Bugs item #3066682, was opened at 2010-09-15 03:48
Message generated for change (Comment added) made by hansonr
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Category: Applet
Group: v11
Status: Open
Resolution: None
Priority: 5
Private: No
Submitted By: lili35 (lili35)
Assigned to: Miguel (migueljmol)
Summary: Bug in secondary prediction
Initial Comment:
Jmol seems to have a problem with some secondary structure prediction.
Some amino acids represented in turn in some molecular graphic software (Pymol,
Chimera, Rasmol, VMD...) are represented in beta sheet in Jmol.
You can see it in attachment.
I think it is a bug. How can I fix it ?
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>Comment By: Bob Hanson (hansonr)
Date: 2010-09-17 12:57
Message:
12.1.15 -- I've added
structure SHEET set [-180,-40, 50, 80, -160, -30, 60, 90] # nonsense
numbers here.
meaning "define SHEET to be phi>=-180 and phi <=-40 and psi >= 50 and psi
< 80 OR phi >=-160 and phi <=-30 and psi >=60 and psi <= 90"
similar --- structure HELIX... structure TURN....
I realize this does not solve the issue that strands are not sheets, but
it is what I propose for now. Ages ago Jmol did attempt to use hydrogen
bonding to identify sheets, but this was only for intra-strand sheets,
which was not very satisfactory. We could still do something along those
lines, but really it is so rarely the issue -- mostly we use PDB files that
have all this defined already -- and the calculation is fairly involved to
get all the hydrogen bonds.
Bob
Bob
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Comment By: Bob Hanson (hansonr)
Date: 2010-09-17 11:02
Message:
I do hate to see you create an all new applet just for this. Why don't we
make it adjustable?
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Comment By: lili35 (lili35)
Date: 2010-09-17 09:42
Message:
Thanks for your help.
On my website, I will use Jmol to visualize hundred of models like this.
So manually disable structure is not easier.
I prefer reduce phi / psi angle allowed in the function 'isSheet' and
create my own JmolApplet. I do this, it works but I can't build the Applet
with build.xml. I work on a Mac OS 10.6.4 and Eclipse Helios (3.6).
I have this error message :
Buildfile: ~/Documents/workspace/Jmol/build.xml
[taskdef] Could not load definitions from resource
net/sf/antcontrib/antlib.xml. It could not be found.
BUILD FAILED
~/Documents/workspace/Jmol/build.xml:54: Cannot find tools/build-i18n.xml
imported from ~/Documents/workspace/Jmol/build.xml
Can you help me again ? ;-)
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Comment By: Nobody/Anonymous (nobody)
Date: 2010-09-16 10:02
Message:
It may not be a bug - as you point out, the torsions are 'strand like' -
but isolated segments like this are definitely not sheets. A sheet has at
least two strands, hbonded to each other. In fact, this stretch of chain is
something like a poly-proline helix conformation, I think.
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Comment By: Bob Hanson (hansonr)
Date: 2010-09-16 09:58
Message:
This is not a bug. Usually Jmol uses the HELIX and SHEET designations in
the PDB file, but this file has no header, so Jmol is doing the calculation
itself. That calculation is simply:
private static boolean isSheet(float psi, float phi) {
return
( (phi >= -180) && (phi <= -10) && (psi >= 70) && (psi <= 180) ) ||
( (phi >= -180) && (phi <= -45) && (psi >= -180) && (psi <= -130) )
||
( (phi >= 140) && (phi <= 180) && (psi >= 90) && (psi <= 180) );
}
In this case we have for phi/psi:
GLU29 -75.46 -41.95
ASN30 -111.74 70.29 *
ILE31 -94.93 109.93 *
PRO32 -52.12 166.21 *
so 30-32 are being tagged as sheet. I'm sure the other programs are using
hydrogen bonding.
If you don't like it, use in this case
structure none {30-32}
cartoons on
Bob
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Comment By: lili35 (lili35)
Date: 2010-09-15 15:15
Message:
It's done !
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Comment By: Bob Hanson (hansonr)
Date: 2010-09-15 10:28
Message:
please upload the PDB file.
----------------------------------------------------------------------
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https://sourceforge.net/tracker/?func=detail&atid=379133&aid=3066682&group_id=23629
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