Re: [Jmol-users] Bug? Secondary structure in PDB/CIF ignored.

[Giuseppe S. <giu...@gm...>]

Hi all, just my two cents.
I noted that the command '$ show structure' gave me different results when
issued before or after '$ calculate structure'.

$ show structure
HELIX    1   1 ALA A   23  ASP A   36  1 strucno= 2

SHEET    1  S1 0 LEU A  12  ALA A  20 strucno= 1
SHEET    2  S2 0 GLU A  42  ASP A  46 strucno= 3
SHEET    3  S3 0 LYS A  50  GLU A  56 strucno= 4

$ calculate structure
....

$ show structure
HELIX    1   1 ALA A   23  ASP A   36  1 strucno= 3

SHEET    1  S1 0 THR A   2  ASN A   8 strucno= 1
SHEET    2  S2 0 LYS A  13  GLU A  19 strucno= 2
SHEET    3  S3 0 GLU A  42  ASP A  46 strucno= 5
SHEET    4  S4 0 THR A  51  THR A  55 strucno= 7

TURN     1   1 ASN A  37  GLY A  38 strucno= 4
TURN     2   2 ASP A  47  LYS A  50 strucno= 6

Maybe as said by m0lviz, in PDB file SHEET 2 have to be marked with 0 and
not SHEET 1.

bye and good vacations to all
Giuseppe

Il giorno dom 17 ago 2025 alle ore 22:21 m0lviz--- via Jmol-users <
jmo...@li...> ha scritto:

> Dear Bob,
>
> In Jmol.jar 16.3.33, 16.2.5:
>
> $ load =1pgb
> $ cartoon only
> $ color structure
>
> [image: Inline image]
>
>
> One strand of the beta sheet, residues 1-9, is not rendered as a beta
> strand, despite being so designated by the authors of the PDB file:
>
> HELIX    1   1 ALA A   23  ASP A   36  1                                  14
> SHEET    1  S1 4 LEU A  12  ALA A  20  0                                        *SHEET    2  S1 4 MET A   1  GLY A   9 -1 *
> SHEET    3  S1 4 LYS A  50  GLU A  56  1
> SHEET    4  S1 4 GLU A  42  ASP A  46 -1
>
>
> (At the end of each SHEET line, 0 means the first strand of a sheet, 1
> means parallel to the preceding strand, and -1 means antiparallel.)
>
> $ calculate structure
> $ cartoon
>
> Now residues 1-9 are rendered as a beta strand.
>
> The same behavior occurs when loading the mmCIF file.
>
> I have not looked for nor observed other examples.
>
> -Eric
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