Re: [Jmol-developers] bug in the script for ligand pockets in PDB

[Robert H. <ha...@st...>]

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 <ha...@st...> 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 <ang...@ua...>
> 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
>
>


-- 
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