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

Thu Jun 18 00:43:15 PDT 2020

Dear Elaine,

Thank you very much for your reply. It helped so much for clarifying the
program.

Yours sincerely,

Yulseung Sung

2020년 6월 18일 (목) 오전 4:55, Elaine Meng <meng at cgl.ucsf.edu>님이 작성:

> 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
> -----
> 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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>
>

-- 
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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