[vtk-developers] caffeine.tcl regression

[Bill Lorensen]

Joachim,

I agree with your analysis. That caffeine file is not a valid PDB file. I
think your patch is a good one. I tried in on several valid PDB files and
it worked great.

Thanks,

Bill

On Tue, Oct 16, 2012 at 3:58 AM, Joachim Pouderoux <
joachim.pouderoux at kitware.com> wrote:

> Hi Bill,
>
> I am not an expert of this domain at all but here is what I understood of
> the situation.
> I also suspect the caffeine file not being a valid PDB file. According thelatest 2011 file format specification<http://www.wwpdb.org/documentation/format33/sect9.html#ATOM>but also the 1998
> one, <http://www.wwpdb.org/documentation/format23/sect9.html> the *element
> *symbol of an atom should be specified at columns 77-78, while the
> caffeine file does not provide it. The previous PDB reader used to take the
> 2 first chars of the *name* field (columns 13-16) to get the atom symbol
> (through the method vtkMoleculeReaderBase::MakeAtomType()) while this
> field use a very specific nomenclature - *"described in the Chemical
> Component Dictionary"* and this caused a misinterpretation of most PDB
> files I fetched on the PDB database.
> So to get the atom symbol with "official" PDB files and with this old and
> may be singular caffeine.pdb file, the latest patch I committed try to use
> the *element *field first and use *name* only of the element field is
> empty.
>
> Regards,
> Joachim
>
>
> 2012/10/14 Bill Lorensen <bill.lorensen at gmail.com>
>
>> Ooops. I wrote this e-mail before I saw that you had updated the gerrit
>> topic: http://review.source.kitware.com/#/t/1451/
>>
>> I just tried your patch and caffeine.tcl produces the correct image.
>>
>> Thanks,
>>
>> Bill
>>
>>
>> On Sun, Oct 14, 2012 at 8:40 AM, Bill Lorensen <bill.lorensen at gmail.com>wrote:
>>
>>> Joachim,
>>>
>>> I noticed that you have a gerrit topic for the caffeine.tcl regression.
>>>
>>> It seems that the file VTKData/Data/caffeine.pdb is not a valid pdb
>>> file. The file has been there since 2003, but I suspect it did not come
>>> from the official PDB. It may have come from here:
>>> http://elchem.kaist.ac.kr/jhkwak/okanaganpdb97/molecule/molecule.html
>>> The author says "I use a commercial programme to obtain x,y,z
>>> coordinates and use these in a format usable by RasMol."
>>>
>>> 1) I suggest we add the missing element symbols to caffeine.pdb.
>>> 2) Since the new PDB code ignores hydrogen (I assume they is some
>>> chemistry reason for this), I suggest we add a new baseline that shows
>>> caffeine without hydrogen.
>>>
>>> With these 2 changes, there is no need to modify the current PDB reader.
>>>
>>> Bill
>>>
>>>
>>
>>
>> --
>> Unpaid intern in BillsBasement at noware dot com
>>
>>
>


-- 
Unpaid intern in BillsBasement at noware dot com
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