[Chimera-users] show mutations in Chimera

[Elaine Meng]

Hello,
Although you can do a simple “mutation” of one protein residue type to another and look at the structure to guess if the change is disruptive, Chimera does not do any sophisticated prediction of whether the mutated protein will be stable or functional.  You have to judge that for yourself based on your knowledge of protein structure in general and any specific information available (e.g. in databases or published papers) about the important residues of that specific protein.

If there is a mutation to stop codon, that’s an even bigger change.  All you can do is to look at the wild-type protein structure and see where the stop (truncation) would occur, and then again use your judgment.

There may be some software that will give you a prediction of functional vs. nonfunctional, but Chimera is not  it.  I don’t have any specific suggestions — maybe other people on this mailing list will have ideas.

If you just want to do the simple sidechain replacement in Chimera, it can be done with the Rotamers tool (in menu under Tools… Structure Editing) or the “swapaa” command:
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/rotamers/rotamers.html>
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/swapaa.html>

Best,
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco


> On Jul 4, 2018, at 9:57 AM, Eslam Nofal <zeiad85eslam at gmail.com> wrote:
> 
>> Hello 
>> Thanks a lot for your effort
>> please help me to know how can I determine My Model for a certain mutated gene
>> (like smn protein for normal sequences,type I,II,III,and IV Spinal muscular atrophy)
>> How can I know the protein model for different seq is functional or non functional?
>> I made models for different affected cases of SMA with A suitable template for pdb  and Recorded The Qmean and GMQE number for each model with but till now I can not be able to determine this sequence produce good functional protein or not
>> especially with gene have Frame shift mutation which produce new protein and also have a lot of stop codon in the sequence
>> I hope you understand the meaning of  my Question ? and hope to guide me to suitable tool or method
>> Thanks