id	summary	reporter	owner	description	type	status	priority	milestone	component	version	resolution	keywords	cc	blockedby	blocking	notify_on_close	platform	project
15832	Arg sidechains	botosi@…	Tristan Croll	"{{{
Hi,

After simulating several EM structures with Isolde, it produces models with outlier Arg sidechains (non planarity of CD with guanidium group; and guanidium angles deviate from 120deg).
Not sure if the lack of these geometric restraints originates from chimeraX or Isolde.
It is reproducible, we had it in five different structures now.

Here is an exerpt from the output of the PDB validation tool:


Residue(model/chain/number/name)    Region not planar

1/A/118/ARG    sidechain

1/B/114/ARG    sidechain

1/B/118/ARG    sidechain

1/C/118/ARG    sidechain



Bond angle outliers



The following bond angles were found to be significantly different from the expected bond angle.



Residue(model/chain/number/name)    Atoms    Expected bond angle (°)    Measured bond angle (°)

1/A/114/ARG    NE-CZ-NH2    120.3 ± 0.5    124.5

1/A/222/ARG    NE-CZ-NH2    120.3 ± 0.5    123.0

1/B/54/ARG    NE-CZ-NH2    120.3 ± 0.5    123.0

1/B/66/ARG    NE-CZ-NH2    120.3 ± 0.5    122.9

1/B/114/ARG    NE-CZ-NH2    120.3 ± 0.5    123.9

1/C/57/ARG    NE-CZ-NH2    120.3 ± 0.5    122.9

1/C/110/ARG    NE-CZ-NH2    120.3 ± 0.5    123.1

1/C/114/ARG    NE-CZ-NH2    120.3 ± 0.5    122.9

Would it be possible to patch this up?

Thanks,
Istvan

}}}
"	defect	assigned	normal		Third Party								all	ChimeraX