Hi, i'm working with chimera for the first time. I need to patch 2 structures that i have the PDBs. I've already read the user guide and try to follow the instructions for making a controlled superimposition of the two structures. These are my two sequence: 1)RKYVYSLYWSTLTLTTIGETPPPVRDSEYFFVVADFLIGVLIFATIVGNIGSMISNMNAARAEFQARIDAIKQYMHFR 2)DSSRRQYQEKYKQVEQYMSFHKLPADFRQKIHDYYEHRYQG-KMFDEDSILGELNGPLREKIVNFNCRKLVASMPLFANADPNFVTAMLTKLKFEVFQP GDYIIREGTIGKKMYFIQHGVVSVLTK-NKEM--KLSDGSYFGEICLLT------RGRRTASVRADTYCRLYSLSVDN FNEVLEEYPMMRRAFETVAIDRLDR/ I need to create a structure like this: RKYVYSLYWSTLTLTTIGETPPPVRDSEYFFVVADFLIGVLIFATIVGNIGSMISNMNAARAEFQARIDAIKQYMHF *RD*SSRRQYQEKYKQVEQYMSFH KLPADFRQKIHDYYEHRYQG-KMFDEDSILGELNGPLREKIVNFNCRKLVASMPLFANADPNFVTAMLTKLKFEVFQP GDYIIREGTIGKKMYFIQHGVVSVLTK-NKEM--KLSDGSYFGEICLLT------RGRRTASVRADTYCRLYSLSVDN FNEVLEEYPMMRRAFETVAIDRLDR/ I know the position of the aa involved but after i launch the command trough command line it gives me errors like match #0:422 #1:442 Unequal numbers of atoms chosen for evalutation What am i doing wrong? Thanks, sincererly Mahad
Hi Mahad, If I read your mail correctly, there is no overlap between the two sequences. You would only use "match" to overlap structures, i.e. to try to put one group of atoms on top of another group of atoms (with exactly the same number of atoms). As the error message said,
match #0:422 #1:442 Unequal numbers of atoms chosen for evaluation
... residue 422 in #0 and residue 442 in #1 do not have the same numbers of atoms, which is not surprising if one is an "R" and the other is "D." You could specify using backbone atoms only to get the same numbers, for example: match #0:422@n,ca,c,o #1:442@n,ca,c,o HOWEVER: from your description it sounds like you do not really want to match (put 422 on top of 442), but instead you want to join the two peptides (add peptide bond between 422 and 442). In that case you should use the Build Structure tool (in menu under Tools... Structure Editing), Join Models section. <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/editing/editing.html> <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/editing/editing.html#join> First select the two atoms you want to bond, maybe something like this: select #0:422@c #1:442@n ... and then use the C-N peptide bond option in Join Models. 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 Jan 25, 2013, at 6:57 AM, mahad iou muddei addò wrote:
Hi, i'm working with chimera for the first time. I need to patch 2 structures that i have the PDBs. I've already read the user guide and try to follow the instructions for making a controlled superimposition of the two structures. These are my two sequence:
1)RKYVYSLYWSTLTLTTIGETPPPVRDSEYFFVVADFLIGVLIFATIVGNIGSMISNMNAARAEFQARIDAIKQYMHFR
2)DSSRRQYQEKYKQVEQYMSFHKLPADFRQKIHDYYEHRYQG-KMFDEDSILGELNGPLREKIVNFNCRKLVASMPLFANADPNFVTAMLTKLKFEVFQP GDYIIREGTIGKKMYFIQHGVVSVLTK-NKEM--KLSDGSYFGEICLLT------RGRRTASVRADTYCRLYSLSVDN FNEVLEEYPMMRRAFETVAIDRLDR/
I need to create a structure like this:
RKYVYSLYWSTLTLTTIGETPPPVRDSEYFFVVADFLIGVLIFATIVGNIGSMISNMNAARAEFQARIDAIKQYMHFRDSSRRQYQEKYKQVEQYMSFH KLPADFRQKIHDYYEHRYQG-KMFDEDSILGELNGPLREKIVNFNCRKLVASMPLFANADPNFVTAMLTKLKFEVFQP GDYIIREGTIGKKMYFIQHGVVSVLTK-NKEM--KLSDGSYFGEICLLT------RGRRTASVRADTYCRLYSLSVDN FNEVLEEYPMMRRAFETVAIDRLDR/
I know the position of the aa involved but after i launch the command trough command line it gives me errors like
match #0:422 #1:442 Unequal numbers of atoms chosen for evalutation
What am i doing wrong? Thanks, sincererly
Mahad
Dear Elaine, thank you so much because i understand my mistakes, but i'm afraid i have to ask you something again. I've done as you said, so i selected the residues and then used join models function but the apply button cannot be clicked. I don't understand if this happens because: -of the selected residues -the 2 proteins have to be already in position for the bond -something to be done before using join models I'm sorry to trouble you so much Sincererly Mahad 2013/1/25 Elaine Meng <meng@cgl.ucsf.edu>
Hi Mahad, If I read your mail correctly, there is no overlap between the two sequences. You would only use "match" to overlap structures, i.e. to try to put one group of atoms on top of another group of atoms (with exactly the same number of atoms). As the error message said,
match #0:422 #1:442 Unequal numbers of atoms chosen for evaluation
... residue 422 in #0 and residue 442 in #1 do not have the same numbers of atoms, which is not surprising if one is an "R" and the other is "D." You could specify using backbone atoms only to get the same numbers, for example:
match #0:422@n,ca,c,o #1:442@n,ca,c,o
HOWEVER: from your description it sounds like you do not really want to match (put 422 on top of 442), but instead you want to join the two peptides (add peptide bond between 422 and 442). In that case you should use the Build Structure tool (in menu under Tools... Structure Editing), Join Models section.
