Bugs item #3066682, was opened at 2010-09-15 10:48
Message generated for change (Comment added) made by lili35
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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: lili35 (lili35)
Date: 2010-09-17 16:42
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 17:02
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 16:58
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 22:15
Message:
It's done !
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Comment By: Bob Hanson (hansonr)
Date: 2010-09-15 17:28
Message:
please upload the PDB file.
----------------------------------------------------------------------
You can respond by visiting:
https://sourceforge.net/tracker/?func=detail&atid=379133&aid=3066682&group_id=23629
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