Angel Herraez wrote:
>Hi to all
>While playing with the PDB files for ribosome (1GIX, 1GIY), I have
>found that some RNAs get an interrupted line for backbone, trace and
>cartoon.
>
>First, the facts (files attached):
>
>1) tRNA, all atoms. 5 break points (residues 7-8, 15-16, 33-34, 37-
>38, 48-49). It seems that the cause is that the 3'O--P bond is not
>set between those due to too long a distance. I thought that could be
>the cause for the broken trace.
>I tried to use Jmol "connect" command, the bonds are created but the
>backbone is still broken.
>Then I added CONECT records in the PDB file, and the backbone is now
>OK.
>
>2) rRNA, only P atoms. 2 break points (residued 1-2, 69-70).
>Similar situation, but given there are only P atoms, no bond can be
>created, so I don't find a way to fix the broken trace.
>
>
>
The distance between the two P atoms (790 pm) is greater than the
maximum allowed distance:
// but some P atoms are up to 7.4 angstroms apart
private static float MAX_ADJACENT_PHOSPHORUS_DISTANCE = 7.5f;
If you think that needs to be increased we can certainly do that. I
don't know why we would ever care that they are not so far apart.
>My thoughts:
>I think that irrespective of bonds, if residue numbers are
>correlative, the backbone should be established. And particularly so
>in P-only models, where there are no bonds anyway.
>
>I will welcome opinions and suggestions to fix this and have a proper
>continuous trace.
>
>
>
>------------------------------------------------------------------------
>
>The following section of this message contains a file attachment
>prepared for transmission using the Internet MIME message format.
>If you are using Pegasus Mail, or any other MIME-compliant system,
>you should be able to save it or view it from within your mailer.
>If you cannot, please ask your system administrator for assistance.
>
> ---- File information -----------
> File: rRNA_5S.pdb.gz
> Date: 19 Nov 2007, 13:01
> Size: 2404 bytes.
> Type: Unknown
>
>
>------------------------------------------------------------------------
>
>The following section of this message contains a file attachment
>prepared for transmission using the Internet MIME message format.
>If you are using Pegasus Mail, or any other MIME-compliant system,
>you should be able to save it or view it from within your mailer.
>If you cannot, please ask your system administrator for assistance.
>
> ---- File information -----------
> File: tRNA_Esite.pdb.gz
> Date: 19 Nov 2007, 13:01
> Size: 27532 bytes.
> Type: Unknown
>
>
>------------------------------------------------------------------------
>
>-------------------------------------------------------------------------
>This SF.net email is sponsored by: Microsoft
>Defy all challenges. Microsoft(R) Visual Studio 2005.
>http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/
>
>------------------------------------------------------------------------
>
>_______________________________________________
>Jmol-users mailing list
>Jmol-users@lists.sourceforge.net
>https://lists.sourceforge.net/lists/listinfo/jmol-users
>
--
Robert M. Hanson
Professor of Chemistry
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr
If nature does not answer first what we want,
it is better to take what answer we get.
-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
-------------------------------------------------------------------------
This SF.net email is sponsored by: Microsoft
Defy all challenges. Microsoft(R) Visual Studio 2005.
http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/
_______________________________________________
Jmol-users mailing list
Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users
