superimposition of DNA moleucles
Dear chimera users, I need to supeimpose a DNA molecule DNA-1.pdb into the protein-DNA complex. I was trying to do this using Mach Maker, but I am getting errors. I am not sure if I can do it using this tool and how should I do it. Thank you in advance for any help and suggestions... best regards Urszula ----------------------------------------- Ta wiadomość została wysłana z serwera Uniwersytetu Gdańskiego http://www.ug.edu.pl/
Hi Urszula, There are several problems… Matchmaker is for automatically pairing chains of same chemical type (both protein or both DNA, for example) and similar sequence. (1) your PDB files are weird: The monomer file has protein + one DNA strand all as chain A and the other DNA strand as chain B. Normally in a PDB file these would have three different chain IDs. The DNA-1 PDB file doesn't have any chain IDs for the two DNA strands, whereas normally these would have two different chain IDs. For Matchmaker, the combination of protein and DNA into the same chain ID is a problem. However... (2) your DNA sequences are not that similar. In that case you wouldn't want to use MatchMaker anyway, but some other method of superimposing the structures. Other methods include the command "match," where you must specify exactly which residues and atoms you want to match, or freezing one structure and moving the other one by hand. The different methods are outlined here: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/framecore.html> For example, assuming you just want to put the DNA helices on top of each other, this command will roughly superimpose your structures if model #0 is your monomer file and model #1 is the DNA-1 file (show Command Line using the Favorites menu): match #0:2-20.a@p #1:2-20@p Manual page for the match command: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/match.html> Or, to move by hand you can use the checkboxes under the Command Line to control which one is frozen (un-check to freeze). <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/mouse.html#activedef> It is possible to use MatchMaker if you change the setting Matrix: to Nucleic, but since it is trying to match only the parts with similar sequences, the DNA helices are offset. You can try it and see what I mean. I thought you probably didn't want that, which is why I suggested the other methods first. 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 Mar 3, 2014, at 6:29 AM, "Urszula Uciechowska" <urszula.uciechowska@biotech.ug.edu.pl> wrote:
Dear chimera users,
I need to supeimpose a DNA molecule DNA-1.pdb into the protein-DNA complex. I was trying to do this using Mach Maker, but I am getting errors. I am not sure if I can do it using this tool and how should I do it. Thank you in advance for any help and suggestions...
best regards Urszula
Hi Elaine, Thank you very much for your help. I was able to superimpose it using your advices. I want to also try it by using command "match" as you also recommended ( please see below). match #DNA-TrfA-complex-NEW-1.pdb:3986-5321@p #nucA-DNA-mina99-ch2-NEW.pdb:1-46@p However I am getting error: "Error in DNA-TrfA-complex-NEW-1.pdb:3986-5321@p value must be intiger" How could I correct the command? /Urszula
Hi Urszula, There are several problems… Matchmaker is for automatically pairing chains of same chemical type (both protein or both DNA, for example) and similar sequence.
(1) your PDB files are weird: The monomer file has protein + one DNA strand all as chain A and the other DNA strand as chain B. Normally in a PDB file these would have three different chain IDs. The DNA-1 PDB file doesn't have any chain IDs for the two DNA strands, whereas normally these would have two different chain IDs. For Matchmaker, the combination of protein and DNA into the same chain ID is a problem. However...
(2) your DNA sequences are not that similar. In that case you wouldn't want to use MatchMaker anyway, but some other method of superimposing the structures. Other methods include the command "match," where you must specify exactly which residues and atoms you want to match, or freezing one structure and moving the other one by hand. The different methods are outlined here: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/framecore.html>
For example, assuming you just want to put the DNA helices on top of each other, this command will roughly superimpose your structures if model #0 is your monomer file and model #1 is the DNA-1 file (show Command Line using the Favorites menu):
match #0:2-20.a@p #1:2-20@p
Manual page for the match command: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/match.html>
Or, to move by hand you can use the checkboxes under the Command Line to control which one is frozen (un-check to freeze). <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/mouse.html#activedef>
It is possible to use MatchMaker if you change the setting Matrix: to Nucleic, but since it is trying to match only the parts with similar sequences, the DNA helices are offset. You can try it and see what I mean. I thought you probably didn't want that, which is why I suggested the other methods first.
