[Chimera-users] Modeller function and MD function in Chimera 1.14

Elaine Meng meng at cgl.ucsf.edu
Wed Jun 17 12:55:15 PDT 2020

Dear Yulseung Sung,
The Modeller interface in Chimera models a new structure from its amino acid sequence.  It is not for refining some structure that you already built.  Maybe this could be done if you used Modeller directly, but the tool in Chimera is meant to be simple and only enables certain specific tasks.

The model looks like more loop because the conformation is different than the original structure and the helices and strands backbone conformation changed enough that they are no longer recognized as helices and strands.  In other words, the structure is probably distorted and the H-bonding changed so they aren't really "good" helices or strands anymore.

Chimera is not really a program for structure prediction:
You cannot get a detailed or energetic prediction of some change that you made in the structure. You may be able to minimize it (Minimize Structure tool) but that will only relax to the nearest local minimum and will not predict any large conformational changes that might occur in reality.  Chimera also has a molecular dynamics simulation tool, but it is also relatively simple and slow, and is not appropriate for the long simulations you might need to run in order to make any decent prediction of structural changes.

In Chimera, you can only do simple first-order prediction by looking at H-bonds and clashes (see for example "structure analysis and comparison tutorial"<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/squalene.html> ) before and after your change.  I.e. if you lose H-bonds or gain lots of clashes, this change might be disruptive or destabilizing.  Sometimes minimization will let you see if simple relaxation might be possible.  However, I would not interpret the minimized structure as "this is how the structure will look after the change."

You may need to use a dedicated molecular simulation program instead, such as AMBER, GROMACS, ...  Or there may be other more appropriate programs for exactly what you want to do that I don't know about.  I can only advise that it sounds like Chimera is not the right tool for detailed predictions of structural and energetic change.

I hope this helps,
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Jun 17, 2020, at 8:53 AM, ‍성열승(대학원학생/일반대학원 약학과) <s.yulseung at yonsei.ac.kr> wrote:
> Daer whom it may concern,
> Hello, I am a graduate student trying out several features in Chimera for structure prediction. I write to you due to repeated problem during my use of Chimera function.
> I currently made a slight alteration in one residue of my protein. I have named it as a another residue, other than an amino acid. Then, I tried going to Modeller function so that the program will predict some energetic difference resulting in a structural modification. However, whenever the function ends, my helices and beta sheets are all converted into loop regions.Therefore, I only selected the loop region of my protein and made it go through the Modeller. Now, the modification was only shown in the loop area, but my alteration in an amino acid residue has been cut off. The residue was nowhere to be seen. I guess the Modeller made it go away. Next I tried selecting all the loop regions except the residue that I made the change and started Modeller, hoping that the altered residue will not be cut off. However, I got a result of it getting cut off again.
> Overall my question could be summed up into the following three:
> 1. Is there any way making Modeller function to have my altered residue not changed but have the program go through?
> 2. Is there a way for refining my protein in the helices and beta sheets area? Modeller function seem to change all of those into loops, and showed excellent prediction in the loop region.
> 3. Do you recommend any other function for my purpose? I built a PTM residue into one of my amino acid and want to see some predicted structure alteration.
> Thank you so much for your time. I really think the Chimera software is awesome and I just need to get used to it and try to learn some tricks.
> I hope to hear from you soon.
> Yours sincerely,
> Yulseung Sung
> -- 
> 성열승
> 연세대학교 약학대학 암대사연구실
> (Yulseung SUNG)
> (Lab of Cancer Metabolism, College of Pharmacy, Yonsei University)
> 연세대학교 약학대학
> 인천광역시 연수구 송도과학로85,
> 연세대학교 국제캠퍼스 진리관D 317-3호, 암대사연구실
> College of Pharmacy, Yonsei University
> 317-3 Veritas D, 85 Songdogwahak-ro, Yeonsu-gu, Inchoen, 406-840, South Korea
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