[Chimera-users] disulfide bonds ?

Marek Maly marek.maly at ujep.cz
Tue Jul 15 13:57:58 PDT 2014

Hi Eric,
thanks for your decisions.

Sorry that I forget to send my files for testing.
I was fully satisfied just with the complete explanation of
this Chimera strange behavior :))

I will send you my input files off-line.

   Best wishes,


Dne Tue, 15 Jul 2014 20:42:39 +0200 Eric Pettersen <pett at cgl.ucsf.edu>  

> Hi Marek,
> 	I'm glad my suggestion worked.  I agree with you assessment, which is  
> why I was hoping you could provide data files for testing.  Nonetheless,  
> I have gone ahead and made changes such that for formats where explicit  
> topology files are provided, such as Amber, Chimera "trusts" the  
> connectivity and does not change excessively long bonds into  
> pseudobonds.  Those changes will be in tonight's daily build and I'm  
> hoping you can test them and let me know if they work.  Look for daily  
> builds dated July 15th or later.
> --Eric
> On Jul 15, 2014, at 4:08 AM, "Marek Maly" <marek.maly at ujep.cz> wrote:
>> 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  
>> connected
>> 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 there
>> 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  
>> trajectory.
>> 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,
>>      Marek
>> Dne Mon, 14 Jul 2014 19:33:51 +0200 Eric Pettersen <pett at cgl.ucsf.edu>  
>> napsal/-a:
>>> 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) __________
>>> Tuto zpravu proveril ESET NOD32 Antivirus.
>>> http://www.eset.cz
>> --
>> Tato zpráva byla vytvořena převratným poštovním klientem Opery:  
>> http://www.opera.com/mail/
> __________ Informace od ESET NOD32 Antivirus, verze databaze 10101  
> (20140715) __________
> Tuto zpravu proveril ESET NOD32 Antivirus.
> http://www.eset.cz

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