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

Mohsen Asadbegi mohsenasad.7091 at gmail.com
Wed Apr 3 12:05:10 PDT 2019

Dear Dr. Elaine

Thanks for your comprehensive answer,

Regarding construction of d-peptide, I have found another answer, that is
provided below:

 In above web page, it is suggested to invert only alpha-carbon of each
residue to convert a L-amino acid to D-amino acid.
Do you confirm this method? Which atoms of a L-amino acid should be
inverted by invert command in CHIMERA?

Mohsen Asadbegi.

On Wed, 3 Apr 2019 at 22:12, Elaine Meng <meng at cgl.ucsf.edu> wrote:

> Hi Mohsen,
> For entirely D-amino acids, I like Mark’s suggestion of inverting the
> coordinates.  However, I think it would work to just invert the sign of X,
> Y, or Z coordinates (rather than all 3) since any of those would reflect
> the molecule across a plane.  There is some python code to flip the sign of
> all X-coordinates in this previous post:
> <
> http://www.cgl.ucsf.edu/pipermail/chimera-users/2010-September/005490.html
> >
> For mixtures of D- and L-amino acids,
> (1) there is a Chimera “invert” command to swap two substituents of an
> atom, which could be used to change chirality.
> <https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/invert.html>
> (2) for a variety of nonstandard or nonnatural amino acid sidechains,
> there is a Chimera plugin available from the SwissSidechain folks for
> adding the sidechains to make D-amino acids, see:
> <https://www.swisssidechain.ch/visualization/chimera.php>
> You could build the residues you want to make into D-amino acids as Gly in
> Chimera and then use this plugin to mutate them.
> I hope this helps,
> Elaine
> -----
> Elaine C. Meng, Ph.D.
> UCSF Chimera(X) team
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
> > On Apr 3, 2019, at 3:05 AM, Mark J van Raaij <mjvanraaij at cnb.csic.es>
> wrote:
> >
> > 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
> > http://wwwuser.cnb.csic.es/~mjvanraaij
> > Section Editor of Acta Crystallographica F, Structural Biology
> Communications
> > http://journals.iucr.org/f/
> >
> >
> >> 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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