Ambiguous bond information is only partially displayed

[ClairePA]

If an ambiguous bond between groups has only some of the attributes defined, only the defined attributes are displayed. This is confusing.

All attributes should be shown.

[scilligence]

Could you paste the HELM notation here? I guess the missing information is not specified. Thanks.

[ClairePA]

The HELM is:

PEPTIDE1{A.C.D.D.P.P}|PEPTIDE2{A.C.D.D.P.P}$PEPTIDE1,PEPTIDE2,1:?-?:?$G3(PEPTIDE1+PEPTIDE2:2)$$V2.0

and the bond attributes are;

So the display is correct, but confusing. It should show which attributes are not specified. Please note that the HELM notation says that if the ratio is not specified the proportion of that component is unknown and you cannot assume a value (e.g. 1).

[scilligence]

Fixed in 2018-01-08 update. It is able to set the default ratio value by changing the value of this variable:

org.helm.webeditor.defaultbondratio = null; // or ?, 1

[ClairePA]

Good start but there is some work to do before this is fully functioning. The main issues are;

• The display for group 1 and group 2 should match. If attributes are displayed for one then the other should also be displayed.
• It must be possible to change a default value to nothing or ? without it reverting to the default. ? Is a valid value in the HELM notation
• Ratio values of 1:1 should not be displayed if the other values are not displayed.
• Null values appear in the HELM for some of the attributes which is causing invalid HELM

	Action	Value	Display	Preferred Display
1	Draw bond	Position = ?	null
		R# = ?	null
		Ratio = 1	Null
1		Position = ?	null
		R# = ?	null
		Ratio = 1	Null
	HELM is invalid - see screenshots below.Â
2	Go into ‘set attributes' and make no changes. Exit 'set attributes'Â	Position = ?	null
		R# = ?	null
		Ratio = 1	Ratio =1	should be as action1 i.e. the ratio should not be displayed.Â
2		Position = ?	null
		R# = ?	null
		Ratio = 1	Ratio =1
3	Go into ‘set attributes' and remove the 1 from the ratio. Save and then go back into the 'set attributes' box. The ratio boxes have 1 in them again, this is incorrect - it must be possible to specify an unknown ratio, either by removing the 1 or by adding ?.Â
4	Change the value of R# for the first group to 1.Â	Position = ?	Pos:?
		R# = 1	R#: R1
		Ratio = 1	Ratio =1
4		Position = ?	null	Pos:? Should be displayed
		R# = ?	null	R# should be displayed
		Ratio = 1	Ratio =1

[scilligence]

Could you write down the steps on how to generate this help?

[ClairePA]

I can't reproduce the nulls, so please take this off the list of issues.

[scilligence]

fixed in 2018-01-10 update

[ClairePA]

The behaviour still looks the same to me. the issues identified in the comment above are still there. Please implement the changes described in the table and the list below:

• The display for group 1 and group 2 should match. If attributes are displayed for one then the other should also be displayed.
• It must be possible to change a default value to nothing or ? without it reverting to the default. ? Is a valid value in the HELM notation
• Ratio values of 1:1 should not be displayed if the other values are not displayed.
• Null values appear in the HELM for some of the attributes which is causing invalid HELM

[scilligence]

Fixed

[ClairePA]

Perfect! Many thanks.