Hello Sunyeping,
I would first point out that if you align on chain A of each molecule, then
chain B of ASFV aligns with chain C of MTUB and vice versa. In other words you
don't have the same assignment of chain ids in your trimer. The alignment of
just alpha carbons of chain A with "align" gives an RMSD of 1.78 Å for 81 atoms
and for "super" gives an RMSD of 1.746 Å for 81 atoms. That may be the best
that you can do, but if you want to align the whole trimer than you need to
rename chain B to chain C and chain C to chain B for one of your molecules.
You can do that renaming within PyMOL with these commands:
PyMOL>alter MTUB_trimer & c. B, chain="D"
PyMOL>alter MTUB_trimer & c. C, chain="B"
PyMOL>alter MTUB_trimer & c. D, chain="C"
(I'm just using "D" as an intermediate name here)
If you do that, then aligning all alpha carbons gives an RMSD of 2.189 Å for
"align" and 1.845 Å for "super".
Cheers,
Rob
On Wed, 2020-06-17 21:04 +0800, sunyeping via PyMOL-users
wrote:
> Hello Julien Cappèle,
>Thank you for your response. I didn't mean to keep the input file
> in secrete. I have changed the access right to them, so you can
> download them freely. Best, Yeping Sun
> ----------
> From:Julien CAPPELE
> Sent At:2020 Jun. 17 (Wed.) 17:05
> To:孙业平
> Subject:Re: [PyMOL] Effect of different align method
>
> Hello Sunyeping,
>
> I would suggest you to try TM-align, and a very good way to use it
> for multi-protein alignment is to use their server mTM-align.
> TM-align is a very robust alignment tool that will in most of the
> case, give you a better structural based alignment with low to zero
> input from the sequence.
> https://can01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fyanglab.nankai.edu.cn%2FmTM-align%2Fdata=02%7C01%7Crobert.campbell%40queensu.ca%7C4e290e0f1c4044d3b1fc08d812bf8cca%7Cd61ecb3b38b142d582c4efb2838b925c%7C1%7C0%7C637279961201881850sdata=EOgyXD4A%2FemFaZHj6eRrx1h3nc%2BoCOHr94cFzpmIE3o%3Dreserved=0
>
>
> Also, if you are not working on secret stuff, you can give me access
> so I can rework the output files from mTM-align server to give you a
> RMSD-colored alignment in PyMOL.
>
> On PyMOL only, I didn't try to implement TM-align because I use
> Windows, but the developers said that a linux implementation could be
> possible if you are a bit familiar with compiling softwares.
>
> -
> Julien Cappèle
> Doctorant - 2ème année - ED C2MP
> Université de Lorraine
> CRM² - UMR CNRS 7036
> julien.capp...@univ-lorraine.fr
> Tel: (+33)6 99 18 59 03
> -
>
> Le mer. 17 juin 2020 à 05:06, sunyeping via PyMOL-users
> a écrit : Dear pymol users,
>
> I am trying to align two very similar trimeric molecules. I tried
> different alignment commands including "align", "cealign" and
> "super", but none of them gives satisfying effect. Athough the
> backbone conformations and orientations of two two molecules look
> very similar, there are obvious displacements between them after
> alignment with these three commands. The rmsd of the two molecules
> for these three methods are 2.250, 4.682, 2.206 and 2.206,
> respectively. I wonder whether there is any better alignment command
> or there are any parameters that can be passed to these three
> alignment commands to improve the effects. Could you help me check
> this? The pdb files of these two molecules, the image for the two
> molecules after using "super" command, and the alignment effect in
> the publication I mentioned can be found at the following link.
>
> https://can01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fdrive.google.com%2Ffile%2Fd%2F1ff3XgTexgdul-SezUz75dVoCx2cL5YPL%2Fview%3Fusp%3Dsharingdata=02%7C01%7Crobert.campbell%40queensu.ca%7C4e290e0f1c4044d3b1fc08d812bf8cca%7Cd61ecb3b38b142d582c4efb2838b925c%7C1%7C0%7C637279961201881850sdata=72dx0AyAPoHLvV4iXbEhmoGY18cXymzJRRWUqC7gdjE%3Dreserved=0
>
> With many thanks.
>
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