[chimerax-users] not showing non-traced amino acids in sequence view after splitting a molecule

[Tom Goddard]

Hi Marta,

   Thanks for the explanation of why you use split.   Suppose Model Panel showed each chain, and you deleted all the unwanted chains.  Would that work as well as split?

   Definitely split should preserve the sequence information for missing structure, so we appreciate you bringing that to our attention.

   Tom

> On Mar 6, 2020, at 3:04 AM, Marta Perez Illana <marta.perez at cnb.csic.es> wrote:
> 
> 
> Thanks a lot for the ideas and opening the topic, that was absolutely great and appreciated. I just wanted to make sure that I was not messing around myself with the splitting+sequence thing. 
> 
> Ideally I wouldn't use the split as you both suggested... However, I frequently use the match maker with several homology proteins coming from big viruses with lots of proteins... and having less proteins  in the session really helps me not to get confused and focus and switching on and of every protein at each time... So I am afraid that I really adore the split command.
> 
> Having the full sequence on the other side helps me out to compare the homology proteins and see which areas are traced in one protein but not in the other (or parts of the protein that are subjected to protease fragmentation and not visualized in the structure) , as well as to get full alignments based on structure...
> 
> I am really grateful for all the help and sorry for being a bit picky on the split+sequence...
> 
> Marta
> 
> 
> 
>> On 05.03.20 20:56, Tom Goddard wrote:
>> Hi Marta,
>> 
>>   The sequence for the missing structure should be preserved by the split command but it currently is not being preserved.  We have opened a request for that
>> 
>> 	https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/2913
>> 
>> I agree with Elaine, that you should rarely need to use the split command.
>> 
>> 	Tom
>> 
>> 
>>> On Mar 2, 2020, at 9:15 AM, Marta Perez Illana  wrote:
>>> 
>>> Hi Elaine
>>> 
>>> Thanks a lot for the quick reply! I though that  maybe there was a way to keep that info of the non-traced amino acids after doing splitting.
>>> 
>>> I use split because we work with huge molecules, and therefore is really convenient for focusing on a particular chain. And as well for fitting as you mention... I will try the alternatives you proposed! now knowing that making/saving new models implies for sure kind of "loosing that info"...
>>> 
>>> Regards
>>> 
>>> Marta
>>> 
>>> 
>>>> On 02/03/2020 18:05, Elaine Meng wrote:
>>>> Hi Marta,
>>>> When you open a structure from PDB or mmCIF format, there is a special part of the file that gives the full sequence of the structure used in the experiment, even if parts of that structure are not visible in the density (and therefore do not have atomic coordinates). This is part of the model information.
>>>> 
>>>> However, “split” makes new models, and it currently loses various kinds of information.  I believe this is the case in both Chimera and ChimeraX.  After splitting, it must only look at the coordinates to get the sequence.
>>>> 
>>>>  My personal opinion is to avoid using “split” unless it is really necessary.
>>>> 
>>>> In Chimera it sometimes helped with molecular surface calculation, but in ChimeraX there is less reason to do it.  You can specify chains individually without splitting.  The main reason one might split is for separately fitting the chains.  However, if having the full sequence is important, you can instead open multiple copies of the original model and just delete the parts of each that you don’t need.
>>>> 
>>>> I hope this helps,
>>>> Elaine
>>>> -----
>>>> Elaine C. Meng, Ph.D.
>>>> UCSF Chimera(X) team
>>>> Department of Pharmaceutical Chemistry
>>>> University of California, San Francisco
>>>> 
>>>>> On Mar 2, 2020, at 8:30 AM, Marta Perez Illana  wrote:
>>>>> 
>>>>> Hi all
>>>>> When I open a cif in chimerax and press the sequence button the window shows up and there is everything within the molecule, including the non-traced amino acids (missing in the structure).
>>>>> 
>>>>> Whereas if I do split the molecule to have just one chain, then the sequence view only shows traced amino acids, but not the non-traced ones anymore... Any ideas on this please?
>>>>> 
>>>>> P.D. With cif files this was a bit confusing in regular chimera for me as well, since when saving the cif it was kind of converted and I guess some info regarding this non-traced aminoacids was missed...
>>>>> 
>>>>> Thank you!!!
>>>>> Marta
>>> 
>>> -- 
>>> Marta Pérez Illana, Ph. D. student
>>> Dept. of Macromolecular Structures Lab 15
>>> Centro Nacional de Biotecnología (CNB-CSIC)
>>> Darwin, 3
>>> 28049-Madrid (SPAIN)
>>> http://wwwuser.cnb.csic.es/~sanmartinlab
>>> 
>>> _______________________________________________
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>> 
> -- 
> Marta Pérez Illana, Ph. D. student
> Dept. of Macromolecular Structures Lab 15
> Centro Nacional de Biotecnología (CNB-CSIC)
> Darwin, 3
> 28049-Madrid (SPAIN)
> Email:  marta.perez at cnb.csic.es
> Phone:  (0034) 91 585 4508
> http://wwwuser.cnb.csic.es/~sanmartinlab
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