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... solving a structure of a cyclic peptide with Ornithine residue, where Orn side-chain participates in an amide bond.

Normally I use Molmol to calculate fitted structure ensembles, but in this case Ornithine is a non-standard residue and is not part of Molmol residue library the the program cannot display it.

Could anyone give an advice - what software could open pdb's or equivalent data formats of arbitrary molecules and fit structures? Is it possible with Molmol?

Will be super thankful for your advice.

asked Jan 28 '10 at 15:10

Evgeny%20Fadeev's gravatar image

Evgeny Fadeev
5571

updated Jan 29 '10 at 11:47


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Ok, answering myself. Turns out MOLMOL opens XYZ files. So I wrote a little program in Python that converts PDB files saved by XPLOR to XYZ format.

XYZ format looks like this:

number_of_atoms
comment
atom_name   x_coor   y_coor   z_coor
...

No residue numbers go into XYZ file, so it will be impossible to make selections by residues - only by atom numbers. Maybe I'll fix up the script above to create selection statements too... If that happens I'll post an update here.

link

answered Feb 02 '10 at 08:36

Evgeny%20Fadeev's gravatar image

Evgeny Fadeev
5571

updated Feb 02 '10 at 08:59

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