[Chimera-users] disulfide bonds ?

Marek Maly marek.maly at ujep.cz
Tue Jul 15 04:08:11 PDT 2014

Hi Eric,
thank you for the prompt and useful answer.

The approach you suggested works !

But I already identified the source of the problem.

In my Amber MD trajectory, there was also the first(starting)
configuration of my protein (that from the *.inpcrd file).

This starting configuration was not so precise as was obtained
by the electron microscopy (not by X-ray or NMR technique).

 From this reason distances of some of the sulfur atoms which should be  
by disulfide bond was not reasonable in this starting configuration but  
higher like 3 A or 6 A.

So in spite the fact that in the Amber topology (*.prmtop) file were
clearly written all the disulfide bonds, Chimera evidently ignored
those bonds in sulfur atom pairs where the distance was not in the
reasonable range (close to 2A). Instead perhaps Chimera considered, that  
are some missing parts or so and used "dashed line" instead "stick".
  So this was the first Chimera "mistake" which should not happen if she  
just simply
  accepted the full topology information from the "*.prmtop" file.

Another problem was that even if in all consequent frames of the trajectory
all the relevant sulfur atoms were in the reasonable distance (2-2.1 A -  
due to the fact
that during the Amber simulation they were bonded), Chimera doesn't care  
about because
she evaluate the overall structure just using the first frame of the  

I would suggest here, that Chimera should not take her own decisions in  
such cases when
molecular topology is fully defined in input files (e.g. Amber *.prmtop,  
mol2 etc.).

Especially in case of the Amber *.prmtop file it is clear that structure  
should be OK,
(e.g. without the missing parts) because otherwise this topology file  
would never be created.

If Chimera find something strange in the structure (even if this structure  
was fully
determined in the input file/s), she can always write the proper warnings,  
and that
should be enough in such specific cases, I think.

   Best wishes,


Dne Mon, 14 Jul 2014 19:33:51 +0200 Eric Pettersen <pett at cgl.ucsf.edu>  

> 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
>                         Eric Pettersen
>                         UCSF Computer Graphics Lab
>                         http://www.cgl.ucsf.edu
> __________ Informace od ESET NOD32 Antivirus, verze databaze 10094  
> (20140714) __________
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