< http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/editing/editing.htm...
< http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/editing/editing.htm...
First select the two atoms you want to bond, maybe something like this:
select #0:422@c #1:442@n
... and then use the C-N peptide bond option in Join Models. 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 Jan 25, 2013, at 6:57 AM, mahad iou muddei addò wrote:
Hi, i'm working with chimera for the first time. I need to patch 2 structures that i have the PDBs. I've already read the user guide and try to follow the instructions for making a controlled superimposition of the two structures. These are my two sequence:
1)RKYVYSLYWSTLTLTTIGETPPPVRDSEYFFVVADFLIGVLIFATIVGNIGSMISNMNAARAEFQARIDAIKQYMHFR
2)DSSRRQYQEKYKQVEQYMSFHKLPADFRQKIHDYYEHRYQG-KMFDEDSILGELNGPLREKIVNFNCRKLVASMPLFANADPNFVTAMLTKLKFEVFQP
GDYIIREGTIGKKMYFIQHGVVSVLTK-NKEM--KLSDGSYFGEICLLT------RGRRTASVRADTYCRLYSLSVDN
FNEVLEEYPMMRRAFETVAIDRLDR/
I need to create a structure like this:
RKYVYSLYWSTLTLTTIGETPPPVRDSEYFFVVADFLIGVLIFATIVGNIGSMISNMNAARAEFQARIDAIKQYMHFRDSSRRQYQEKYKQVEQYMSFH
KLPADFRQKIHDYYEHRYQG-KMFDEDSILGELNGPLREKIVNFNCRKLVASMPLFANADPNFVTAMLTKLKFEVFQP
GDYIIREGTIGKKMYFIQHGVVSVLTK-NKEM--KLSDGSYFGEICLLT------RGRRTASVRADTYCRLYSLSVDN
FNEVLEEYPMMRRAFETVAIDRLDR/
I know the position of the aa involved but after i launch the command trough command line it gives me errors like
match #0:422 #1:442 Unequal numbers of atoms chosen for evalutation
What am i doing wrong? Thanks, sincererly
Mahad
Hi Mahad, I can't tell what exactly is the problem, but make sure that you have only two atoms selected (not the whole residues), the C at the end of one peptide and the N at the start of the other. Then you should be able to choose the "C-N peptide bond" option, and then apply. You do not need to position the structures before joining them. Something like the example "select" command I gave in the earlier message should select only two atoms. Or, if you prefer to use the mouse to select from the screen, you would first need to show the atoms... for example: preset apply int 2 ... use Ctrl-click to select the carbonyl C at the end of the first peptide, then Shift-Ctrl-click to select the amino N at the start of the second peptide. Then choose "C-N peptide bond" in the Join Models part of Build Structure, then click Apply. 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 Jan 26, 2013, at 4:06 AM, mahad iou muddei addò wrote:
Dear Elaine, thank you so much because i understand my mistakes, but i'm afraid i have to ask you something again. I've done as you said, so i selected the residues and then used join models function but the apply button cannot be clicked. I don't understand if this happens because:
-of the selected residues -the 2 proteins have to be already in position for the bond -something to be done before using join models
I'm sorry to trouble you so much Sincererly
Mahad
2013/1/25 Elaine Meng <meng@cgl.ucsf.edu> Hi Mahad, If I read your mail correctly, there is no overlap between the two sequences. You would only use "match" to overlap structures, i.e. to try to put one group of atoms on top of another group of atoms (with exactly the same number of atoms). As the error message said,
match #0:422 #1:442 Unequal numbers of atoms chosen for evaluation
... residue 422 in #0 and residue 442 in #1 do not have the same numbers of atoms, which is not surprising if one is an "R" and the other is "D." You could specify using backbone atoms only to get the same numbers, for example:
match #0:422@n,ca,c,o #1:442@n,ca,c,o
HOWEVER: from your description it sounds like you do not really want to match (put 422 on top of 442), but instead you want to join the two peptides (add peptide bond between 422 and 442). In that case you should use the Build Structure tool (in menu under Tools... Structure Editing), Join Models section.
