Hi--
I've figured out the cause of your problem writing a pdb which
contains unknown atoms.
>
> The dg_sub_embed.pdb was like this:
> ATOM 1 CA MET 1 26.143 1.718 -0.064 1.00 0.00
> ATOM 2 HA MET 1 25.066 1.605 0.128 1.00 0.00
> ATOM 3 CB MET 1 26.399 1.588 -1.559 1.00 0.00
> ATOM 4 HB1 MET 1 ************************ 1.00 0.00
> ATOM 5 HB2 MET 1 ************************ 1.00 0.00
> ATOM 6 CG MET 1 25.154 1.922 -2.340 1.00 0.00
>
> When I run the xplor3.8 instead of xplor-nih, the *** were replaced by
> 9999.0, and the problem is gone.
>
This is a bug in xplor-nih in versions up to and including 2.0.3. It
will be fixed in version 2.0.4, which I will try to release in the
next week.
Until then, here's a workaround:
In the xplor script, before the write coor statement, place the
following three lines:
command("vector do (x=9999) (not known)")
command("vector do (y=9999) (not known)")
command("vector do (z=9999) (not known)")
regards--
Charles
--
Charles Schwieters email: [email protected]
www: http://schwieters.org/cds
phone: (301) 402-4914 FAX: (301) 402-2867
