Yes, those two commands I gave worked fine on my own example, but you may need to modify them if your model numbers and chain IDs are different.

You must have a sequence alignment before you can calculate sequence identity.  As I mentioned in the previous message, using "sequence align" is only one way to get the sequence alignment.  You should look at the resulting sequence alignment and see if it makes sense to you.  If the sequences are not similar it may fail to align them well and you may need to use different parameters and/or a totally different program to make the alignment.  If you use some other program to make the sequence alignment file, you can open the sequence alignment file in ChimeraX and then calculate sequence identity.

The sequence alignment with "sequence align" only uses the sequences and "sequence identity" only uses the letters in the sequence alignment.  It does not use the 3D structures.

You can read the help pages (links in previous message) for details on how they work.

Elaine

> On Jul 17, 2024, at 10:52 AM, NUR AIDA SAKINAH via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
>
> From what I understand, we need to use the "sequence align" command first, then can calculate % using sequence identity, is it right?
> Does the sequence identity can calculate for the structural alignment?
>
> Thank you for be patient with me and I am sorry if I have asked some obvious questions. I really appreciate it.
>
>
>
> On Thu, 18 Jul 2024 at 00:58, Elaine Meng <meng@cgl.ucsf.edu> wrote:
> Hi,
> The sequences all have to be aligned in the same sequence window (see example in image below) - there is only one alignment ID.
>
> <Screen Shot 2024-07-17 at 9.46.53 AM.png>
>
>
> 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!
>
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