Kumardeep,
At daliLite, you get this:
*
First Structure & Chain: mol1A
* No.Second Structure & ChainZ-ScoreAligned ResiduesRMSD [Å]Seq. Identity
[%]Structural AlignmentSuperimposed C-alpha TracesPDB Files: mol2 is
rotated / translated to mol1 position 1mol2A0.6343.215click
here<http://www.ebi.ac.uk/Tools/es/cgi-bin/jobresults.cgi/dalilite/dalilite-20120714-2227229381/aln.html#alignment-1>
CA_1.pdb<http://www.ebi.ac.uk/Tools/es/cgi-bin/jobresults.cgi/dalilite/dalilite-20120714-2227229381/CA_1.pdb>
mol1_original.pdb<http://www.ebi.ac.uk/Tools/es/cgi-bin/jobresults.cgi/dalilite/dalilite-20120714-2227229381/mol1_original.pdb>
mol2_1.pdb<http://www.ebi.ac.uk/Tools/es/cgi-bin/jobresults.cgi/dalilite/dalilite-20120714-2227229381/mol2_1.pdb>
so there are your two files -- specifically mol2_1.pdb. Just download that
and load it into Jmol along with your first pdb file.
Say my first file name was 1crn.pdb. Then I would do this:
1) "copy link location" for that second file or just download the file
2) in Jmol:
load =1crn # (or whatever file you used as "model 1")
load append
http://www.ebi.ac.uk/Tools/es/cgi-bin/jobresults.cgi/dalilite/dalilite-20120714-2227229381/mol2_1.pdb
# (or whatever link that is)
model *
and go from there.
If you then save that as a PNGJ file, it will encapsulate both model files
so that you don't need to worry about losing the file on the server even if
you don't download it.
No need for PyMOL, I think.
Bob
On Sat, Jul 14, 2012 at 2:19 PM, Kumardeep Chaudhary
<[email protected]>wrote:
> Hi all
> I am trying to use Jmol applet for representing the 2 aligned pdb files.
> The files have been aligned using DaliLite on the local. but I am unable to
> locate the aligned coordinate file. Basically, DaliLite sends link to its
> own site for Jmol visualization of aligned files. But I want to give link
> to my local web page containg Jmol applet. So how to go for that.
> I tried pymol to align these 2 files and get the session file as .pse
> extension. Is there any way to load this .pse file to jmol ?
>
> Thanks in advance
> Kumardeep
>
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--
Robert M. Hanson
Larson-Anderson Professor of Chemistry
Chair, Chemistry Department
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
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