Re: [Jmol-users] new DSSR
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/
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Re: [Jmol-users] Support of 'alchemy' format for rectangular schematic base-pair geometry
OpenBabel reads the Alchemy format http://openbabel.org/wiki/Alchemy which makes me wonder if Jmol could use the versatility of Open Babel and avoid writing new code. Xavier I have been using 'openbabel' for a long while, and know that it supports alchemy format. However, it can't read my schematic base-pair geometry. I know my alchemy file does not have 'proper' chemistry. The chemistry-related tools are too intelligent to handle such a simple case. Date: Mon, 08 Dec 2008 23:52:21 +0100 From: Angel Herr?ez [EMAIL PROTECTED] Subject: Re: [Jmol-users] Support of 'alchemy' format for rectangular schematic base-pair geometry To: jmol-users@lists.sourceforge.net Message-ID: [EMAIL PROTECTED] Content-Type: text/plain; charset=US-ASCII Xiang, I would suggest that whatever software you use to produce the ALC files is changed so that it produces MOL files. These have a well documented format specification and will be read by Jmol as well as RasMol. It seems that Alchemy format is rather old (there isn't even a mention of the program at the Tripos website) and there is no documentation about the format details, so it is difficult and unlikely that Jmol will read it. MDL MOL format specifies atoms and bonds as well, and you can easily instruct Jmol to render those bonds only. I guess you could even use plain text files making use of the DATA command in Jmol to draw the boxes you need. * As I mentioned in my previous message, I am playing tricks with the alchemy format Yes, that was clear. But the brief answer is: Jmol does not understand the alc format. In relation to Jmol, I am hoping Jmol could render such non-chemistry-based alchemy file properly. In essence, the render just needs to respect the node and linkage information explicitly defined in the file: it does not try to be clever to deduce some chemistry from it. Yes, that is perfectly possible. But you need a file format that Jmol understands. Maybe you can use some utility like OpenBabel to convert ALC to MDL files? or http://www.webqc.org/molecularformatsconverter.php I know alchemy is not as well-supported/documented as the one your mentioned. I picked alchemy up instead of other options for some random reason I can't recall. I initially figured out the alchemy format by going through RasMol code and played with some examples that RasMol writes out. It is a simple format, and I am using it in the simplest possible way. RasMol likes it, and I have been using RasMol for interactive visualization purpose only, without any problem. As far as Jmol's support for alchemy is concerned, I converted a sample PDB file to alchemy using 'openbabel' and Jmol can read it without a problem. That's why I thought Jmol does support standard alchemy in my initial post, and qualified my subject line with 'alchemy' format for rectangular schematic base-pair geometry. Thanks so much to all of you for for your feedbacks. I still hope Jmol could support this un-chemical alchemy format. It could be taken as an extreme case to validate an alchemy reader. Xiang-Jun -- Xiang-Jun Lu (Ph. D.) Creator Maintainer of 3DNA Email: [EMAIL PROTECTED] http://3dna.rutgers.edu:8080/forum -- SF.Net email is Sponsored by MIX09, March 18-20, 2009 in Las Vegas, Nevada. The future of the web can't happen without you. Join us at MIX09 to help pave the way to the Next Web now. Learn more and register at http://ad.doubleclick.net/clk;208669438;13503038;i?http://2009.visitmix.com/___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Support of 'alchemy' format for rectangular schematic base-pair geometry
Dear Bob,
Thank you so much for your detailed explanations.
Date: Tue, 9 Dec 2008 18:19:09 -0600
From: Robert Hanson [EMAIL PROTECTED]
Subject: Re: [Jmol-users] Support of 'alchemy' format for rectangular
schematic base-pair geometry
To: jmol-users@lists.sourceforge.net
Message-ID:
[EMAIL PROTECTED]
Content-Type: text/plain; charset=ISO-8859-1
Before I write this reader, can I ask if it's possible you could use
another format?
I could, but I really do not have a solid reason to (see below).
Do you have all these files already made, so you are eager to use them
exactly, or do you have a program that produces them?
Yes, I have several (utility) programs within 3DNA that produce and read
such alchemy files for various (internal) purposes. It is nice that RasMol
can render them properly, but essentially, 3DNA is a suite of command-line
driven programs which do not rely on RasMol for using the alchemy files.
Because if it's a program that produces them, I suggest doing a little
modification to that program to produce Jmol scripts instead. That
would be far more efficient, and it should be pretty easy to make them
- probably just one small subroutine. Then you could do all sorts of
interesting things in relation to dynamically changing them,
displaying them, measuring them, etc., within Jmol. For example, that
one you show as a demo could be something like this:
pt1={-2.2500 5. 0.2500}
pt2={-2.2500 -5. 0.2500}
pt3={-2.2500 -5. -0.2500}
pt4={-2.2500 5. -0.2500}
pt5={2.2500 5. 0.2500}
pt6={2.2500 -5. 0.2500}
pt7={2.2500 -5. -0.2500}
pt8={2.2500 5. -0.2500}
draw box line @pt1 @pt2 @pt3 @pt4 @pt1 @pt5 @pt6 @pt7 @pt8 @pt5
draw side1 plane @pt1 @pt2 @pt3 @pt4
(not complete, but you get the idea)
But even better, you could define a Jmol function that draws the boxes
for you give the eight points:
function drawbox(name, pt1, pt2, pt3, pt4, pt5, pt6, pt7, pt8)
draw ID @{name + _box} line @pt1 @pt2 @pt3 @pt4 @pt1 @pt5 @pt6
@pt7 @pt8 @pt5
draw ID @{name + _side1} plane @pt1 @pt2 @pt3 @pt4
etc.
end function
then just
drawbox({-2.2500 5. 0.2500},{-2.2500 -5. 0.2500}
,{-2.2500 -5. -0.2500} ,\
{-2.2500 5. -0.2500},{2.2500 5. 0.2500},{2.2500
-5. 0.2500},\
{2.2500 -5. -0.2500},{2.2500 5. -0.2500})
for each box. It seems to me, for that matter, you only need three
points to define the box. So that would be even easier.
Now, if you are really fancy, what you do is embed those commands in
the pdb files themselves, so when the pdb file is loaded, the boxes
are all drawn automatically. Rolf can show you how he does that at
Jena.
And, better, if you are doing this based on some simple criterion in
PDB files, then you should be able to define a function that allows
drawing of such boxes for the entire model all within Jmol. That would
be REALLY COOL, because then anyone could do it with any PDB file. I
have such a function (somewhere), for example, for drawing all the
peptide planes.
Bob
Given the amazing support of Jmol from you and others, I have been
considering to use Jmol (and eventually switch to it), and then came cross
the alchemy format issue. All the cool stuffs you mentioned are very
impressive, and I will surely dig more deeply into Jmol in the future.
However, I still think a simple render of the alchemy format in Jmol would
be ideal. Then people like me could simply load the alchemy file into Jmol
to visualize it without writing any Jmol-specific scripts.
I have checked RasMol v2.6.4 source code, and found the alchemy reader is
via function LoadAlchemyMolecule() in infile.c, and it is pretty short. The
data directory even has an example file 'asprin.alc'.
Since there is no official alchemy document, and given the problem that
'openbabel' has with my non-chemistry oriented alchemy file (see my previous
post), maybe one could forget the complexity of atom/bond types, just take
them as nodes and linkages, and Jmol would render the file at face value.
Thanks,
Xiang-Jun
--
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Creator Maintainer of 3DNA
Email: [EMAIL PROTECTED]
http://3dna.rutgers.edu:8080/forum
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