Topics

1

General discussions (Q&As) / Curves link

« on: June 27, 2010, 10:07:55 am »

The link to Curves on the Links page is no longer active.  You probably want to change it to:

http://gbio-pbil.ibcp.fr/Curves_plus/Curves+.html

Mike

2

General discussions (Q&As) / superimpose original structure with rebuilt structure

« on: June 26, 2010, 10:34:12 pm »

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

3

General discussions (Q&As) / Suggestions

« on: June 25, 2010, 10:55:37 am »

Could find_pair be modified to recognize explicit ribonucleotide abreviations (RG,RA,RC,RU,RG5,...,RC3,...)?  These are used by AMBER's ptraj and have to be substituted with single-letter base desigations before find_pair recognizes them.

Is it intended that when you enter "find_pair -h" the previous set of files from a find_pair analysis are erased?

Mike Bruist

4

General discussions (Q&As) / relative phase of two helicies

« on: June 25, 2010, 10:45:41 am »

HI!  I have just joined and am seeking advice on applying 3DNA to analysis of molecular dynamics runs on small RNAs.  I want to measure the relative orientation of two helical segments of an RNA.  I will analyze the two helicies separately, fitting thenm to the full molecule, and then use the "Global linear helical axis coordinates to get the relative angle of the two segments.  

What is described by the three numers follwing "Helix:" in this section?

I am not sure how to get relativet twists (helical phases) of the two segments.  I am considering fitting helices in a trajectory to a standard average helix and then compare the RN9/YN1 lines of the first base pair in each fit helix.  Any better sugestions?

Mike Bruist, University of the Sciences in Philadelphia (mfb)