2011/3/9 Angel Herráez <[email protected]>
> I realize that this may be difficult or impossible to implement, but I'll
> write it here at least for
> the record.
>
> I'm working on base pairing in RNA molecules, both canonical and
> noncanonical pairs.
> Example: 5S rRNA from E.coli, which is chain A in 2WWQ.pdb
>
> There are several reported GU pairs. One is between residues 9 and 111.
> When I look at it in Jmol and give
> calculate hbonds
> two Hbonds are created, between
>
> [U]111:A.N3 #7670 -30.643002 -82.178 -45.936
> [G]9:A.N1 #5486 -28.97 -83.12399 -42.726
>
> [U]111:A.O2 #7669 -28.472 -82.802 -45.579
> [G]9:A.N2 #5488 -26.938 -84.215996 -42.416
>
> both of them sprout at a funny angle relative to the rings and over 3.7
> angstroms length.
> Visual inspection suggests another 2 bonds as more reasonable, both are ca.
> 3 angstroms
>
> [G]9:A.O6 #5485 -30.924 -81.826 -42.938
> [U]111:A.N3 #7670 -30.643002 -82.178 -45.936
>
> [U]111:A.O2 #7669 -28.472 -82.802 -45.579
> [G]9:A.N1 #5486 -28.97 -83.12399 -42.726
>
> So it seems to me that Jmol is generating suboptimal Hbonds, based maybe on
> atom names
> rather that distance and aligning. I remember discussion on this list about
> admissible angles
> and distances when calculated Hbonds were implemented, but that was
> centered on
> proteins. Are nucleic acids out of those rules?
>
It's based on distance and aligning, but it is between those specific atoms.
If you want, you can use "real" H-bond calculation using
set hbondsRasmol false
calculate hbonds
At least see how that looks.
Bob
>
> I am attaching the state script.
>
>
> 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: 9-111_pair.spt
> Date: 9 Mar 2011, 21:30
> Size: 8437 bytes.
> Type: Unknown
>
>
> ------------------------------------------------------------------------------
> Colocation vs. Managed Hosting
> A question and answer guide to determining the best fit
> for your organization - today and in the future.
> http://p.sf.net/sfu/internap-sfd2d
> _______________________________________________
> Jmol-users mailing list
> [email protected]
> https://lists.sourceforge.net/lists/listinfo/jmol-users
>
>
--
Robert M. Hanson
Professor of Chemistry
St. Olaf College
1520 St. Olaf Ave.
Northfield, MN 55057
http://www.stolaf.edu/people/hansonr
phone: 507-786-3107
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
------------------------------------------------------------------------------
Colocation vs. Managed Hosting
A question and answer guide to determining the best fit
for your organization - today and in the future.
http://p.sf.net/sfu/internap-sfd2d
_______________________________________________
Jmol-users mailing list
[email protected]
https://lists.sourceforge.net/lists/listinfo/jmol-users