<http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/editing/editing.html> <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/editing/editing.html#join>
First select the two atoms you want to bond, maybe something like this:
select #0:422@c #1:442@n
... and then use the C-N peptide bond option in Join Models. 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 Jan 25, 2013, at 6:57 AM, mahad iou muddei addò wrote:
Hi, i'm working with chimera for the first time. I need to patch 2 structures that i have the PDBs. I've already read the user guide and try to follow the instructions for making a controlled superimposition of the two structures. These are my two sequence:
1)RKYVYSLYWSTLTLTTIGETPPPVRDSEYFFVVADFLIGVLIFATIVGNIGSMISNMNAARAEFQARIDAIKQYMHFR
2)DSSRRQYQEKYKQVEQYMSFHKLPADFRQKIHDYYEHRYQG-KMFDEDSILGELNGPLREKIVNFNCRKLVASMPLFANADPNFVTAMLTKLKFEVFQP GDYIIREGTIGKKMYFIQHGVVSVLTK-NKEM--KLSDGSYFGEICLLT------RGRRTASVRADTYCRLYSLSVDN FNEVLEEYPMMRRAFETVAIDRLDR/
I need to create a structure like this:
RKYVYSLYWSTLTLTTIGETPPPVRDSEYFFVVADFLIGVLIFATIVGNIGSMISNMNAARAEFQARIDAIKQYMHFRDSSRRQYQEKYKQVEQYMSFH KLPADFRQKIHDYYEHRYQG-KMFDEDSILGELNGPLREKIVNFNCRKLVASMPLFANADPNFVTAMLTKLKFEVFQP GDYIIREGTIGKKMYFIQHGVVSVLTK-NKEM--KLSDGSYFGEICLLT------RGRRTASVRADTYCRLYSLSVDN FNEVLEEYPMMRRAFETVAIDRLDR/
I know the position of the aa involved but after i launch the command trough command line it gives me errors like
match #0:422 #1:442 Unequal numbers of atoms chosen for evalutation
What am i doing wrong? Thanks, sincererly
Mahad
Perfect! now it worked! but if i want to make 4 bonds for for chains how am i suppose to do? Thank you so much anyway 2013/1/28 Elaine Meng <meng@cgl.ucsf.edu>
Hi Mahad, I can't tell what exactly is the problem, but make sure that you have only two atoms selected (not the whole residues), the C at the end of one peptide and the N at the start of the other. Then you should be able to choose the "C-N peptide bond" option, and then apply. You do not need to position the structures before joining them.
Something like the example "select" command I gave in the earlier message should select only two atoms. Or, if you prefer to use the mouse to select from the screen, you would first need to show the atoms... for example:
preset apply int 2
... use Ctrl-click to select the carbonyl C at the end of the first peptide, then Shift-Ctrl-click to select the amino N at the start of the second peptide. Then choose "C-N peptide bond" in the Join Models part of Build Structure, then click Apply.
