id	summary	reporter	owner	description	type	status	priority	milestone	component	version	resolution	keywords	cc	blockedby	blocking	notify_on_close	platform	project
502	findclash misleading and wrong	Elaine Meng	Conrad Huang	"ChimeraX findclash gives different results from Chimera findclash and it is not easy for a user to figure out why.  I understand that certain things may not be implemented yet, but it should be clearer what's different. For example, the following gives 19 contacts in Chimera and 108 contacts in ChimeraX.

open 1zik
findclash protein overlap 0 hb 0

(Difference #1) ChimeraX uses “test self” as the default and does not let the user enter a “test” option (Chimera default is “test other”). Log should report which ""test"" option is being used.  Ideally ""test other"" would be implemented (I could be wrong but guess it wouldn't be much work) and made the default.  Further,

ChimeraX: findclash protein ov 0  ... gives 11 contacts
Chimera equivalent: findclash protein ov 0 test self ... gives 56 contacts

(Difference #2) ChimeraX apparently subtracts ""hb"" value from the overlap of every pair of atoms even if they are not potentially H-bonding. Default ""hb"" value is 0.4, as reported in the log (or if user specifies a value, that value is used and reported in the log).  Instead should say ""hb"" is not implemented and set it to 0 and report it as such.  (Last time I tested it was wrong in a different way: it claimed the value was 0.4 or whatever the user specified, yet always really used 0.)

"	defect	closed	major		Structure Analysis		fixed		Eric Pettersen Tom Goddard Scooter Morris				all	ChimeraX