[chimerax-users] addh and phenix

[Elaine Meng]

Hi Daniel,
To rename that hydrogen from HD2 to HD21 in ChimeraX, you could do it with command:

setattr :asn at hd2 atom name HD21

I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco


> On Apr 24, 2020, at 12:55 AM, Tristan Croll <tic20 at cam.ac.uk> wrote:
> 
> It’s the naming. Phenix is absolutely strict in its rule that atom names must match their CCD templates. AddH doesn’t use the templates, so in general outside of protein and nucleic acids the hydrogen names won’t be acceptable to Phenix. For now it’s best to just save a file without hydrogens:
> 
> sel ~H
> save file.pdb sel true
> 
> I have a tool mostly ready to correct residues against their template... will try to make it ready for the next ISOLDE release.
> 
> — Tristan
> 
> 
> 
> 
>> On 24 Apr 2020, at 08:47, Daniel Asarnow <asarnow at msg.ucsf.edu> wrote:
>> 
>> Hi,
>> Seems like with NAG glycans the addh result is incompatible with phenix real space refinement. It's easy enough to fix by deleting HD2 - the offending hydrogen - manually.
>> 
>> I was wondering if anyone had an opinion about this, before I report a phenix bug.
>> 
>> Error looks like:
>> 
>> Number of atoms with unknown nonbonded energy type symbols: 5
>>    "ATOM   2629  HD2 ASN A 362 .*.     H  "
>> 
>> (4 more similar lines).
>> 
>> Best,
>> -da
>>