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 Jan 26, 2013, at 4:06 AM, mahad iou muddei addò wrote:
Dear Elaine, thank you so much because i understand my mistakes, but i'm afraid i have to ask you something again. I've done as you said, so i selected the residues and then used join models function but the apply button cannot be clicked. I don't understand if this happens because:
-of the selected residues -the 2 proteins have to be already in position for the bond -something to be done before using join models
I'm sorry to trouble you so much Sincererly
Mahad
2013/1/25 Elaine Meng <meng@cgl.ucsf.edu> Hi Mahad, If I read your mail correctly, there is no overlap between the two sequences. You would only use "match" to overlap structures, i.e. to try to put one group of atoms on top of another group of atoms (with exactly the same number of atoms). As the error message said,
match #0:422 #1:442 Unequal numbers of atoms chosen for evaluation
... residue 422 in #0 and residue 442 in #1 do not have the same numbers of atoms, which is not surprising if one is an "R" and the other is "D." You could specify using backbone atoms only to get the same numbers, for example:
match #0:422@n,ca,c,o #1:442@n,ca,c,o
HOWEVER: from your description it sounds like you do not really want to match (put 422 on top of 442), but instead you want to join the two peptides (add peptide bond between 422 and 442). In that case you should use the Build Structure tool (in menu under Tools... Structure Editing), Join Models section.
< http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/editing/editing.htm...
< http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/editing/editing.htm...
First select the two atoms you want to bond, maybe something like this:
select #0:422@c #1:442@n
... and then use the C-N peptide bond option in Join Models. 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 Jan 25, 2013, at 6:57 AM, mahad iou muddei addò wrote:
Hi, i'm working with chimera for the first time. I need to patch 2 structures that i have the PDBs. I've already read the user guide and try to follow the instructions for making a controlled superimposition of the two structures. These are my two sequence:
1)RKYVYSLYWSTLTLTTIGETPPPVRDSEYFFVVADFLIGVLIFATIVGNIGSMISNMNAARAEFQARIDAIKQYMHFR
2)DSSRRQYQEKYKQVEQYMSFHKLPADFRQKIHDYYEHRYQG-KMFDEDSILGELNGPLREKIVNFNCRKLVASMPLFANADPNFVTAMLTKLKFEVFQP
GDYIIREGTIGKKMYFIQHGVVSVLTK-NKEM--KLSDGSYFGEICLLT------RGRRTASVRADTYCRLYSLSVDN
FNEVLEEYPMMRRAFETVAIDRLDR/
I need to create a structure like this:
RKYVYSLYWSTLTLTTIGETPPPVRDSEYFFVVADFLIGVLIFATIVGNIGSMISNMNAARAEFQARIDAIKQYMHFRDSSRRQYQEKYKQVEQYMSFH
KLPADFRQKIHDYYEHRYQG-KMFDEDSILGELNGPLREKIVNFNCRKLVASMPLFANADPNFVTAMLTKLKFEVFQP
GDYIIREGTIGKKMYFIQHGVVSVLTK-NKEM--KLSDGSYFGEICLLT------RGRRTASVRADTYCRLYSLSVDN
FNEVLEEYPMMRRAFETVAIDRLDR/
I know the position of the aa involved but after i launch the command trough command line it gives me errors like
match #0:422 #1:442 Unequal numbers of atoms chosen for evalutation
What am i doing wrong? Thanks, sincererly
Mahad
Not sure I understand the question. You could just repeat the process as many times as you need to. If you meant that you want to join multiple chains from one structure to multiple chains in another structure (for example, A from first structure to A in second structure, B from the same first structure to B in the same second structure, ...) I think you would have to first split the second structure to make each of its chains a separate model. For example, if the second structure is open as model 1, you could split it with the command: split #1 <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/split.html> Then, you could use Join Models several times to combine the chains of the second structure (which are now separate models) with the chains of the first structure. After each join, you would need to select one atom from the new combined model and then one atom from the next chain of the second structure. Another way to add bonds is with the Adjust Bonds section of the same tool, but that only works on atoms that are already within the same model. <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/editing/editing.html> Elaine On Jan 28, 2013, at 10:15 AM, mahad iou muddei addò wrote:
Perfect! now it worked! but if i want to make 4 bonds for for chains how am i suppose to do?
Thank you so much anyway
2013/1/28 Elaine Meng <meng@cgl.ucsf.edu> Hi Mahad, I can't tell what exactly is the problem, but make sure that you have only two atoms selected (not the whole residues), the C at the end of one peptide and the N at the start of the other. Then you should be able to choose the "C-N peptide bond" option, and then apply. You do not need to position the structures before joining them.
Something like the example "select" command I gave in the earlier message should select only two atoms. Or, if you prefer to use the mouse to select from the screen, you would first need to show the atoms... for example:
preset apply int 2
... use Ctrl-click to select the carbonyl C at the end of the first peptide, then Shift-Ctrl-click to select the amino N at the start of the second peptide. Then choose "C-N peptide bond" in the Join Models part of Build Structure, then click Apply.
