[Chimera-users] how to build missing loops

Elaine Meng meng at cgl.ucsf.edu
Mon Sep 30 10:18:43 PDT 2013

I forgot to mention an easy way to get  the sequence file in FASTA format: 

(1) open your PDB file, then show its Sequence (Chimera menu: Tools… Sequence… Sequence)

(2) save the sequence as FASTA  file (sequence window menu: File… Save As, choose file type: aligned FASTA)

(3) in a text-editing program, edit the FASTA file to add the GGG… part.  Save yourfile.fasta as plain text from the text-editing program.

Quit from the first sequence window.  Open your new fasta file (yourfile.fasta) in Chimera.  Associate it with the structure (sequence window menu: Structure… Associations, change from "none" to the hlaa1… sequence, OK.  Then use the Modeller interface (sequence window menu:  Structure… Modeller (loops/refinement)) to model "non-terminal missing structure" or "all missing structure"


On Sep 30, 2013, at 9:45 AM, Elaine Meng <meng at cgl.ucsf.edu> wrote:

> Dear Haiping Zhang,
> I see, your PDB file does not have SEQRES.  My previous instructions assumed you had a structure from the PDB database that was missing coordinates for residues that were in SEQRES.
> In your case, PDB file without SEQRES, you need to make a sequence file that has the GGGGGG included in the sequence where you want it, in plain text FASTA format:
> <http://www.ncbi.nlm.nih.gov/BLAST/fasta.shtml>
> Then open both the structure PDB file (yourfile.pdb) and the sequence FASTA file (yourfile.fasta) in Chimera.  Make sure the sequence is associated with the structure (sequence window menu: Structure… Associations), 
> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/multalignviewer.html#association>
> and then proceed to use the Modeller loop-building interface as in my previous message.
> If you never used Modeller with Chimera before, you have to get a Modeller license key to enter into the interface (it is free for noncommercial use, you just have to go to the Modeller website and sign up, they will email it to you).
> 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 6:29 PM, 张海平 <spr8249618 at 163.com> wrote:
>> Dear professor Elaine Meng:
>>   I can not add a GGGGGGG sequence to the place between 182 and 183 residues by the Modeller interface for building loops. My structure is in a attachment file. Thanks for your help. 
>> best wishes
>> Haiping zhang
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