[Chimera-users] disulfide bonds ?

Eric Pettersen pett at cgl.ucsf.edu
Mon Jul 14 10:33:51 PDT 2014

On Jul 14, 2014, at 8:57 AM, "Marek Maly" <marek.maly at ujep.cz> wrote:

> Hellow,
> I just visualized my Amber MD trajectory with protein containing
> several disulfide bonds. These bonds as well as all the other bonds are
> written in the given Amber topology (*.prmtop) file, which is read in
> by Chimera. Moreover the distance of sulfur atoms connected by disulfide bond
> is in all cases quite reasonable ( 2-2.1 A). In spite these facts Chimera
> draws some of those bonds in "stick" and some of them in "dashed line" style,
> even if one sets globally "stick" or "ball & stick" representation.
> Please see the attached illustrations.
> Why Chimera is doing such unwanted differences in graphical representations here ?
> It is possible, to force Chimera to draw all of those bonds unanimously in "stick"
> representation ?

Hi Marek,
	My best guess is that Chimera is mistakenly converting some of the the disulphide bonds into "missing structure" pseudobonds, which are supposed to be used to represent parts of a chain that missing because is couldn't be located in the experimental data -- which obviously is not the case here!  The workaround to make those pseudobonds be depicted as stick is to open the Pseudobond Panel (in Tools/General Controls) and the double click on the "missing structure" group to bring up its attribute inspector.  In that inspector, click the check box next to "Component Pseudobond Attributes" to reveal those options and then change "bond style" from wire to stick.  There is an equivalent command:  "setattr pb drawMode 1".
	Obviously the better solution is to have Chimera not make this mistake in the first place.  As far as I know it shouldn't be already.  So, I would need your prmtop file and at least a subset of your coordinate file in order to investigate.  Also, what version of Chimera are you using?


                        Eric Pettersen
                        UCSF Computer Graphics Lab

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