[Chimera-users] problem with showing broken peptide after residues with alternative conformation

[Wangshu Jiang]

Dear Elaine,

Thank you so much for your help! The commands work like a charm:-) I am happy that you did not regard my question as a Halloween prank. Very grateful to have support from you guys so fast!

I will have a look at your new program ChimeraX. May I ask if I install ChimeraX on my mac, does it mean it will replace my previous Chimera or can they exist at the same time?

Thanks again and hope you have a lovely day!


Best Regards,
Wangshu Jiang

PhD student
Dept Cell and Molecular Biology
BMC Box 596
Husargatan 3
751 24 Uppsala Sweden

On 31 Oct 2017, at 23:58, Elaine Meng <meng at cgl.ucsf.edu<mailto:meng at cgl.ucsf.edu>> wrote:

Dear Wangshu Jiang,
I’m not sure exactly what’s going on with 3LR2, but you can add the missing bonds, for example with commands (also attached as a command file for your convenience):

bond :42.a at c :43.a at n
bond :47.a at c :48.a at n
bond :51.a at c :52.a at n
bond :125.a at c :126.a at n
bond :47.b at c :48.b at n
bond :48.b at c :49.b at n

I think I got all of the breaks. Hey, seems like this a good protein for Halloween (spider silk)!  :-)

Sorry for the hassle.  Our newer program ChimeraX doesn’t have this problem with 3LR2, but it handles alternate locations differently.
I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco


> On Oct 31, 2017, at 3:18 PM, Wangshu Jiang <wangshu.jiang at icm.uu.se<mailto:wangshu.jiang at icm.uu.se>> wrote:
>
> Dear Chimera Support,
> I am using Chimera to performing structural analysis for a manuscript. I have been struggling to show the protein structure with PDB entry 3LR2, the peptide bond between residue with alternative conformations and the next residue was shown broken, both in backbone and in ribbon presentation. I am not sure what went wrong here, I compared the PDB text file to other PDB entries with alternative conformations and I did not find obvious differences.  It would be nice to show all the rotamers in the PDB instead of manually deleting by coot just from ‘eyeballing'.
>
> Could you please help me to solve this issue? Any suggestion is deeply appreciated! I attached an image illustrating the problem I described. I hope to hear from you soon!
>
> Best Regards,
> Wangshu Jiang
>
> PhD student
> Dept Cell and Molecular Biology
> BMC Box 596
> Husargatan 3
> 751 24 Uppsala Sweden
>
> <BrokenPeptide.png>

<bondit.cmd>

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