Hi,
In addition to what Bob and Rolf have said, you may find the following
information relevant regarding the 'new DSSR' and the 'strange' residue
identifier.
1. Rolf is correct to 'suspect the "1" being the model number'. The full
documentation about the so-called "Unit Id Format" (UnitId) is at URL:
http://www.bgsu.edu/research/rna/help/rna-3d-hub-help/unit-ids.html
2. Accordingly to Bob, UnitId is the new identifier adopted by EBI in a
project he has been involved. Per his request, I added support for the
UnitID in DSSR *specifically* for the updated DSSR-Jmol integration based
on JSON. So the actual DSSR command option is (using 1msy as an example):
"x3dna-dssr -i=1msy.pdb --json=ebi".
3. DSSR offers a set of different ways to specify nucleotides, via the
"--idstr" option. See the DSSR user manual for more details (
http://x3dna.bio.columbia.edu/docs/dssr-manual.pdf). In particular, the
list includes "--idstr=jmol" for output with identifiers like [G]2673:A.
Try: "x3dna-dssr -i=1msy.pdb --json --idstr=jmol". Moreover, the above
"--json=ebi" option is actually a shorthand for "--json --idstr=ebi"
4. As of DSSR v1.4.9-2016jan25 (the current downloadable version), the
option "--jmol" to facilitate the original DSSR-Jmol integration is still
available. Simply run "x3dna-dssr -i=1msy.pdb -jmol" to see what the output
looks like. The obsolete "--jmol" option will be removed from DSSR v1.5
since "--json" is the way to go.
5. See my blogpost "Integrating DSSR into Jmol and PyMOL" (
http://x3dna.org/highlights/integrating-dssr-into-jmol-and-pymol) and links
therein for more information.
HTH,
Xiang-Jun
Date: Thu, 28 Jan 2016 14:25:10 -0500
>
> From: Pshemak Maslak <p...@chem.psu.edu>
> Subject: [Jmol-users] Fwd: Re: new DSSR
> To: "jmol-users@lists.sourceforge.net"
> <jmol-users@lists.sourceforge.net>
> Message-ID: <56aa6b16.1040...@chem.psu.edu>
> Content-Type: text/plain; charset=windows-1252; format=flowed
> Thanks Rolf!
> PM
> Forwarded per Rolf's request
> On 01/28/2016 07:08 PM, Pshemak Maslak wrote:
> >
> > The new DSSR has base pairs and nucleotide indexed by numbers, For
> > example (the 9th base-pair):
> >
> > auxiliaryinfo.models[1].dssr.pairs[9].bp "A-T"
> > auxiliaryinfo.models[1].dssr.pairs[9].nt1 "|1|D|A|10||||"
> > auxiliaryinfo.models[1].dssr.pairs[9].nt2 "|1|E|T|29||||"
> >
> > What is the proper syntax to select any one of these"
> >
> From the example I showed in the previous thread regarding the DSSR
> change I would suspect that the first base would be residue "A" number
> "10" from chain "D". And I would suspect the "1" being the model number.
> But because it wasn't included in the former residue selection
> expression I am not really sure.
> The syntax for the selection expression is the same as before:
> select [A]10:D
> select [T]29:E
> Or if you would add the (suspected) model number it would look like this:
> select [A]10:D/1
> select [T]29:E/1
> You can split the 'nt1' and 'nt2' strings by "|" into an array and then
> build the selection expression as a string:
> ----- Jmol commands ----------
> nt1 = auxiliaryinfo.models[1].dssr.pairs[9].nt1.split("|");
> nt2 = auxiliaryinfo.models[1].dssr.pairs[9].nt2.split("|");
> res_nt1 = "[" + nt1[4] + "]" + nt1[5] + ":" + nt1[3] + "/" + nt1[2];
> res_nt2 = "[" + nt2[4] + "]" + nt2[5] + ":" + nt2[3] + "/" + nt2[2];
> select @res_nt1;
> select @res_nt2;
> ------------------------------
> I currently cannot post to the 'jmol-users' list because my recent email
> address change wasn't confirmed there yet. Please forward my answer to
> the list so that others can also see it.
> Regards,
> Rolf
> --
> Xiang-Jun Lu (PhD)
>
> Email: xiang...@x3dna.org
Web: http://x3dna.org/
Forum: http://forum.x3dna.org/
------------------------------------------------------------------------------
Site24x7 APM Insight: Get Deep Visibility into Application Performance
APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month
Monitor end-to-end web transactions and take corrective actions now
Troubleshoot faster and improve end-user experience. Signup Now!
http://pubads.g.doubleclick.net/gampad/clk?id=267308311&iu=/4140
_______________________________________________
Jmol-users mailing list
Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users
