[PyMOL] nucleic acid (one or two letter) residue names

[Pascal A. <p.a...@ib...>]

Hi Jason,

A more difficult one (at least for me)
Pymol seems to write (through save command) nucleic acid residue names not
as suggested by PDB convention.

Here is an extract of a PDB file (any PDB file containing nucleic acid
residues shows the same ­ try 100D for example)

ATOM      1  O5'   C A   1      -4.549   5.095   4.262  1.00 28.71  O
ATOM      2  C5'   C A   1      -4.176   6.323   3.646  1.00 27.35  C
ATOM      3  C4'   C A   1      -3.853   7.410   4.672  1.00 24.41  C

When I save this file (save command in pymol) i get this

Output from pymol

                 XXXXX (this is added by me)
ATOM      1  O5' C   A   1      -4.549   5.095   4.262  1.00 28.71  O
ATOM      2  C5' C   A   1      -4.176   6.323   3.646  1.00 27.35  C
ATOM      3  C4' C   A   1      -3.853   7.410   4.672  1.00 24.41  C

In one instance, the "C" residue name is left justified and right justified
in the other.
Of course, this cannot happen for the three letter residue names.
Any clue ?

I tried the following :

pdb_truncate_residue_name (boolean, default: off) controls whether or not
PDB residue names are truncated to three letters only.

with no effect

Thanks for help

Pascal
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