Way to compute residue wise RMSD using python script in chimera:
Dear sir/madam, I would like to superimpose the two structures and compute the residue wise RMSD values. With Gui support in chimera, I opened the two structures and used Matchmaker to superimpose two structures. In Matchmaker, I checked the box 'Show pairwise alignment(s)' and click Apply, subsequently it displays MultAlignViewer dialogue box, where --> Headers --> RMSD : backbone --> Save --> filenamegiven. This process would give me residue wise RMSD score only for backbone atoms in .hdr format. I wants to write python script to do the same, so that I will compare large number of structures, and my script is able to perform till the procedure of superimposition using matchmaker and display MultAlignViewer dialogue box. I don't know the way to store the RMSD : backbone and RMSD : calpha in .hdr format using python script through chimera. Can some one please help me in this. The reason why I specifically want to do in this approach is, because among the two structures, some residues of one structure is missing. Since this approach will compute RMSD only for the matching residues, I am interested in this. Hope my question is not confusing. Thanks in advance. Best regards, Kamalesh D.
Hi Kamalesh, If you are familiar with Python, there is a script attached to this previous mailing-list message: [Chimera-users] Writing alignment and RMSD out <http://www.cgl.ucsf.edu/pipermail/chimera-users/2007-December/002090.html> that would be easy to modify to do what you want. You would just remove the parts the parts that used Multalign Viewer to write the sequence alignment. The RMSD that the MatchMaker.match() function returns is a carbon-alpha RMSD, so if you needed a full-backbone RMSD that would be more work. Let me know and I can offer guidance on that. Also, match() returns the overall RMSD of the match. To get the per-residue RMSD you would loop over the atom lists returned by the match() function and for corresponding pairs get the distance (== RMSD for two atoms) with: atom1.xformCoord().distance(atom2.xformCoord()). For output purposes you can get a string representation of an atom’s residue with str(atom.residue). Also, unfortunately the attachment to the message has a “.bin” suffix despite being from a Python file that had a “.py” suffix, so if that’s a problem let me know and I can send you the .py file directly. —Eric Eric Pettersen UCSF Computer Graphics Lab
On Aug 31, 2019, at 7:20 AM, Kamalesh Damodaran <kamaleshdams@gmail.com> wrote:
Dear sir/madam,
I would like to superimpose the two structures and compute the residue wise RMSD values. With Gui support in chimera, I opened the two structures and used Matchmaker to superimpose two structures. In Matchmaker, I checked the box 'Show pairwise alignment(s)' and click Apply, subsequently it displays MultAlignViewer dialogue box, where --> Headers --> RMSD : backbone --> Save --> filenamegiven. This process would give me residue wise RMSD score only for backbone atoms in .hdr format.
I wants to write python script to do the same, so that I will compare large number of structures, and my script is able to perform till the procedure of superimposition using matchmaker and display MultAlignViewer dialogue box. I don't know the way to store the RMSD : backbone and RMSD : calpha in .hdr format using python script through chimera.
Can some one please help me in this. The reason why I specifically want to do in this approach is, because among the two structures, some residues of one structure is missing. Since this approach will compute RMSD only for the matching residues, I am interested in this.
Hope my question is not confusing. Thanks in advance.
Best regards, Kamalesh D. _______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Hi Eric, Thank you so much for your guidance and the python script. I got everything what I was looking for. Thanks and regards, Kamalesh D. On Wed, 4 Sep 2019 at 04:54, Eric Pettersen <pett@cgl.ucsf.edu> wrote:
Hi Kamalesh, If you are familiar with Python, there is a script attached to this previous mailing-list message: [Chimera-users] Writing alignment and RMSD out <http://www.cgl.ucsf.edu/pipermail/chimera-users/2007-December/002090.html> that would be easy to modify to do what you want. You would just remove the parts the parts that used Multalign Viewer to write the sequence alignment. The RMSD that the MatchMaker.match() function returns is a carbon-alpha RMSD, so if you needed a full-backbone RMSD that would be more work. Let me know and I can offer guidance on that. Also, match() returns the overall RMSD of the match. To get the per-residue RMSD you would loop over the atom lists returned by the match() function and for corresponding pairs get the distance (== RMSD for two atoms) with: atom1.xformCoord().distance(atom2.xformCoord()). For output purposes you can get a string representation of an atom’s residue with str(atom.residue). Also, unfortunately the attachment to the message has a “.bin” suffix despite being from a Python file that had a “.py” suffix, so if that’s a problem let me know and I can send you the .py file directly.
