[chimerax-users] Labeling canine Apolipoprotein A-I

[Elaine Meng]

Hi Tiglath, 
Are you using Chimera or ChimeraX??  Please e-mail questions to chimera-users at cgl.ucsf.edu if you are using Chimera, chimerax-users at cgl.ucsf.edu if you are using ChimeraX.

Either way, however,  don't model the sequence directly from Uniprot.  Download a fasta file of that sequence, then delete (with a text-editor) the residues you don't want in your model, and then open the resulting edited fasta file instead of opening the uniprot sequence directly.  Then do the modeling steps.

I hope this helps,
Elaine

> On Jan 29, 2021, at 10:24 AM, Moradkhan, Tiglath A <tmoradkhan at csus.edu> wrote:
> 
> Hi
> 
> I'm trying to model the N-terminus of mature canine Apolipoprotein A-I using Chimera. However the actual sequence in uniprot is not that of the mature protein. Here is the sequence:
> 
> MKAALLTLAVLFLTGSQARHFWQQDEPQSPWDRVKDLATVYVDAVKDSGRDYVAQFEASA
> LGKQLNLKLLDNWDSLSSTVTKLREQIGPVTQEFWDNLEKETEVLRQEMSKDLEEVKQKV
> QPYLDDFQKKWQEEVELYRQKVAPLGSELREGARQKLQELQEKLSPLAEELRDRARTHVD
> ALRAQLAPYSDDLRERLAARLEALKEGGGASLAEYHARASEQLSALGEKARPALEDLRQG
> LLPVLESFKVSLLAAIDEATKKLNAQ
> 
> 
> The sequence of the mature form is:
> DEPQSPWDRVKDLATVYVDAVKDSGRDYVAQFEASA
> LGKQLNLKLLDNWDSLSSTVTKLREQIGPVTQEFWDNLEKETEVLRQEMSKDLEEVKQKV
> QPYLDDFQKKWQEEVELYRQKVAPLGSELREGARQKLQELQEKLSPLAEELRDRARTHVD
> ALRAQLAPYSDDLRERLAARLEALKEGGGASLAEYHARASEQLSALGEKARPALEDLRQG
> LLPVLESFKVSLLAAIDEATKKLNAQ
> 
> 
> According to how the sequence is labeled in uniprot the first aspartate residue of mature canine
> Apolipoprotein A-I starts at position 25, and this what Chimera uses. However, for the mature
> protein this should start at position 1. How can I change the numbering system so the first
> aspartate residue starts at position 1?
> 
> I would be very glad for your advice.
> 
> Thank you.
> Tiglath
>