Hi,

The sequences all have to be aligned in the same sequence window (see example in image below) - there is only one alignment ID.

In other words, you have to actually create a sequence alignment before you can calculate % sequence identity.  There are lots of ways you can get sequence alignments (download from databases, use other programs or web servers) but if you want a way to do it in ChimeraX, see the "sequence align" command.  For example

seq align #1/A,B #2/A

... to create a sequence alignment of model 1 chains A and B and model 2 chain A. Then you can calculate identity, for example

seq identity 1 denominator nongap

Please see the "sequence" command help for the options on these commands:

<https://rbvi.ucsf.edu/chimerax/docs/user/commands/sequence.html#align>

<https://rbvi.ucsf.edu/chimerax/docs/user/commands/sequence.html#identity>

I hope this helps,

Elaine

On Jul 17, 2024, at 9:37 AM, NUR AIDA SAKINAH via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:

Hi, 
If I want to use the sequence identity command for two or more different sequences, should the command look like this "sequence identity 1/A 1/B 2/B denominator nongap" ?

On Wed, 17 Jul 2024 at 06:49, NUR AIDA SAKINAH <nuraida14599@gmail.com> wrote:
Oh, that’s how it works. Thank you so much Elaine!

On Wed, 17 Jul 2024 at 03:26, Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hi,
If the sequence window title bar says "[ID: 1]" that means the alignment ID is just "1", not "alignment-1"

However, I don't understand what you are trying to calculate.

If you show only a single sequence as the alignment there is nothing to calculate the % identity with.  You would need the alignment to contain two or more different sequences.

I hope this makes sense.
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Resource for Biocomputing, Visualization, and Informatics
Department of Pharmaceutical Chemistry
University of California, San Francisco


> On Jul 16, 2024, at 2:49 AM, NUR AIDA SAKINAH via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
> 
> Hai, 
> I want to use the sequence identity command in ChimeraX but in the log said "Missing or invalid "src1" argument: Expected alignment-id or [alignment-id]:sequence-name-or-number". 
> The input I gave is "sequence identity alignment-1" after open the tools>sequence>show sequence viewer and then select model e.g. #1/a and it show the ID as [ID: 1] but i got error. How to solve this problem?
> 
> Hope ChimeraX teams can help. Thank you!