Re: [Jmol-developers] bug in the script for ligand pockets in PDB
It's not general because within Jmol there are over 225 references to .toLowerCase() and over 150 to .toUpperCase(), and any of these are potential problems in that regard, not just that one script or scripts in general. And I think it is not possible to do this in JavaScript without an explicit check for Turkish, which probably is not going to happen. But it is a good idea to at least fix that one. cc'ing Jesse Woo (RCSB/San Diego) for that. Bob On Thu, Jun 5, 2014 at 12:45 AM, Angel Herráez angel.herr...@uah.es wrote: yes, OK, but that's not a general solution. I suppose that happens in Java and JavaScript? Not sure, but I will try to check today. It is happening in the PDB site, I think it was Java Jmol. I guess I can use the ?_USE=HTML5 there for testing. Why is it not general? Just avoid uppercase in scripts. -- Learn Graph Databases - Download FREE O'Reilly Book Graph Databases is the definitive new guide to graph databases and their applications. Written by three acclaimed leaders in the field, this first edition is now available. Download your free book today! http://p.sf.net/sfu/NeoTech ___ Jmol-developers mailing list Jmol-developers@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-developers -- Robert M. Hanson Larson-Anderson Professor of Chemistry 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 -- Learn Graph Databases - Download FREE O'Reilly Book Graph Databases is the definitive new guide to graph databases and their applications. Written by three acclaimed leaders in the field, this first edition is now available. Download your free book today! http://p.sf.net/sfu/NeoTech___ Jmol-developers mailing list Jmol-developers@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-developers
Re: [Jmol-developers] bug in the script for ligand pockets in PDB
yes, short of redesigning all the code references of .toLowerCase() and .toUpperCase() just for our friends in Turkey, there's not much we can do about this. On Wed, Jun 4, 2014 at 1:36 AM, Angel Herráez angel.herr...@uah.es wrote: Yes, I had read about such a problem. The issue is, however, that it is not a user-given ID with Turkish characters, but the ID token in the source code. -- Learn Graph Databases - Download FREE O'Reilly Book Graph Databases is the definitive new guide to graph databases and their applications. Written by three acclaimed leaders in the field, this first edition is now available. Download your free book today! http://p.sf.net/sfu/NeoTech ___ Jmol-developers mailing list Jmol-developers@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-developers -- Robert M. Hanson Larson-Anderson Professor of Chemistry 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 -- Learn Graph Databases - Download FREE O'Reilly Book Graph Databases is the definitive new guide to graph databases and their applications. Written by three acclaimed leaders in the field, this first edition is now available. Download your free book today! http://p.sf.net/sfu/NeoTech___ Jmol-developers mailing list Jmol-developers@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-developers
Re: [Jmol-developers] bug in the script for ligand pockets in PDB
Bob, I think you are not getting my point.
I think this happens because there is an upercase ID text in the source
code of that gotoligand function.
For some reason, Jmol goes later to convert that to lowercase.
But if the gotoligand function had just lowercase id, then I believe no
harm
would happen.
That is,
http://www.rcsb.org/pdb/Viewers/jmol-14.1.1//jsmol/spt/ext/rcsb/gotoLigand.s
pt
has these:
// contact surface
contact ID surf {ligandAtoms} surface
contact slab 60 fullylit
// hydrogen bonds
contact ID hb {ligandAtoms} hbond
select within(3.3,ligandAtoms)
Those two 'contact ID ' should be changed to 'contact id ' and see if the
problem goes away.
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Re: [Jmol-developers] bug in the script for ligand pockets in PDB
yes, OK, but that's not a general solution. I suppose that happens in Java
and JavaScript?
On Wed, Jun 4, 2014 at 2:20 PM, Angel Herráez angel.herr...@uah.es wrote:
Bob, I think you are not getting my point.
I think this happens because there is an upercase ID text in the source
code of that gotoligand function.
For some reason, Jmol goes later to convert that to lowercase.
But if the gotoligand function had just lowercase id, then I believe
no harm would happen.
That is,
http://www.rcsb.org/pdb/Viewers/jmol-14.1.1//jsmol/spt/ext/rcsb/gotoLigand.spt
has these:
// contact surface
contact ID surf {ligandAtoms} surface
contact slab 60 fullylit
// hydrogen bonds
contact ID hb {ligandAtoms} hbond
select within(3.3,ligandAtoms)
Those two 'contact ID ' should be changed to 'contact id ' and see if
the problem goes away.
