id	summary	reporter	owner	description	type	status	priority	milestone	component	version	resolution	keywords	cc	blockedby	blocking	notify_on_close	platform	project
3116	computeSs documented as computeSS	vadim.kotov@…	Elaine Meng	"{{{
The following bug report has been submitted:
Platform:        Linux-3.10.0-1062.9.1.el7.x86_64-x86_64-with-centos-7.7.1908-Core
ChimeraX Version: 0.93 (2020-04-03)
Description
""computeSS true"" option is not recognized as a valid option for coordset; ""comp true"" is recognized. I guess this is a typo in the documentation, the recongized option is ""computeSs true"" (2nd s is lowercase). Attached a script to reproduce the bug

Log:
UCSF ChimeraX version: 0.93 (2020-04-03)  
© 2016-2020 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open2 /beegfs/cssb/user/kotovvad/200210_XylE_movie/bug3.cxc

> open 6n3i

6n3i title:  
Crystal structure of a double Trp XylE mutants (G58W/L315W) [more info...]  
  
Chain information for 6n3i #1  
---  
Chain | Description  
A | D-xylose transporter  
  
  

> open 4gby

Summary of feedback from opening 4gby fetched from pdb  
---  
note |  
  
  
| Summary of feedback from opening
/home/kotovvad/Downloads/ChimeraX/PDB/4gby.cif  
  
---  
  
  
  
  
warning | Unable to infer polymer connectivity due to unspecified label_seq_id
for residue ""XYP"" near line 4750  
  
  
  
  
  
4gby title:  
The structure of the MFS (major facilitator superfamily) proton:xylose
symporter XylE bound to D-xylose [more info...]  
  
Chain information for 4gby #2  
---  
Chain | Description  
A | D-xylose-proton symporter  
  
Non-standard residues in 4gby #2  
---  
BNG — B-nonylglucoside  
XYP — β-D-xylopyranose  
  
  

> mmaker #1 to #2

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 4gby, chain A (#2) with 6n3i, chain A (#1), sequence alignment
score = 2376.8  
RMSD between 415 pruned atom pairs is 0.832 angstroms; (across all 475 pairs:
2.152)  
  

> morph #1-2 frames 10 play false

Computed 11 frame morph #3  

> coordset #3 1,-1,1 computeSs true

Expected a keyword  

> coordset #3 1,-1,1 computeSs true




OpenGL version: 3.3.0 NVIDIA 440.33.01
OpenGL renderer: Quadro M6000/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: Supermicro
Model: SYS-1028GQ-TRT
OS: CentOS Linux 7 Core
Architecture: 64bit ELF
CPU: 40 Intel(R) Xeon(R) CPU E5-2640 v4 @ 2.40GHz
Cache Size: 25600 KB
Graphics:
	02:00.0 VGA compatible controller [0300]: NVIDIA Corporation GM200GL [Quadro M6000] [10de:17f0] (rev a1)
	Subsystem: NVIDIA Corporation Device [10de:1129]
	Kernel driver in use: nvidia
File attachment: bug3.cxc

}}}

[attachment:""bug3.cxc""]
"	defect	closed	normal		Documentation		fixed						all	ChimeraX