Merge the protein sequences of two different chains
Dear all: I am a new beginner of Chemira software package. By using "Multalign Viewer", I would like to merge the protein sequences of two different chains (200~300 a.a.). After that, I want to map some epitopes (8 ~ 20 a.a.) to this merged sequence. How can I do? Thanks for any kind help further. Hsih-Te
Hi Hsih-Te, Welcome to Chimera! Can you explain more about what you want to do? Are the chains in two different PDB files or in the same PDB file, and why do you want a single chain in Multalign Viewer? Did you just want one chain stuck on the end of the other, or mixed together somehow? You may be able to do what you want without merging any chains. You can just show the sequence of each chain in a separate window (Favorites.. Sequence), and both of those will automatically interact with your structure: if you highlight some residues in the sequence window, the corresponding part of your structure will be selected and vice versa. If you really need a merged single chain, the details depend on what you have to start with. Multalign Viewer editing does not allow merging chains directly, so you might have to do text-editing manually (in your favorite text editor outside of Chimera). Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Apr 3, 2012, at 9:10 AM, Hsih-Te Yang wrote:
Dear all: I am a new beginner of Chemira software package. By using "Multalign Viewer", I would like to merge the protein sequences of two different chains (200~300 a.a.). After that, I want to map some epitopes (8 ~ 20 a.a.) to this merged sequence. How can I do? Thanks for any kind help further. Hsih-Te
Hi, Elaine: Thanks for your kind reply that is very informative. Eventually, I found the solution to mapping the epitopes to reference/merged protein which is combined by text editor. Please see the enclosed results analysed by "Blast 2 seqs" (HTY_HA_B2Seq). I spent a couple of days to study the docs of "Chimera". Finally , I came out of the command lines to map epitops to protein structure: open 3LZG split #0 preset apply int 3 col magenta r #0.1:322-330 col magenta #0.2:1-11 ========================= However, I found a very unexpected region which is colored by the epitope segment. See the "red question marks" in the PPT file (HTY_HA_Chimera.pdf) Thanks again, Hsih-Te On Wed, Apr 4, 2012 at 2:19 PM, Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hi Hsih-Te, Welcome to Chimera!
Can you explain more about what you want to do? Are the chains in two different PDB files or in the same PDB file, and why do you want a single chain in Multalign Viewer? Did you just want one chain stuck on the end of the other, or mixed together somehow?
You may be able to do what you want without merging any chains. You can just show the sequence of each chain in a separate window (Favorites.. Sequence), and both of those will automatically interact with your structure: if you highlight some residues in the sequence window, the corresponding part of your structure will be selected and vice versa.
If you really need a merged single chain, the details depend on what you have to start with. Multalign Viewer editing does not allow merging chains directly, so you might have to do text-editing manually (in your favorite text editor outside of Chimera).
Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco
On Apr 3, 2012, at 9:10 AM, Hsih-Te Yang wrote:
Dear all: I am a new beginner of Chemira software package. By using "Multalign Viewer", I would like to merge the protein sequences of two different chains (200~300 a.a.). After that, I want to map some epitopes (8 ~ 20 a.a.) to this merged sequence. How can I do? Thanks for any kind help further. Hsih-Te
Hi Hsih-Te, In 3lzg, the protein chain A (#0.1 after splitting) ends at 325. When you color residues 325-330 it includes a nonprotein residue NAG 330, which is a glycosylation on a different area of the chain. One way to see what you are coloring is to display the atoms of those residues when the surface is not shown, for example: alias epi1 #0.1:322-330 color magenta epi1 show epi1 You can put the mouse over the atoms to see the residue name and number. Or, you could check first to see what residues are in some chain of your protein structure by using the Sequence tool (under Favorites menu) to show the sequence of that chain and then putting the mouse cursor over the sequence to see what the structure residue numbers are. Some other advice for making your figure... (1) 3lzg has two hemagglutinin trimers, the first one is chains A-F, the second one is chains G-L. Might as well delete the second copy before splitting and doing the other stuff, for example commands: open 3lzg delete :.g-l split (2) instead of using the preset to show the surface with orange-white-blue coloring by hydrophobicity, just show the surface and color it one color. Then it will be easier to see the epitope locations when you color the epitopes some other colors. For example: surface color tan,s alias epi1 #0.1:322-325 alias epi2 #0.2:1-11 color magenta epi1 color cyan epi2 I like to use aliases because it is then easier to try other colors or do other things to those sets of residues without typing the residue numbers again. (3) After you have the structure coloring as you like it, you can use a publication preset to make the surface smoother and color the background white. It will keep the structure coloring the same. I hope this helps, Elaine On Apr 4, 2012, at 2:39 PM, Hsih-Te Yang wrote:
Hi, Elaine: Thanks for your kind reply that is very informative. Eventually, I found the solution to mapping the epitopes to reference/merged protein which is combined by text editor. Please see the enclosed results analysed by "Blast 2 seqs" (HTY_HA_B2Seq). I spent a couple of days to study the docs of "Chimera". Finally , I came out of the command lines to map epitops to protein structure:
open 3LZG split #0 preset apply int 3 col magenta r #0.1:322-330 col magenta #0.2:1-11 =========================
However, I found a very unexpected region which is colored by the epitope segment. See the "red question marks" in the PPT file (HTY_HA_Chimera.pdf) Thanks again, Hsih-Te
Good morning, Elaine: You really solved my problem as well as I expected. The Chimera is such a powerful software with kind support to the scientist who doesn't know much about structure biology. Thank you again. Cheers, Hsih-Te On Wed, Apr 4, 2012 at 7:00 PM, Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hi Hsih-Te, In 3lzg, the protein chain A (#0.1 after splitting) ends at 325. When you color residues 325-330 it includes a nonprotein residue NAG 330, which is a glycosylation on a different area of the chain.
One way to see what you are coloring is to display the atoms of those residues when the surface is not shown, for example:
alias epi1 #0.1:322-330 color magenta epi1 show epi1
You can put the mouse over the atoms to see the residue name and number.
Or, you could check first to see what residues are in some chain of your protein structure by using the Sequence tool (under Favorites menu) to show the sequence of that chain and then putting the mouse cursor over the sequence to see what the structure residue numbers are.
Some other advice for making your figure...
(1) 3lzg has two hemagglutinin trimers, the first one is chains A-F, the second one is chains G-L. Might as well delete the second copy before splitting and doing the other stuff, for example commands:
open 3lzg delete :.g-l split
(2) instead of using the preset to show the surface with orange-white-blue coloring by hydrophobicity, just show the surface and color it one color. Then it will be easier to see the epitope locations when you color the epitopes some other colors. For example:
surface color tan,s alias epi1 #0.1:322-325 alias epi2 #0.2:1-11 color magenta epi1 color cyan epi2
I like to use aliases because it is then easier to try other colors or do other things to those sets of residues without typing the residue numbers again.
(3) After you have the structure coloring as you like it, you can use a publication preset to make the surface smoother and color the background white. It will keep the structure coloring the same.
I hope this helps, Elaine
On Apr 4, 2012, at 2:39 PM, Hsih-Te Yang wrote:
Hi, Elaine: Thanks for your kind reply that is very informative. Eventually, I found the solution to mapping the epitopes to reference/merged protein which is combined by text editor. Please see the enclosed results analysed by "Blast 2 seqs" (HTY_HA_B2Seq). I spent a couple of days to study the docs of "Chimera". Finally , I came out of the command lines to map epitops to protein structure:
open 3LZG split #0 preset apply int 3 col magenta r #0.1:322-330 col magenta #0.2:1-11 =========================
However, I found a very unexpected region which is colored by the epitope segment. See the "red question marks" in the PPT file (HTY_HA_Chimera.pdf) Thanks again, Hsih-Te
participants (2)
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Elaine Meng -
Hsih-Te Yang