Hi, I have never used Chimera so please bear with me. I have this short peptide sequence (8 aa) that I want to locate in the secondary structure of a protein which I have opened in chimera. Is there a way to highlight the sequence in a particular color in the 3D model and/or only have the aminoacid numbering in this region? Also, I would like to view a linear alignment of the entire protein sequence with my peptide sequence of interest. I was able to do that and see that the peptide sequence falls in a beta-sheet (green color). Is there any way know which strand it is exactly? It is supposed to be in strand 5 but I don't know how to display strand numbers, or verify with certainty that it is indeed strand 5 and not strand 6 for example. Thanks, Bodvael
Hi Bodvael, Please check out my answer in blue color for your query. I have never used Chimera so please bear with me. I have this short peptide sequence (8 aa) that I want to locate in the secondary structure of a protein which I have opened in chimera. Is there a way to highlight the sequence in a particular color in the 3D model and/or only have the aminoacid numbering in this region? ** Yes, you can highlight the desired region using Chimera. After loading your structure, goto *Tools -> Sequence -> Sequence * to display the sequence. Here, you can find that by default, alpha - helices are highlighted in yellow, sheets in green in the sequence window. Now, to highlight the region of your interest, just drag on the residues that you want. You can see that the residues you have selected are highlighted in green in the structure window. Now goto *Actions -> Color -> choose a color of your choice * To have the amino acid numbering, goto * Actions -> Label -> Residue -> Specifier (you can select 1-letter code + specifier to have the amino acid residue and residue number labelled). * I have never used Chimera so please bear with me. I have this short peptide sequence (8 aa) that I want to locate in the secondary structure of a protein which I have opened in chimera. Is there a way to highlight the sequence in a particular color in the 3D model and/or only have the aminoacid numbering in this region? I am unsure, if you can display the strand numbers in Chimera. The best way is to identify the N- and C- terminal and count the strand from N- terminal. * -Suda * On Tue, Nov 15, 2011 at 7:12 AM, bodvael email <bodvael@gmail.com> wrote:
Hi,
I have never used Chimera so please bear with me. I have this short peptide sequence (8 aa) that I want to locate in the secondary structure of a protein which I have opened in chimera. Is there a way to highlight the sequence in a particular color in the 3D model and/or only have the aminoacid numbering in this region?
Also, I would like to view a linear alignment of the entire protein sequence with my peptide sequence of interest. I was able to do that and see that the peptide sequence falls in a beta-sheet (green color). Is there any way know which strand it is exactly? It is supposed to be in strand 5 but I don't know how to display strand numbers, or verify with certainty that it is indeed strand 5 and not strand 6 for example.
Thanks, Bodvael
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Thanks Suda! Hi Bodvael, I would only add: (A) To get strand number, it is probably best to do what Suda suggested: if looking at the sequence, just count the strands (green boxes) from N to C, or if looking at the structure, follow the ribbon from N to C. It may help to rainbow-color the structure, which by default goes from blue at the C-term to red at the N-term (Tools... Depiction... Rainbow in the menu, or command rainbow. Currently in Chimera the strand numbering is not necessarily from N->C... they are numbered in order of appearance in the PDB SHEET records, and sometimes the order of the strands in a sheet is different from N->C order. Keeping that in mind, you could select strands by number (will be shown with green highlighting on the structure) with commands, for example: select :/ssId=1 & strand (B) After you show the whole protein sequence as Suda said, you can search for some string of residues by choosing "Edit... Find Subsequence" from the sequence window menu. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco
Hi Elaine, Thanks a lot for your answer, it works. The reason I asked about the beta sheet numbers is because when I count the number regions highlighted in green from the N-term, my stretch of amino acids corresponds to beta sheet 7 instead of 5 (based on the original manuscript). Thus, it appears that the numbering of the beta sheets in the linear sequence is different from their numbering in the ribbon diagram. My question is then, what is the best way to get the numbering of the secondary structure in the linear sequence but based on the "official" numbering in the ribbon diagram. Else it is a bit confusing to have different numbers for the same beta sheets. Thanks, Bodvael On Tue, Nov 15, 2011 at 12:32 PM, Elaine Meng <meng@cgl.ucsf.edu> wrote:
Thanks Suda!
Hi Bodvael, I would only add:
(A) To get strand number, it is probably best to do what Suda suggested: if looking at the sequence, just count the strands (green boxes) from N to C, or if looking at the structure, follow the ribbon from N to C. It may help to rainbow-color the structure, which by default goes from blue at the C-term to red at the N-term (Tools... Depiction... Rainbow in the menu, or command rainbow.
Currently in Chimera the strand numbering is not necessarily from N->C... they are numbered in order of appearance in the PDB SHEET records, and sometimes the order of the strands in a sheet is different from N->C order. Keeping that in mind, you could select strands by number (will be shown with green highlighting on the structure) with commands, for example:
select :/ssId=1 & strand
(B) After you show the whole protein sequence as Suda said, you can search for some string of residues by choosing "Edit... Find Subsequence" from the sequence window menu.
