id	summary	reporter	owner	description	type	status	priority	milestone	component	version	resolution	keywords	cc	blockedby	blocking	notify_on_close	platform	project
2603	Fragmented surface after adding hydrogens	goddard@…	Tom Goddard	"{{{
The following bug report has been submitted:
Platform:        Darwin-19.0.0-x86_64-i386-64bit
ChimeraX Version: 0.91 (2019-10-25)
Description
Fragmented surface after adding hydrogens.

Log:
UCSF ChimeraX version: 0.91 (2019-10-25)  
© 2016-2019 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /Users/goddard/Downloads/ChimeraX/PDB/1a0m.cif

1a0m.cif title:  
1.1 angstrom crystal structure of A-conotoxin [TYR15]-epi [more info...]  
  
Chain information for 1a0m.cif #1  
---  
Chain | Description  
A B | α-conotoxin [TYR15]-epi  
  
Non-standard residues in 1a0m.cif #1  
---  
NH2 — amino group  
  

> surface

> addh

Summary of feedback from adding hydrogens to 1a0m.cif #1  
---  
warning | Not adding hydrogens to /A ARG 7 CB because it is missing heavy-atom
bond partners  
notes | Termini for 1a0m.cif (#1) chain A determined from SEQRES records  
Termini for 1a0m.cif (#1) chain B determined from SEQRES records  
Chain-initial residues that are actual N termini: /A GLY 1, /B GLY 1  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini: /A NH2 17, /B NH2 17  
Chain-final residues that are not actual C termini:  
107 hydrogen bonds  
271 hydrogens added  
  

> show surfaces

> save /Users/goddard/Desktop/image1.png supersample 3




OpenGL version: 4.1 ATI-3.2.24
OpenGL renderer: AMD Radeon Pro Vega 20 OpenGL Engine
OpenGL vendor: ATI Technologies Inc.
File attachment: image1.png

}}}

[attachment:""image1.png""]
"	defect	closed	normal		Surface		fixed						all	ChimeraX