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 Mar 3, 2014, at 6:29 AM, "Urszula Uciechowska" <urszula.uciechowska@biotech.ug.edu.pl> wrote:
Dear chimera users,
I need to supeimpose a DNA molecule DNA-1.pdb into the protein-DNA complex. I was trying to do this using Mach Maker, but I am getting errors. I am not sure if I can do it using this tool and how should I do it. Thank you in advance for any help and suggestions...
best regards Urszula
----------------------------------------- Ta wiadomość została wysłana z serwera Uniwersytetu Gdańskiego http://www.ug.edu.pl/
Hi Urszula, You would type the "match" command exactly as I did in the earlier message (do not insert the name of the files!). That command assumes you opened the monomer file first and then the DNA-1 file. Best, Elaine On Mar 5, 2014, at 4:55 AM, Urszula Uciechowska wrote:
Hi Elaine,
Thank you very much for your help. I was able to superimpose it using your advices. I want to also try it by using command "match" as you also recommended ( please see below).
match #DNA-TrfA-complex-NEW-1.pdb:3986-5321@p #nucA-DNA-mina99-ch2-NEW.pdb:1-46@p
However I am getting error: "Error in DNA-TrfA-complex-NEW-1.pdb:3986-5321@p value must be intiger"
How could I correct the command?
/Urszula
Hi Urszula, There are several problems… Matchmaker is for automatically pairing chains of same chemical type (both protein or both DNA, for example) and similar sequence.
(1) your PDB files are weird: The monomer file has protein + one DNA strand all as chain A and the other DNA strand as chain B. Normally in a PDB file these would have three different chain IDs. The DNA-1 PDB file doesn't have any chain IDs for the two DNA strands, whereas normally these would have two different chain IDs. For Matchmaker, the combination of protein and DNA into the same chain ID is a problem. However...
(2) your DNA sequences are not that similar. In that case you wouldn't want to use MatchMaker anyway, but some other method of superimposing the structures. Other methods include the command "match," where you must specify exactly which residues and atoms you want to match, or freezing one structure and moving the other one by hand. The different methods are outlined here: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/framecore.html>
For example, assuming you just want to put the DNA helices on top of each other, this command will roughly superimpose your structures if model #0 is your monomer file and model #1 is the DNA-1 file (show Command Line using the Favorites menu):
match #0:2-20.a@p #1:2-20@p
Manual page for the match command: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/match.html>
Or, to move by hand you can use the checkboxes under the Command Line to control which one is frozen (un-check to freeze). <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/mouse.html#activedef>
It is possible to use MatchMaker if you change the setting Matrix: to Nucleic, but since it is trying to match only the parts with similar sequences, the DNA helices are offset. You can try it and see what I mean. I thought you probably didn't want that, which is why I suggested the other methods first.
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 Mar 3, 2014, at 6:29 AM, "Urszula Uciechowska" <urszula.uciechowska@biotech.ug.edu.pl> wrote:
Dear chimera users,
I need to supeimpose a DNA molecule DNA-1.pdb into the protein-DNA complex. I was trying to do this using Mach Maker, but I am getting errors. I am not sure if I can do it using this tool and how should I do it. Thank you in advance for any help and suggestions...
best regards Urszula
Hi Elanie, I corrected the command: match #0:DNA-TrfA-complex-NEW-1.pdb:3986-5321 #1:nucA-DNA-mina99-ch2-NEW.pdb:1-1369 However the number of my atoms is not equal, can I still do it using this command? /Urszula
Hi Urszula, There are several problems… Matchmaker is for automatically pairing chains of same chemical type (both protein or both DNA, for example) and similar sequence.
(1) your PDB files are weird: The monomer file has protein + one DNA strand all as chain A and the other DNA strand as chain B. Normally in a PDB file these would have three different chain IDs. The DNA-1 PDB file doesn't have any chain IDs for the two DNA strands, whereas normally these would have two different chain IDs. For Matchmaker, the combination of protein and DNA into the same chain ID is a problem. However...
