Re: [Jmol-users] pickcallback UNK bug?

[Robert H. <ha...@st...>]

The reason it is doing that is that it has become customary to use UNK for
all atoms in a PDB-format file that has nothing to do with structural
biology.  Fixed -- to release tonight or tomorrow.


Jmol.___JmolVersion="14.27.2"

bug fix: [UNK] missing in atom identities, even when part of actual
structures such as 3A0B



On Thu, Dec 14, 2017 at 4:21 PM, Eric Martz <em...@mi...>
wrote:

> Dear Bob,
>
> There are 598 entries in the PDB that have coordinates for unknown amino
> acids "UNK". An example is *155c*.
>
> ATOM    922  N   UNK A 122      12.620  16.758  24.013  1.00  0.00           N
> ATOM    923  CA  UNK A 122      12.950  15.573  24.817  1.00  0.00           C
> ATOM    924  C   UNK A 122      12.225  15.298  26.135  1.00  0.00           C
> ATOM    925  O   UNK A 122      12.755  14.617  27.025  1.00  0.00           O
> ATOM    926  N   UNK A 123      11.023  15.833  26.242  1.00  0.00           N
> ATOM    927  CA  UNK A 123      10.220  15.652  27.459  1.00  0.00           C
> ATOM    928  C   UNK A 123      10.677  16.835  28.313  1.00  0.00           C
> ATOM    929  O   UNK A 123       9.868  17.473  29.003  1.00  0.00           O
>
> The pickcallback for these atoms appears to me to have a bug (in both
> 2017-12-07 and 2016-05-27 releases of Jmol). For the CA atom it is e.g.
>
> CA #923 12.950 15.573 24.817
>
> but I think it should be
>
> *[UNK]122:A.*CA #923 12.950 15.573 24.817
>
> This can be contrasted with the 576 entries that contain UNX. An example
> is 1zuu which contains a single such atom.
>
> HETATM  538  UNK UNX A1001      14.657   8.674   6.997  0.50 11.24           X
>
> The pickcallback report is as one would wish:
>
> [UNX]1001:A.UNK #538 14.657 8.674 6.997
>
> Thanks,
> -Eric
>
> ------------------------------------------------------------
> ------------------
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
> _______________________________________________
> Jmol-users mailing list
> Jmo...@li...
> https://lists.sourceforge.net/lists/listinfo/jmol-users
>
>


-- 
Robert M. Hanson
Professor of Chemistry
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr


If nature does not answer first what we want,
it is better to take what answer we get.

-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900