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Hi Robbie,
maybe it is good not to use coordinates for calculations if you cannot
measure the coordinates?
Cheers,
Tim
On 06/13/2014 12:35 PM, Robbie Joosten wrote:
> Hi Tim,
>
> The problem with missing atoms in ligands is that you cannot use
> the coordinates for any follow-up calculation that requires ligand
> topology (e.g. restraint generation). That forces you to rely on
> the annotation of the compound, for instance at the PDB. That can
> be quite messy and leaves extra room for errors and
> misunderstandings.
>
> Cheers, Robbie
>
>> -----Original Message----- From: CCP4 bulletin board
>> [mailto:[log in to unmask]] On Behalf Of Tim Gruene Sent:
>> Friday, June 13, 2014 12:04 To: [log in to unmask] Subject:
>> Re: [ccp4bb] Invisible atoms in ligands
>>
> Hi Frank,
>
> if you can calculate their position, i.e. it is part of a rigid
> group, I would leave it. If it is flexible, I would remove it
> because the reader of my deposited structure may not be a
> crystallographer and misinterpret the result.
>
> If it is obvious that some atoms are missing, it is even better
> because it is more likely to make the reader think about the
> reasons why part of the ligand is not displayed in the model.
>
> Cheers, Tim
>
> On 06/13/2014 11:45 AM, Frank von Delft wrote:
>>>> Hi all - talking about ligands, a quick question on that old
>>>> conundrum, of what to do about invisible atoms -- build them
>>>> with occ=0, or omit them?
>>>>
>>>> For bits of protein, I know all the arguments; personally I
>>>> prefer omitting atoms because:
>>>>
>>>> * for amino acid sidechains, their presence is implied in the
>>>> residue name. * for whole residues, their presence is implied
>>>> in the sequence numbering
>>>>
>>>> However: what about ligands? Nowhere else in the PDB file
>>>> is their presence implied - or have I missed something?
>>>>
>>>> (Certainly disorder in a ligand is important information that
>>>> needs to be captured!)
>>>>
>>>> Cheers phx
>>>>
>
>
- --
- --
Dr Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen
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