[Chimera-users] Mutation in Chimera

Elaine Meng meng at cgl.ucsf.edu
Thu Nov 17 15:38:12 PST 2016


What????  those are not the links I sent…. I have no idea what is wrong with your email, but the links were fine in the copy of the mail that I received.

I  was about to send another link that contains the original posting from me, but now I’m afraid something will go crazy along the way.  Hmm.

OK, try this, how to get the page with that original posting.  Go to UCSF Chimera homepage (you can google “ucsf chimera".  Then near the bottom of the lefthand Quick Links section, click the “Contact Us” link.  Then click the link to “view” the whole archive of chimera-users.  Then click Thread in the November 2016 row, then scroll down to my first reply to you, and click to view it.  In that page, I see the links just as I sent them, and when I click them they go to the correct places.

Elaine


> On Nov 17, 2016, at 2:46 PM, Islam, Tanzila <tanzila.islam at wsu.edu> wrote:
> 
> Thanks a lot for your email. But the 2 links you gave are not working and leading to the same page named 'Red Angus Society'.
> Is this the correct site?
> 
> 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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