Re: [PyMOL] Protein structures in 2D?

[Jarrett J. <jar...@sc...>]

As the first command
```
set matrix_mode, 1
fetch 2blx
fetch 2bly
symexp sym2blx, 2blx, (2blx), 4
symexp sym2bly, 2bly, (2bly), 4
align 2bly, 2blx
matrix_copy 2bly, sym2bly*
```

[image: image.png]
Assuming this is what you want.

Best,
Jarrett J.

On Fri, Feb 20, 2026 at 8:34 PM Francisco Murphy Pérez <
fra...@ib...> wrote:

> before matrix_copy...it moves the symmetry mates to other places...(not
> around the original coordinates)
>
> El vie, 20 feb 2026 a la(s) 7:25 p.m., Francisco Murphy Pérez (
> fra...@ib...) escribió:
>
>> before all commands...or just before the matrix_copy command?
>>
>> El vie, 20 feb 2026 a la(s) 4:29 p.m., Jarrett Johnson (
>> jar...@sc...) escribió:
>>
>>> HI Francisco,
>>>
>>> Yes, this is definitely a bug. We'll address this in the next patch. In
>>> the meantime, can you run `set matrix_mode, 1` before doing these commands
>>> and see if that helps?
>>>
>>> Best,
>>> Jarrett J
>>>
>>> On Fri, Feb 20, 2026 at 4:55 PM Francisco Murphy Pérez <
>>> fra...@ib...> wrote:
>>>
>>>> Dear PYMOL users...I found a bug...
>>>> or.. Am I doing something wrong?
>>>>
>>>> got this
>>>> ```
>>>> fetch 2blx
>>>> fetch 2bly
>>>> symexp sym2blx, 2blx, (2blx), 4
>>>> symexp sym2bly, 2bly, (2bly), 4
>>>> align 2bly, 2blx
>>>> matrix_copy 2bly, sym2bly*
>>>> ```
>>>>
>>>> Attached are 2 screenshots, before and after the last command
>>>>
>>>> How do I align symmetry mates?
>>>> Most importantly... is this a feature or a bug?
>>>> (joking...)
>>>>
>>>> Any help is appreciated!
>>>> Thanks
>>>>
>>>> _______________________________________________
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>>>
>>>
>>>
>>> --
>>>
>>> *Jarrett Johnson* | Staff Developer, PyMOL
>>>
>>>

-- 

*Jarrett Johnson* | Staff Developer, PyMOL