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 <pymol-users@lists.sourceforge.net> 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 <julien.capp...@univ-lorraine.fr> > Sent At:2020 Jun. 17 (Wed.) 17:05 > To:孙业平 <sunyep...@aliyun.com> > 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%2F&data=02%7C01%7Crobert.campbell%40queensu.ca%7C4e290e0f1c4044d3b1fc08d812bf8cca%7Cd61ecb3b38b142d582c4efb2838b925c%7C1%7C0%7C637279961201881850&sdata=EOgyXD4A%2FemFaZHj6eRrx1h3nc%2BoCOHr94cFzpmIE3o%3D&reserved=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 > <pymol-users@lists.sourceforge.net> 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%3Dsharing&data=02%7C01%7Crobert.campbell%40queensu.ca%7C4e290e0f1c4044d3b1fc08d812bf8cca%7Cd61ecb3b38b142d582c4efb2838b925c%7C1%7C0%7C637279961201881850&sdata=72dx0AyAPoHLvV4iXbEhmoGY18cXymzJRRWUqC7gdjE%3D&reserved=0 > > With many thanks. > > _______________________________________________ > PyMOL-users mailing list > Archives: > https://can01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.mail-archive.com%2Fpymol-users%40lists.sourceforge.net&data=02%7C01%7Crobert.campbell%40queensu.ca%7C4e290e0f1c4044d3b1fc08d812bf8cca%7Cd61ecb3b38b142d582c4efb2838b925c%7C1%7C0%7C637279961201881850&sdata=PS%2BRq2rFtONyOjTtIS59OZnLnYEAG2spdQJXLzlpGzA%3D&reserved=0 > Unsubscribe: > https://can01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fsourceforge.net%2Fprojects%2Fpymol%2Flists%2Fpymol-users%2Funsubscribe&data=02%7C01%7Crobert.campbell%40queensu.ca%7C4e290e0f1c4044d3b1fc08d812bf8cca%7Cd61ecb3b38b142d582c4efb2838b925c%7C1%7C0%7C637279961201881850&sdata=FMqipuYNGRnLNirUNl5hMdQtsm%2F%2F9GRkhNxzMKjP0LE%3D&reserved=0 > -- Robert L. Campbell, Ph.D. Academic Advisor, BHSc Program Assistant Professor, Dept. of Biomedical & Molecular Sciences, Queen's University, Kingston, ON K7L 3N6 Canada Botterell Hall Rm 644 Tel: 613-533-6821 <robert.campb...@queensu.ca> http://pldserver1.biochem.queensu.ca/~rlc _______________________________________________ PyMOL-users mailing list Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
