[Chimera-users] Question about Model Loops Option in Chimera

[Eric Pettersen]

This seems like a bug in both Chimera and ChimeraX.  I will open a ticket in our bug-tracking database with you cc'ed so that you will be notified when it gets fixed.

--Eric

	Eric Pettersen
	UCSF Computer Graphics Lab


> On Dec 12, 2022, at 11:15 AM, Elaine Meng via Chimera-users <chimera-users at cgl.ucsf.edu> wrote:
> 
> Hi Ece,
> As far as I know they should not move.
> 
> If you are showing ribbons (not just atomic coordinates) it might seem like there are changes because the ribbon is interpolated over multiple positions, so the ribbon might be in a slightly different place even at residues where the atoms have not moved, just because the ribbon path calculation now has more atoms to use.
> 
> Otherwise I would not expect anything to move.  Hide ribbons, show all atoms... if you still see atoms in different positions then you could use Help... Report a Bug and attach data like the session, if you are willing to share the data.
> Elaine
> 
>> On Dec 12, 2022, at 11:08 AM, Ecem Güngör via Chimera-users <chimera-users at cgl.ucsf.edu> wrote:
>> 
>> Dear Elanie, 
>> 
>> Thanks for your answer.
>> 
>> Even if I set the option you mentioned to 0, it still moves some positions of the atoms. That's why I could not comprehend the reason. 
>> 
>> Ece
>> 
>> 
>> Elaine Meng <meng at cgl.ucsf.edu>, 12 Ara 2022 Pzt, 17:39 tarihinde şunu yazdı:
>> Hi Ece,
>> There is an option "Allow this many residues adjacent to missing regions to move" which you can change to zero instead of the default of one.  Then it should not change any atom positions. 
>> 
>> See the documentation:
>> <https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/modeller.html#building>
>> 
>> I don't know the details of the "standard" option, maybe others can elaborate. As mentioned in the documentation, if you choose the DOPE option instead, it may produce higher-quality results, but it takes longer and is also more prone to calculation failure.
>> 
>> I hope this helps,
>> Elaine
>> -----
>> Elaine C. Meng, Ph.D.                       
>> UCSF Chimera(X) team
>> Department of Pharmaceutical Chemistry
>> University of California, San Francisco
>> 
>>> On Dec 12, 2022, at 5:38 AM, Ecem Güngör via Chimera-users <chimera-users at cgl.ucsf.edu> wrote:
>>> 
>>> Hello,
>>> 
>>> I have a protein crystal structure where some regions are not resolved in the crystal. Therefore, I want to predict and fill these regions, without touching the rest, by using the Model Loops/Refine Structure option of Modeller in Chimera. When I select the non-terminal missing structure as a model and standard as a loop modeling protocol, some atoms in the rest of the structure are shifted from the original positions. However, I want to keep them as they are. Here I would like to ask what standard loop modeling protocol corresponds to. Does it also refine or optimize the structure as a whole? What does it actually correspond to? 
>>> 
>>> Any help would be appreciated. Thanks. 
>>> 
>>> Ece
>> 
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