VMD-L Mailing List

From: Paul T. Bauman (pbauman_at_ices.utexas.edu)
Date: Wed Sep 03 2008 - 11:53:37 CDT

I should have mentioned I started counting from zero, so the "ATOM"
number is less than or equal to 99999 (i.e. I'm not violating the column
limitation of the .pdb format).

After playing a bit more, it seems that if the number of atoms are <
99999 (i.e. <=99998 ) then it will be fine. For some reason 99999 is
not included.

Thanks,

Paul

Paul T. Bauman wrote:
> Hello,
>
> I'm using VMD 1.8.6 on Linux_AMD64_OPENGL. I tried looking through the
> archive for some discussion of the following, but couldn't find it.
>
> I've noticed recently that if there are many atoms in my .pdb file,
> that the "CONECT" records do not seem to be processed correctly and
> the bonds are not plotted. Note that "autobonds" are still plotted.
> The magic number is somewhere between 3,000 "ATOM"'s (bonds are
> plotted) and 100,000 (greater than or equal, bonds are not plotted).
> Is there a maximum number of "ATOM"'s that can be in the .pdb file for
> "CONECTS" to be plotted? I only use "ATOM" and "CONECT" records in my
> .pdb file.
>
> I didn't want to send the file over the list because it's pretty
> large, but please let me know if you'd like it.
>
> Any assistance is most appreciated.
>
> Thanks,
>
> Paul
>