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

‍성열승(대학원학생/일반대학원 약학과) s.yulseung at yonsei.ac.kr
Wed Jun 17 08:53:16 PDT 2020

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

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

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
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