[Chimera-users] PDB file of D-amino acids

Mark J van Raaij mjvanraaij at cnb.csic.es
Wed Apr 3 03:05:15 PDT 2019

may not the smartest way, but you could generate a peptide of L-amino acids and then make the mirror image by inverting the sign of all the x, y, z coordinates.
Either by hand in a text editor or with a program (I know of PDBSET from CCP4, but there are probably other options). The program may complain that you are doing something that is "not allowed" in protein structure, but you can probably override that.
In protein crystallography this is sometimes needed when heavy atom positions have been determined, sometimes we don't know if the given coordinates are correct or if the mirror image is it.

Mark J van Raaij
Dpto de Estructura de Macromoleculas
Centro Nacional de Biotecnologia - CSIC
calle Darwin 3
E-28049 Madrid, Spain
tel. (+34) 91 585 4616
Section Editor of Acta Crystallographica F, Structural Biology Communications

> On 3 Apr 2019, at 12:47, Mohsen Asadbegi <mohsenasad.7091 at gmail.com> wrote:
> Hello every one!
> I want to convert a sequence of d-amino acids or a sequence of d-amino acids and L-amino acids to a PDB file.
>  How can I construct such PDB file? I know that this is possible to enter the sequence of L-amino acids in CHIMERA (uppercase characters of the amino acids for example: LFVVA), But regarding d-peptides and retro-inverso peptides I don't know the exact way of building PDB files.
> Regards,
> Mohsen Asadbegi
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