--
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applications. Written by three acclaimed leaders in the field,
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--
Robert M. Hanson
Larson-Anderson Professor of Chemistry
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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Re: [Jmol-developers] bug in the script for ligand pockets in PDB
Yes, that makes sense. Funny that we just talked about this.
string.lowerCase() apparently chokes with Turkish.
Go figure.
Bob
On Tue, Jun 3, 2014 at 2:13 PM, Angel Herráez angel.herr...@uah.es wrote:
Dear Bob,
You're going to love this bug report. It's thrilling!
I was today demonstrating the new PDB ligand pocket view that uses the
contact command. Guess what... it breaks in Turkish computers, nothing is
displayed but the standard protein rendering.
I think I have tracked down the issue. This is the error in the console
history:
line 23 command 20 of function gotoligand:
contact ıd surf { ligandatoms } surface
gotoligand ( , IBP )
Note that Turkish i without the dot. I guess the uppercase ID (that
you usually use) is being somewhere converted to lowercase, and in Turkish
that means without the dot on the i, and Jmol chokes.
That happens while working directly on the PDB site (Jmol Java), at
least with Chrome and Firefox, and does not happen on my Spanish laptop in
the same room and network. This means all Turkish users are deprived of the
nice display of ligands within the contact-colored surface.
For clarification, Turkish is unique in having 2 kinds of i in both
upper and lowercase and the matching makes it different:
i -- İ
ı -- I
while in any other language:
i -- I
(I hope the Unicode characters don't get lost in the email)
Probably changing the original code into lowercase id will avoid the
issue.
We can test up to next Friday.
Cheers,
--
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Robert M. Hanson
Larson-Anderson Professor of Chemistry
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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Graph Databases is the definitive new guide to graph databases and their
applications. Written by three acclaimed leaders in the field,
this first edition is now available. Download your free book today!
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Re: [Jmol-developers] bug in the script for ligand pockets in PDB
here it is:
http://mattryall.net/blog/2009/02/the-infamous-turkish-locale-bug
On Tue, Jun 3, 2014 at 3:21 PM, Robert Hanson hans...@stolaf.edu wrote:
Yes, that makes sense. Funny that we just talked about this.
string.lowerCase() apparently chokes with Turkish.
Go figure.
Bob
On Tue, Jun 3, 2014 at 2:13 PM, Angel Herráez angel.herr...@uah.es
wrote:
Dear Bob,
You're going to love this bug report. It's thrilling!
I was today demonstrating the new PDB ligand pocket view that uses
the contact command. Guess what... it breaks in Turkish computers,
nothing is displayed but the standard protein rendering.
I think I have tracked down the issue. This is the error in the console
history:
line 23 command 20 of function gotoligand:
contact ıd surf { ligandatoms } surface
gotoligand ( , IBP )
Note that Turkish i without the dot. I guess the uppercase ID (that
you usually use) is being somewhere converted to lowercase, and in Turkish
that means without the dot on the i, and Jmol chokes.
That happens while working directly on the PDB site (Jmol Java), at
least with Chrome and Firefox, and does not happen on my Spanish laptop in
the same room and network. This means all Turkish users are deprived of the
nice display of ligands within the contact-colored surface.
For clarification, Turkish is unique in having 2 kinds of i in both
upper and lowercase and the matching makes it different:
i -- İ
ı -- I
while in any other language:
i -- I
(I hope the Unicode characters don't get lost in the email)
Probably changing the original code into lowercase id will avoid the
issue.
We can test up to next Friday.
Cheers,
--
Learn Graph Databases - Download FREE O'Reilly Book
Graph Databases is the definitive new guide to graph databases and their
applications. Written by three acclaimed leaders in the field,
this first edition is now available. Download your free book today!
http://p.sf.net/sfu/NeoTech
___
Jmol-developers mailing list
Jmol-developers@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-developers
--
Robert M. Hanson
Larson-Anderson Professor of Chemistry
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
--
Robert M. Hanson
Larson-Anderson Professor of Chemistry
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
--
Learn Graph Databases - Download FREE O'Reilly Book
Graph Databases is the definitive new guide to graph databases and their
applications. Written by three acclaimed leaders in the field,
this first edition is now available. Download your free book today!
http://p.sf.net/sfu/NeoTech___
Jmol-developers mailing list
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