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