[Chimera-users] Mutation in Chimera

Islam, Tanzila tanzila.islam at wsu.edu
Thu Jan 5 12:12:13 PST 2017


Hello Elaine


How is everything going?

I need a little help regarding modeller service with Chimera.

I was able to perform some insertions to the protein structure using your methods. Your emails were very helpful.


But the modeller is not working properly for last 2 days. Its showing error-


But liiks like the service is down for last couple of days.

.........................................................................................
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NonChimeraError: Web service appears to be down.  See Reply Log for more details.
Service 'opal:Modeller9v8Service' is unavailable.  See Reply Log for more details.


Is there any problem with the web service that you know of? Will that be resolved soon?

If you can tell me when I will be able to use the service, that will be very helpful.


Thanks


Tanzila Islam

Graduate Student
Washington State University
________________________________
From: Elaine Meng <meng at cgl.ucsf.edu>
Sent: Thursday, November 17, 2016 2:08:16 PM
To: Islam, Tanzila
Cc: chimera-users at cgl.ucsf.edu
Subject: Re: [Chimera-users] Mutation in Chimera

Hi Tanzila Islam,
To add more residues instead of just changing the residues that are already in the structure, probably the best way is to use the Modeller interface of Chimera.  This runs a Modeller web service, for which you have to register to get a “license key” to enter into the dialog … this is free for noncommercial users, but it may take a while for them to respond with the key.  To get the key, see:
<https://urldefense.proofpoint.com/v2/url?u=http-3A__www.rbvi.ucsf.edu_chimera_docs_ContributedSoftware_multalignviewer_modeller.html-23modeller-2Dlicense&d=DgIF-g&c=C3yme8gMkxg_ihJNXS06ZyWk4EJm8LdrrvxQb-Je7sw&r=zA9st_jbqMZ-6qaduW-fZ6ZgnxlqIQlkWFNGnI1qgus&m=qnzukRr71oE5Ot_xJugoDK0hgwfxK0qI7QPmc0Xates&s=V51J9advE8qkJUtFSQ9Yx1k6yK_iOdgZx6gREEKVuIs&e= >

After you get the key, then the steps would be:

(1) make a sequence file (plain text file in FASTA format) containing the sequence that you want, including the insertion, and open it in Chimera.  The filename should end in “.fa” to indicate the format.  The sequence will appear in a separate Chimera window.

(2) make sure the sequence is associated with your starting structure.  It will probably happen automatically when both the sequence and structure are opened in Chimera.  You can check by seeing if the sequence window menu: "Structure… Modeller (loops/refinement)”  is grayed out.  If it is grayed out,  use sequence window menu: “Structure… Associations” to manually associate the structure with the sequence.

(3) Choose sequence window menu: "Structure… Modeller (loops/refinement)”   and in the resulting dialog choose to model “non-terminal missing structure” or “all missing structure” … doesn’t matter which one of those since you are modeling an insertion.  For information on the options in that dialog, see:
<https://urldefense.proofpoint.com/v2/url?u=http-3A__www.rbvi.ucsf.edu_chimera_docs_ContributedSoftware_multalignviewer_modeller.html-23building&d=DgIF-g&c=C3yme8gMkxg_ihJNXS06ZyWk4EJm8LdrrvxQb-Je7sw&r=zA9st_jbqMZ-6qaduW-fZ6ZgnxlqIQlkWFNGnI1qgus&m=qnzukRr71oE5Ot_xJugoDK0hgwfxK0qI7QPmc0Xates&s=CVGkyCc5pUx7kCxie2lSflYKg3LlbbIxPJcq_oOL5OY&e= >

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 Nov 17, 2016, at 10:59 AM, Islam, Tanzila <tanzila.islam at wsu.edu> wrote:
>
> Hi
> I am learning Chimera and I have gone through soe online tutorials. The tutorials showed how to introduce point mutation by Rotamers command. But it only allows to replace 1 ammino acid residue at a time.
>
> I want to insert 4-5 ammino acid residues in a gap of a sequence. Is there any standard procedure, command in Chimera that will let me do this type of residue insertion? This is really crucial for my research work.
> Thanks
> Tanzila Islam
> Graduate Student
> Washington State University

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