HETATM vs. ATOM

[Tristan Croll]

The following bug report has been submitted:
Platform:        Linux-3.10.0-1127.13.1.el7.x86_64-x86_64-with-centos-7.8.2003-Core
ChimeraX Version: 1.0 (2020-06-04 23:15:07 UTC)
Description
When saving as mmCIF, unusual amino acids such as TYS in a protein sequence and capping residues like NH2 are incorrectly written as HETATM. Saving as PDB writes them as ATOM.

Log:
UCSF ChimeraX version: 1.0 (2020-06-04)  
© 2016-2020 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open 2rll

Summary of feedback from opening 2rll fetched from pdb  
---  
warning | Atom H1 is not in the residue template for SER /A:7  
note | Fetching compressed mmCIF 2rll from
http://files.rcsb.org/download/2rll.cif  
  
2rll title:  
CCR5 Nt(7-15) [more info...]  
  
Chain information for 2rll #1  
---  
Chain | Description  
A | 9-mer from C-C chemokine receptor type 5  
  

> save test.cif #1

> save test.pdb #1




OpenGL version: 3.3.0 NVIDIA 450.51.05
OpenGL renderer: TITAN Xp/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: Dell Inc.
Model: Precision T5600
OS: CentOS Linux 7 Core
Architecture: 64bit ELF
CPU: 32 Intel(R) Xeon(R) CPU E5-2687W 0 @ 3.10GHz
Cache Size: 20480 KB
Memory:
	              total        used        free      shared  buff/cache   available
	Mem:            62G        8.2G         42G        349M         12G         53G
	Swap:          4.9G          0B        4.9G

Graphics:
	03:00.0 VGA compatible controller [0300]: NVIDIA Corporation GP102 [TITAN Xp] [10de:1b02] (rev a1)	
	Subsystem: NVIDIA Corporation Device [10de:11df]	
	Kernel driver in use: nvidia
PyQt version: 5.12.3
Compiled Qt version: 5.12.4
Runtime Qt version: 5.12.8

[pett]

Hi Tristan,

I suspect the problem is the reverse. PDB should be writing those out as HETATM records. Certainly in the RCSB 2rll PDB entry, TYS is in HETATM records. NH2 and ACE residues are always in HETATM records. What makes you believe they should be in ATOM records?

--Eric

[Tristan Croll]

Oh, I see. My bad - you're right.


On 2020-08-25 17:10, ChimeraX wrote:

[Tristan Croll]

Turns out the *actual* bug I ran into was on the Phenix side: it seems 
it doesn't bother to write the LINK records for in-chain protein-hetatm 
bonds. If I feed it a structure with these residues as HETATM, loading 
the resulting PDB into ChimeraX leaves the C-terminal NH2 unbonded 
(although interestingly my mid-chain TYS does still get bonded). If I 
change them to ATOMs in the Phenix input, it spits them out as ATOM and 
ChimeraX bonds everything correctly.

On 2020-08-25 17:30, ChimeraX wrote:

[pett]

Okay, the actual ChimeraX bug is that TYS is output in ATOM records. Will get to that sometime.

FYI, I think you mean CONECT records, not LINK records. LINK records are for non-local connectivity like SS bonds ("Inter-residue linkages not implied by the primary structure are listed").

[Tristan Croll]

If I look at the header for 2rll in the wwPDB as an example of a 
TYS-containing protein, I see:

LINK         C   ILE A   9                 N   TYS A  10     1555   1555 
  1.31
LINK         C   TYS A  10                 N   ASP A  11     1555   1555 
  1.31
LINK         C   ASN A  13                 N   TYS A  14     1555   1555 
  1.31
LINK         C   TYS A  14                 N   TYR A  15     1555   1555 
  1.31


On 2020-08-25 18:58, ChimeraX wrote:

[pett]

Yes, for non-standard residues, all the inter-residue bonds would be in LINK records. CONECT records have both those plus all the intra-residue bonds for TYS.

--Eric

[Tristan Croll]

I was referring to the inter-residue bonds. The problem that I 
originally hit was that the C-terminal NH2 (treated by the PDB as a bona 
fide separate residue) was not being bonded to the preceding amino acid.

On 2020-08-25 19:08, ChimeraX wrote: