hlx.pdb" so others can follow the steps.

Note that both analyze and rebuild generate the file "ref_frames.dat"; however, they are in different coordinate system.

Xiang-Jun

[mfb]

Xian-Jun,

That helps a lot. I did not realize rebuild rewrote ref_frames.dat.   I now must confess that I do not know how to attach a file to a post.  How do I attach the bot_hlx.pdb file?

Mike

[xiangjun]

Did you notice the "Upload attachment" tab below the post composition window? Simply click on it, and follow the instructions. Attachments, along with step-by-step instructions, are required to allow for reproducible examples.

Xiang-Jun

[mfb]

Attached is the pdb file with which I have been working.
This is an AMBER pdb file, which has designations for RNA that are distinct and differentiate terminal and internal residues.  The attached baselist.dat file contains all of these designations.


Xiang-Jun,

Your series of commands produces full and rebuilt molecules with the same coordinate frame.  But the helix axis from the *.out file is still in a different coordinate frame.  I need that axis for the fitting routine that uses this standard helix.  I solved that problem simply by analyzing the rebuilt bases and getting the axes from that out file.

Mike[attachment=1:35yw4frl]bot_hlx.pdb[/attachment:35yw4frl][attachment=0:35yw4frl]baselist.dat[/attachment:35yw4frl]

[xiangjun]

Dear Mike,

Thanks for sharing your knowledge of AMBER PDB format, which "which has designations for RNA that are distinct and differentiate terminal and internal residues".

Your series of commands produces full and rebuilt molecules with the same coordinate frame.

Glad to know that my command script works.

But the helix axis from the *.out file is still in a different coordinate frame. I need that axis for the fitting routine that uses this standard helix. I solved that problem simply by analyzing the rebuilt bases and getting the axes from that out file.

That's expected, and I am happy you have solved your the problem with helix axis.

Did you also notice that that parameters (in .out file) of the rebuilt structure are virtually identical to those from analyzing the original PDB file? This is another way to verify that the analyze/rebuild pair in 3DNA are rigorously defined and completely reversible.

Xiang-Jun