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco
Hi Bodvael, I don't understand the question. Which numbering is the official numbering? Chimera has no way of knowing how a structure was described in the manuscript about the structure. It only knows what is in the PDB file, and will number strands consecutively in the order in which they are listed in the SHEET lines of the PDB file. To tell what numbers Chimera assigned, use select commands such as: select :/ssId=1 & strand You can manually reassign "ssId" to something different than what Chimera assigned, using the command "setattr" -- for example, if you want to change ssId of strand currently assigned as 2 to 3, command: setattr r ssId 3 strand&:/ssId=2 ... but you would have to be very careful about the order in which you do things. The original strand 3 would still be 3 unless you had changed it beforehand. Also, does it ultimately matter which numbers Chimera has assigned? Not really, unless you are going to use them for something. You could simply choose the strand you want to act on by dragging in the sequence window, without using its number. Numbering in terms of N->C, which may or may not be different from what Chimera assigned using the order in the PDB file, can be obtained by simply counting from N to C while viewing the structure or sequence as described in my earlier message. I hope this helps, 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 Nov 15, 2011, at 12:32 PM, bodvael email wrote:
Hi Elaine,
Thanks a lot for your answer, it works.
The reason I asked about the beta sheet numbers is because when I count the number regions highlighted in green from the N-term, my stretch of amino acids corresponds to beta sheet 7 instead of 5 (based on the original manuscript).
Thus, it appears that the numbering of the beta sheets in the linear sequence is different from their numbering in the ribbon diagram. My question is then, what is the best way to get the numbering of the secondary structure in the linear sequence but based on the "official" numbering in the ribbon diagram. Else it is a bit confusing to have different numbers for the same beta sheets.
Thanks, Bodvael
On Tue, Nov 15, 2011 at 12:32 PM, Elaine Meng <meng@cgl.ucsf.edu> wrote: Thanks Suda!
Hi Bodvael, I would only add:
(A) To get strand number, it is probably best to do what Suda suggested: if looking at the sequence, just count the strands (green boxes) from N to C, or if looking at the structure, follow the ribbon from N to C. It may help to rainbow-color the structure, which by default goes from blue at the C-term to red at the N-term (Tools... Depiction... Rainbow in the menu, or command rainbow.
Currently in Chimera the strand numbering is not necessarily from N->C... they are numbered in order of appearance in the PDB SHEET records, and sometimes the order of the strands in a sheet is different from N->C order. Keeping that in mind, you could select strands by number (will be shown with green highlighting on the structure) with commands, for example:
select :/ssId=1 & strand
(B) After you show the whole protein sequence as Suda said, you can search for some string of residues by choosing "Edit... Find Subsequence" from the sequence window menu.
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco
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Hi Bodvael, Since it seems that numbering the strands in N->C order rather than SHEET record order would be an improvement, I am opening an enhancement-request in our bug-tracking database with you on the cc list so that you know when it gets implemented. You should go ahead and use Elaine's suggestions since it will probably take awhile before it gets implemented. --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu On Nov 15, 2011, at 4:44 PM, Elaine Meng wrote:
Hi Bodvael, I don't understand the question. Which numbering is the official numbering? Chimera has no way of knowing how a structure was described in the manuscript about the structure. It only knows what is in the PDB file, and will number strands consecutively in the order in which they are listed in the SHEET lines of the PDB file. To tell what numbers Chimera assigned, use select commands such as:
select :/ssId=1 & strand
You can manually reassign "ssId" to something different than what Chimera assigned, using the command "setattr" -- for example, if you want to change ssId of strand currently assigned as 2 to 3, command:
setattr r ssId 3 strand&:/ssId=2
... but you would have to be very careful about the order in which you do things. The original strand 3 would still be 3 unless you had changed it beforehand. Also, does it ultimately matter which numbers Chimera has assigned? Not really, unless you are going to use them for something. You could simply choose the strand you want to act on by dragging in the sequence window, without using its number.
Numbering in terms of N->C, which may or may not be different from what Chimera assigned using the order in the PDB file, can be obtained by simply counting from N to C while viewing the structure or sequence as described in my earlier message.
I hope this helps, 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 Nov 15, 2011, at 12:32 PM, bodvael email wrote:
Hi Elaine,
Thanks a lot for your answer, it works.
The reason I asked about the beta sheet numbers is because when I count the number regions highlighted in green from the N-term, my stretch of amino acids corresponds to beta sheet 7 instead of 5 (based on the original manuscript).
Thus, it appears that the numbering of the beta sheets in the linear sequence is different from their numbering in the ribbon diagram. My question is then, what is the best way to get the numbering of the secondary structure in the linear sequence but based on the "official" numbering in the ribbon diagram. Else it is a bit confusing to have different numbers for the same beta sheets.
Thanks, Bodvael
On Tue, Nov 15, 2011 at 12:32 PM, Elaine Meng <meng@cgl.ucsf.edu> wrote: Thanks Suda!
Hi Bodvael, I would only add:
(A) To get strand number, it is probably best to do what Suda suggested: if looking at the sequence, just count the strands (green boxes) from N to C, or if looking at the structure, follow the ribbon from N to C. It may help to rainbow-color the structure, which by default goes from blue at the C-term to red at the N-term (Tools... Depiction... Rainbow in the menu, or command rainbow.
Currently in Chimera the strand numbering is not necessarily from N-
C... they are numbered in order of appearance in the PDB SHEET records, and sometimes the order of the strands in a sheet is different from N->C order. Keeping that in mind, you could select strands by number (will be shown with green highlighting on the structure) with commands, for example:
select :/ssId=1 & strand
(B) After you show the whole protein sequence as Suda said, you can search for some string of residues by choosing "Edit... Find Subsequence" from the sequence window menu.
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco
_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
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participants (4)
-
bodvael email -
Elaine Meng -
Eric Pettersen -
Suda Parimala Ravindran