save command option to exclude hydrogens

[Tristan Croll]

Wanting to save only heavy atoms from a model with hydrogens is a very common scenario (for example, PHENIX balks if you attempt to refine a model where hydrogens have been added to a truncated sidechain). Would be great to have it as an optional argument to the save command.

[Eric Pettersen]

I'm not going to implement this for two reasons:

1) As of yesterday, ChimeraX no longer adds protons to the truncation-point atom of truncated residues

2) This behavior is easily accomplished using the 'selectedOnly' keyword when saving PDBs, e.g. "sel ~H ; save x.pdb sel true". Now that example doesn't actually work right now because of a bug with atom specs, but that's a different kettle of fish. :-)

--Eric

[Eric Pettersen]

Scratch the part about the bug -- it's working. I was misled because of a bug in the selection of bonds -- the H atoms were selected (/not selected) correctly.

[tic20@…]

“1) As of yesterday, ChimeraX no longer adds protons to the truncation-
point atom of truncated residues”

That’s going to cause problems for me/ISOLDE (OpenMM treats truncated-but-protonated residues as Ala or Gly, but doesn’t know what to do if the hydrogens simply aren’t there). Is there any chance the old behaviour can be maintained as an option?

 
 
Tristan Croll
Research Fellow
Cambridge Institute for Medical Research
University of Cambridge CB2 0XY
 

 

[tic20@…]

... although come to think about it, it would be fairly easy to work around (just need to define forcefield entries for common truncations).

 
 
Tristan Croll
Research Fellow
Cambridge Institute for Medical Research
University of Cambridge CB2 0XY
 

 

[Eric Pettersen]

Adding that option would be easy but it was added in the first place because otherwise some structures cause AddH to throw errors.  For example, ARG 71 in chain A of 2iab is truncated at the NE.  ChimeraX knows that NE is planar, but all the atoms it is planar _with_ are gone, so an error occurs.  Surely OpenMM can’t treat that residue as ALA or GLY?

It would seem that extending the forcefield would be the better plan, but I can add an option if you feel you really need it.

—Eric

[Eric Pettersen]

Doesn’t ISOLDE do rotamer replacement of truncated side chains?

[tic20@…]

Last two replies went directly to Eric (damned phone...). Repeating for the record:

No, a truncation like that would be treated as an error (and rightly so - I can see few reasons for creating a monstrosity like that. If you want to truncate, truncate properly, otherwise just build the whole darned sidechain...)

Ahem

Anyway, the only special cases I envision handling are truncations back to CB or CA. Anything else will get flagged as an unrecognized residue, and ISOLDE will point it out so the user can rebuild it properly.

 
 
Tristan Croll
Research Fellow
Cambridge Institute for Medical Research
University of Cambridge CB2 0XY
 

 

[Eric Pettersen]

So is the upshot “more forcefield” rather than “more option”?

—Eric

[tic20@…]

Yes, I think “more forcefield” is probably going to be the best approach. Just to be clear: the official 0.8 release still uses the old behaviour, correct?

 
 
Tristan Croll
Research Fellow
Cambridge Institute for Medical Research
University of Cambridge CB2 0XY
 

 

[Eric Pettersen]

Yes, this change went in just after 0.8.

—Eric

[tic20@…]

I’ll be adding a “build in missing sidechains” option eventually (sooner rather than later), but for this release my focus has been making *re*building as smooth and painless as problem. Actual *building* is one of the next big steps.

More generally, the question of whether to build in sidechains that aren’t visible in the density is one that has spawned many a heated argument over the years. Whichever side of the debate I fall on (build them in), I have to provide both options.

 
 
Tristan Croll
Research Fellow
Cambridge Institute for Medical Research
University of Cambridge CB2 0XY