(2) your DNA sequences are not that similar. In that case you wouldn't want to use MatchMaker anyway, but some other method of superimposing the structures. Other methods include the command "match," where you must specify exactly which residues and atoms you want to match, or freezing one structure and moving the other one by hand. The different methods are outlined here: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/framecore.html>
For example, assuming you just want to put the DNA helices on top of each other, this command will roughly superimpose your structures if model #0 is your monomer file and model #1 is the DNA-1 file (show Command Line using the Favorites menu):
match #0:2-20.a@p #1:2-20@p
Manual page for the match command: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/match.html>
Or, to move by hand you can use the checkboxes under the Command Line to control which one is frozen (un-check to freeze). <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/mouse.html#activedef>
It is possible to use MatchMaker if you change the setting Matrix: to Nucleic, but since it is trying to match only the parts with similar sequences, the DNA helices are offset. You can try it and see what I mean. I thought you probably didn't want that, which is why I suggested the other methods first.
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 Mar 3, 2014, at 6:29 AM, "Urszula Uciechowska" <urszula.uciechowska@biotech.ug.edu.pl> wrote:
Dear chimera users,
I need to supeimpose a DNA molecule DNA-1.pdb into the protein-DNA complex. I was trying to do this using Mach Maker, but I am getting errors. I am not sure if I can do it using this tool and how should I do it. Thank you in advance for any help and suggestions...
best regards Urszula
----------------------------------------- Ta wiadomość została wysłana z serwera Uniwersytetu Gdańskiego http://www.ug.edu.pl/
Hi Urszula, If you enter exactly the command that I showed earlier, it specifies the same numbers of atoms. That command only used some of the residues. Open monomer file, open DNA-1 file and then enter *exactly* this command:
match #0:2-20.a@p #1:2-20@p
Elaine On Mar 5, 2014, at 5:08 AM, Urszula Uciechowska wrote:
Hi Elanie,
I corrected the command:
match #0:DNA-TrfA-complex-NEW-1.pdb:3986-5321 #1:nucA-DNA-mina99-ch2-NEW.pdb:1-1369
However the number of my atoms is not equal, can I still do it using this command?
/Urszula
Hi Urszula, There are several problems… Matchmaker is for automatically pairing chains of same chemical type (both protein or both DNA, for example) and similar sequence.
(1) your PDB files are weird: The monomer file has protein + one DNA strand all as chain A and the other DNA strand as chain B. Normally in a PDB file these would have three different chain IDs. The DNA-1 PDB file doesn't have any chain IDs for the two DNA strands, whereas normally these would have two different chain IDs. For Matchmaker, the combination of protein and DNA into the same chain ID is a problem. However...
(2) your DNA sequences are not that similar. In that case you wouldn't want to use MatchMaker anyway, but some other method of superimposing the structures. Other methods include the command "match," where you must specify exactly which residues and atoms you want to match, or freezing one structure and moving the other one by hand. The different methods are outlined here: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/framecore.html>
For example, assuming you just want to put the DNA helices on top of each other, this command will roughly superimpose your structures if model #0 is your monomer file and model #1 is the DNA-1 file (show Command Line using the Favorites menu):
match #0:2-20.a@p #1:2-20@p
Manual page for the match command: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/match.html>
Or, to move by hand you can use the checkboxes under the Command Line to control which one is frozen (un-check to freeze). <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/mouse.html#activedef>
It is possible to use MatchMaker if you change the setting Matrix: to Nucleic, but since it is trying to match only the parts with similar sequences, the DNA helices are offset. You can try it and see what I mean. I thought you probably didn't want that, which is why I suggested the other methods first.
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 Mar 3, 2014, at 6:29 AM, "Urszula Uciechowska" <urszula.uciechowska@biotech.ug.edu.pl> wrote:
Dear chimera users,
I need to supeimpose a DNA molecule DNA-1.pdb into the protein-DNA complex. I was trying to do this using Mach Maker, but I am getting errors. I am not sure if I can do it using this tool and how should I do it. Thank you in advance for any help and suggestions...
best regards Urszula
----------------------------------------- Ta wiadomość została wysłana z serwera Uniwersytetu Gdańskiego http://www.ug.edu.pl/
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participants (2)
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Elaine Meng -
Urszula Uciechowska