[Chimera-users] how to build missing loops

Elaine Meng meng at cgl.ucsf.edu
Thu Sep 26 13:16:42 PDT 2013


Dear Haiping Zhang,
You can use the Modeller interface for building loops.  First show the Sequence for that protein chain (menu: Tools… Sequence… Sequence).  This sequence comes from the SEQRES in the PDB file and includes the whole sequence.  The part that is missing from the structure is shown with a red outline box.  To build the missing part, from the Sequence window menu choose Structure… Modeller (loops/refinement).  The Modeller loop-building interface is described here:

<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/modeller.html#building>

I hope this helps,
Elaine
----------
Elaine C. Meng, Ph.D. 
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco


On Sep 26, 2013, at 2:59 AM, 张海平 <spr8249618 at 163.com> wrote:

> Dear professor Elaine C. Meng:
>    I have a structure that miss some resides, I want to add a loop to fed the gap. How can I accomplish this by chimera? The structure is as bellow, I want to add some residus to the place where shows dot line. Thanks for your help.
> 
> <截图1.png>




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