Read Amber format

[J.R.Lewandowsk@…]

as per summary

[pett]

Tomorrow's daily build will read Amber netCDF coordinate files (.nc suffix), not "formatted" ASCII coordinates. If you have the latter, I suggest you use cpptraj to convert. If that really is problematic, let me know and I will consider adding direct support for formatted ASCII coordinates.

[slochower@…]

Nope, we have binary netCDF. Great! I'll check it out tomorrow, thanks :)

On Tue, Sep 22, 2020 at 5:05 PM ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
wrote:

[pett]

For other reasons, the Windows build failed and the Linux build effectively failed (won't start), so you can only try it out today if you have a Mac. Will try to get things into better shape by tomorrow.

[slochower@…]

I just tried it (Mac build) and am running into an atom mismatch between
structure and trajectory (see screenshot). I didn't try with a smaller
trajectory (sorry, can do that later if necessary) but since I see 99999,
I'm guessing I'm hitting some sort of hard limit with indexing or
bookkeeping. What do you think?

[image: image.png]

On Wed, Sep 23, 2020 at 8:28 AM ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
wrote:

[slochower@…]

Added by email2trac

[pett]

I'm guessing you're using a PDB file for the structure? What wrote the PDB file? A standard PDB file only supports 99,999 atoms, so maybe whatever program you used to write it stopped there. There are various non-standard tricks for getting more atoms into a PDB file, and ChimeraX supports several of those, but the program outputting the PDB file has to use such tricks for that to matter.

[pett]

Can you attach the PDB file?

[slochower@…]

Yes, exactly! I just rewrote the file with `cpptraj` afresh and it does
work! I can see the trajectory. I think the previous one was written by
ParmEd (ParmEd and tleap seem to have slightly different conventions for
placing TER cards, e.g., between waters). I was using PDB because you had
previously mentioned it will be a bear to support `prmtop` files (I tend to
agree). So in the meantime, as long as this... unsupported behavior... of
using PDBs with >99,999 atoms works... I'm happy. What do you think?

On Wed, Sep 23, 2020 at 8:55 AM ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
wrote:

[pett]

Sounds good to me!