Jmol users,
[reader warning: This is in very active development. It is changing day by
day. No guarantees.]
I thought I would say a bit about an exciting development in the
biomolecule area. We all are fairly well versed in protein secondary
structure -- helices, sheets, loops -- but what about RNA and DNA? Yes,
there are a couple of kinds of helix, and in general there is a lot of
flexibility and twistiness to the structure of nucleic acids. But what
else?
Lots else. Some time ago I met Xiang-Jun Lu, of Columbia University, and he
and I decided it was time to bring nucleic acid secondary structure to the
masses -- via Jmol. (see http://x3dna.org/index.php)
Well, this week has been the week to get our heads together and see what we
can do. I'm most excited about a VERY simple way to pull nucleic acid
secondary structure into Jmol. Xiang-Lun's DSSR (Determination of Secondary
Structure of RNA) algorithms are now directly available when you download a
structure from the PDB. All you have to do is add "/dssr" to an RCSB
request:
load =1msy/dssr # patience, though -- that's the ribosome! Better start
smaller!
What this does is send a call to Xiang-Jun's server at Columbia along with
the call to RCSB and combines the information in the form of a model and a
data structure. The report looks something like this:
DSSR: a software program for Defining the Secondary
Structures of RNA from three-dimensional coordinates
v1.1.0-2014apr09, Xiang-Jun Lu ([email protected])
Date and time: Tue Apr 8 22:04:52 2014
File name: dssr-O7chF1
no. of DNA/RNA chains: 2 [0=2754,9=122]
no. of nucleotides: 2876
no. of atoms: 98543
no. of waters: 7893
no. of metals: 210 [Na=86,Mg=117,K=2,Cd=5]
List of 1435 base pairs
List of 233 multiplets
List of 107 helices
List of 179 stems
List of 50 lone WC/wobble pairs
List of 40 coaxial stacks
List of 68 hairpin loops
List of 38 bulges
List of 67 internal loops
List of 35 junctions
List of 31 non-loop single-stranded segments
List of 3 kissing loop interactions
List of 106 A-minor motifs
List of 46 ribose zippers
List of 9 (possible) kink turns
[big secondary structure linear diagram section here]
List of 10181 H-bonds
You can see the full data structure (I would not recommend doing this with
the ribosome, by the way):
show dssr
show dssr "bulges"
show dssr "multiplets.5"
etc.
So what can you do? Lots of new capabilities. First, you select anything in
RNA or DNA based on structure:
select within(dssr,"stems")
display within(dssr,"kinkTurns.4");zoomto {displayed} 0
select within(dssr,"kinkTurns[SELECT basePairs where turnType=Normal]")
display selected
rotate best
zoomto {visible} 0
(OOOH -- That's right -- we now have minimal SQL-like support in Jmol!)
select within(dssr, "multiplets.3")
What you can select within dssr include:
$ print getProperty("auxiliaryInfo.models.1.dssr").keys
aMinorMotifs
basePairs
bulges
coaxialStacks
hBonds
hairpinLoops
helices
internalLoops
junctions
kinkTurns
kissingLoops
lonePairs
multiplets
riboseZippers
singleStranded
stems
summary
btw:
$ print getProperty("auxiliaryInfo.models.1.dssr").keys.all
will give you all the details of what is available:
aMinorMotifs
aMinorMotifs.106.data
aMinorMotifs.106.info
aMinorMotifs.106.motiftype
basePairs
basePairs.1435.DSSR
basePairs.1435.LW
basePairs.1435.Saenger
basePairs.1435.bp
basePairs.1435.bpPar1
basePairs.1435.bpPar2
basePairs.1435.bpPar3
basePairs.1435.bpPar4
basePairs.1435.bpPar5
basePairs.1435.bpPar6
basePairs.1435.helixId
basePairs.1435.id
basePairs.1435.info
basePairs.1435.name
basePairs.1435.nt1
basePairs.1435.nt2
basePairs.1435.res1
basePairs.1435.res2
bulges
bulges.38.basePairs
.... etc.
(The syntax xxx.keys.all is new and works on all arrays.)
What about visualization? just starting in on that. Anyone want to suggest
a color scheme for
color structure
?
I've added a new rendering option:
set backboneSteps
This creates a ladder-diagram for RNA that is pretty neat. Add a few balls
and labels on phosphorus, and you basically have a 3D stem diagram:
load =1msy/dssr
set backboneSteps
backbone -0.2
select _P; spacefill 1.5
label %[group1]; set labelOffset 0 0
color labels grey; font labels 16 bold
Loads of fun! (Hmm, I wonder what would happen if you turned that diagram
into a "molecule" and minimized it.... Would it unwrap the ribosome??)
Anyway, if you are interested in giving us good ideas, don't be shy.
Tonight's upload has the capability:
http://chemapps.stolaf.edu/jmol/zip/jmol-14.1.14_2014.04.08b.zip
should be working... Have at it. Feedback much appreciated!
Bob
--
Robert M. Hanson
Larson-Anderson 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
------------------------------------------------------------------------------
Put Bad Developers to Shame
Dominate Development with Jenkins Continuous Integration
Continuously Automate Build, Test & Deployment
Start a new project now. Try Jenkins in the cloud.
http://p.sf.net/sfu/13600_Cloudbees
_______________________________________________
Jmol-users mailing list
[email protected]
https://lists.sourceforge.net/lists/listinfo/jmol-users
