My Idea:
May be not direct but may work :)
PDB files generally does not have Hydrogen atoms. In such case u can use
'REDUCE ' program from RICHARDSON Lab.
Convert it to MOL2 format using Openbabel, which retains the atom
nomenclature(This is the case only for PDB to MOL2, in all othercase, it
gives atom type)
Hope it will help you
PRASUN (ASHOKA)
Desire + stability = Resolution
Resolution + Hard work = Success
On Fri, Jul 4, 2014 at 3:16 PM, Ooker <ganuongp...@gmail.com> wrote:
> I think Pybel is just Open Babel for Python, which means there is no
> different in the output between them. Anyway, I'll try to numbering the H
> atoms incrementally. Thanks for your help :D.
>
>
> On Fri, Jul 4, 2014 at 3:13 PM, Pascal Muller <pascal.jm.mul...@gmail.com>
> wrote:
>
>> Hi,
>>
>>
>>> And what's your definition of "ligand" in the PDB? :)
>>>>
>>>
>>> Well, it's on HETATM lines and not a familiar molecule like HOH or PO4
>>> for example.
>>>
>>
>> Ok, if it's not yet the case, be aware that there is a lot of garbage
>> (PEG, detergents, strange ions, deuterated water, modified aminoacids and
>> so on) too.
>>
>>
>>> Anyway, if you don't want to write a script to modify H atom names
>>>> (should be easy)
>>>>
>>>
>>> I'm not saying that I don't want to wirte a script. I just wonder how
>>> should I modify it appropriately. Should it respect the heavy atoms whose H
>>> or just mark continuously like H1, H2, H3 from top to bottom?
>>>
>>
>> I would go for incremental numbering of H... but probably doesn't matter?
>>
>>
>>>
>>> I don't know.
>>>>
>>>
>>> Well, aren't you a developer of it? I'm sorry if this is too directly.
>>>
>>
>> Myself, no, I'm mainly using pybel, and that's it :)
>> But some other people here are active and skilled developpers.
>>
>> Regards,
>> Pascal
>>
>
>
>
> ------------------------------------------------------------------------------
> Open source business process management suite built on Java and Eclipse
> Turn processes into business applications with Bonita BPM Community Edition
> Quickly connect people, data, and systems into organized workflows
> Winner of BOSSIE, CODIE, OW2 and Gartner awards
> http://p.sf.net/sfu/Bonitasoft
> _______________________________________________
> OpenBabel-discuss mailing list
> OpenBabel-discuss@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
>
>
------------------------------------------------------------------------------
Open source business process management suite built on Java and Eclipse
Turn processes into business applications with Bonita BPM Community Edition
Quickly connect people, data, and systems into organized workflows
Winner of BOSSIE, CODIE, OW2 and Gartner awards
http://p.sf.net/sfu/Bonitasoft
_______________________________________________
OpenBabel-discuss mailing list
OpenBabel-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