—Eric
Eric Pettersen UCSF Computer Graphics Lab
On Aug 31, 2019, at 7:20 AM, Kamalesh Damodaran <kamaleshdams@gmail.com> wrote:
Dear sir/madam,
I would like to superimpose the two structures and compute the residue wise RMSD values. With Gui support in chimera, I opened the two structures and used Matchmaker to superimpose two structures. In Matchmaker, I checked the box 'Show pairwise alignment(s)' and click Apply, subsequently it displays MultAlignViewer dialogue box, where --> Headers --> RMSD : backbone --> Save --> filenamegiven. This process would give me residue wise RMSD score only for backbone atoms in .hdr format.
I wants to write python script to do the same, so that I will compare large number of structures, and my script is able to perform till the procedure of superimposition using matchmaker and display MultAlignViewer dialogue box. I don't know the way to store the RMSD : backbone and RMSD : calpha in .hdr format using python script through chimera.
Can some one please help me in this. The reason why I specifically want to do in this approach is, because among the two structures, some residues of one structure is missing. Since this approach will compute RMSD only for the matching residues, I am interested in this.
Hope my question is not confusing. Thanks in advance.
Best regards, Kamalesh D. _______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Great! —Eric
On Sep 9, 2019, at 6:31 AM, Kamalesh Damodaran <kamaleshdams@gmail.com> wrote:
Hi Eric,
Thank you so much for your guidance and the python script. I got everything what I was looking for.
Thanks and regards, Kamalesh D.
On Wed, 4 Sep 2019 at 04:54, Eric Pettersen <pett@cgl.ucsf.edu <mailto:pett@cgl.ucsf.edu>> wrote: Hi Kamalesh, If you are familiar with Python, there is a script attached to this previous mailing-list message: [Chimera-users] Writing alignment and RMSD out <http://www.cgl.ucsf.edu/pipermail/chimera-users/2007-December/002090.html> that would be easy to modify to do what you want. You would just remove the parts the parts that used Multalign Viewer to write the sequence alignment. The RMSD that the MatchMaker.match() function returns is a carbon-alpha RMSD, so if you needed a full-backbone RMSD that would be more work. Let me know and I can offer guidance on that. Also, match() returns the overall RMSD of the match. To get the per-residue RMSD you would loop over the atom lists returned by the match() function and for corresponding pairs get the distance (== RMSD for two atoms) with: atom1.xformCoord().distance(atom2.xformCoord()). For output purposes you can get a string representation of an atom’s residue with str(atom.residue). Also, unfortunately the attachment to the message has a “.bin” suffix despite being from a Python file that had a “.py” suffix, so if that’s a problem let me know and I can send you the .py file directly.
—Eric
Eric Pettersen UCSF Computer Graphics Lab
On Aug 31, 2019, at 7:20 AM, Kamalesh Damodaran <kamaleshdams@gmail.com <mailto:kamaleshdams@gmail.com>> wrote:
Dear sir/madam,
I would like to superimpose the two structures and compute the residue wise RMSD values. With Gui support in chimera, I opened the two structures and used Matchmaker to superimpose two structures. In Matchmaker, I checked the box 'Show pairwise alignment(s)' and click Apply, subsequently it displays MultAlignViewer dialogue box, where --> Headers --> RMSD : backbone --> Save --> filenamegiven. This process would give me residue wise RMSD score only for backbone atoms in .hdr format.
I wants to write python script to do the same, so that I will compare large number of structures, and my script is able to perform till the procedure of superimposition using matchmaker and display MultAlignViewer dialogue box. I don't know the way to store the RMSD : backbone and RMSD : calpha in .hdr format using python script through chimera.
Can some one please help me in this. The reason why I specifically want to do in this approach is, because among the two structures, some residues of one structure is missing. Since this approach will compute RMSD only for the matching residues, I am interested in this.
Hope my question is not confusing. Thanks in advance.
Best regards, Kamalesh D. _______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu <mailto:Chimera-users@cgl.ucsf.edu> Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users <http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users>
participants (2)
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Eric Pettersen -
Kamalesh Damodaran