[Chimera-users] disulfide bonds ?
marek.maly at ujep.cz
Tue Jul 15 13:57:58 PDT 2014
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.
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.
> 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
>> 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
>> 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:
>>>> I just visualized my Amber MD trajectory with protein containing
>>>> several disulfide bonds. These bonds as well as all the other bonds
>>>> 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
>>>> 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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