Messages

1

General discussions (Q&As) / Re: analysis along the md trajectories

« on: August 02, 2010, 02:45:45 pm »

Aneesh,

I am attaching two perl scripts that may be of use.  These will convert a group of pdb files created by ptraj and concatenate then into a single multi-model pdb file.  One version is for DNA where two strands are expected.  The other is for RNA, where a single chain is expected.  These scripts will convert the multi-letter base designations to one-letter designations and insert TER lines at the ends of chains. These are in-house and have only limited comments.

I had to change the extensions from the standard *.pl to *.txt in order to attach the files.

Mike Bruist (mfb)

2

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

« on: June 30, 2010, 10:42:46 pm »

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]

3

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

« on: June 28, 2010, 05:47:22 pm »

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

4

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The link to Curves on the Links page is no longer active.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

5

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

« on: June 26, 2010, 10:36:23 pm »

Thanks for explaining dd.  It is simple enough.

I haven't had a chance to look at Curves+.  I will get back with details on the phasing problem.

Mike

6

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

7

General discussions (Q&As) / Re: Suggestions

« on: June 26, 2010, 06:48:44 pm »

Your suggestion works very well.  I have added all of the deoxyribose, ribose and terminus specific nucleotide desigantions.  I can now read the AMBER ptraj pdb files without running them through a tailor.

Thanks

8

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

9

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)