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 Jan 26, 2013, at 4:06 AM, mahad iou muddei addò wrote:
Dear Elaine, thank you so much because i understand my mistakes, but i'm afraid i have to ask you something again. I've done as you said, so i selected the residues and then used join models function but the apply button cannot be clicked. I don't understand if this happens because:
-of the selected residues -the 2 proteins have to be already in position for the bond -something to be done before using join models
I'm sorry to trouble you so much Sincererly
Mahad
2013/1/25 Elaine Meng <meng@cgl.ucsf.edu> Hi Mahad, If I read your mail correctly, there is no overlap between the two sequences. You would only use "match" to overlap structures, i.e. to try to put one group of atoms on top of another group of atoms (with exactly the same number of atoms). As the error message said,
match #0:422 #1:442 Unequal numbers of atoms chosen for evaluation
... residue 422 in #0 and residue 442 in #1 do not have the same numbers of atoms, which is not surprising if one is an "R" and the other is "D." You could specify using backbone atoms only to get the same numbers, for example:
match #0:422@n,ca,c,o #1:442@n,ca,c,o
HOWEVER: from your description it sounds like you do not really want to match (put 422 on top of 442), but instead you want to join the two peptides (add peptide bond between 422 and 442). In that case you should use the Build Structure tool (in menu under Tools... Structure Editing), Join Models section.
<http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/editing/editing.html> <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/editing/editing.html#join>
First select the two atoms you want to bond, maybe something like this:
select #0:422@c #1:442@n
... and then use the C-N peptide bond option in Join Models. 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 Jan 25, 2013, at 6:57 AM, mahad iou muddei addò wrote:
Hi, i'm working with chimera for the first time. I need to patch 2 structures that i have the PDBs. I've already read the user guide and try to follow the instructions for making a controlled superimposition of the two structures. These are my two sequence:
1)RKYVYSLYWSTLTLTTIGETPPPVRDSEYFFVVADFLIGVLIFATIVGNIGSMISNMNAARAEFQARIDAIKQYMHFR
2)DSSRRQYQEKYKQVEQYMSFHKLPADFRQKIHDYYEHRYQG-KMFDEDSILGELNGPLREKIVNFNCRKLVASMPLFANADPNFVTAMLTKLKFEVFQP GDYIIREGTIGKKMYFIQHGVVSVLTK-NKEM--KLSDGSYFGEICLLT------RGRRTASVRADTYCRLYSLSVDN FNEVLEEYPMMRRAFETVAIDRLDR/
I need to create a structure like this:
RKYVYSLYWSTLTLTTIGETPPPVRDSEYFFVVADFLIGVLIFATIVGNIGSMISNMNAARAEFQARIDAIKQYMHFRDSSRRQYQEKYKQVEQYMSFH KLPADFRQKIHDYYEHRYQG-KMFDEDSILGELNGPLREKIVNFNCRKLVASMPLFANADPNFVTAMLTKLKFEVFQP GDYIIREGTIGKKMYFIQHGVVSVLTK-NKEM--KLSDGSYFGEICLLT------RGRRTASVRADTYCRLYSLSVDN FNEVLEEYPMMRRAFETVAIDRLDR/
I know the position of the aa involved but after i launch the command trough command line it gives me errors like
match #0:422 #1:442 Unequal numbers of atoms chosen for evalutation
What am i doing wrong? Thanks, sincererly
Mahad
_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Everytime i'm getting closer to what i need and it's all thanks to you! i used the "Adjust Bonds" command (after i manually put the 2 proteins in the position i wanted and combine them in a single structure) because it maintains the structure of my two protein and only adds the bond. Instead using "Join Models" every chain was bonded indipendently and this results in a conformation that is non useful for my work because the various chains moved following the bond but non according to each other (sorry for my bad explanation). Now i'm searching a way to rename every residue of the new model in a sequential way (Example: sequence residues number before 300-351 aa renamed in 1-51 aa) but i don't have the solution right now. There is a function with chimera? And if i use the function "Minimize Structure" it will change the bonds added and make them better? Regards Mahad 2013/1/29 Elaine Meng <meng@cgl.ucsf.edu>
Not sure I understand the question. You could just repeat the process as many times as you need to. If you meant that you want to join multiple chains from one structure to multiple chains in another structure (for example, A from first structure to A in second structure, B from the same first structure to B in the same second structure, ...) I think you would have to first split the second structure to make each of its chains a separate model.
For example, if the second structure is open as model 1, you could split it with the command:
split #1 <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/split.html>
Then, you could use Join Models several times to combine the chains of the second structure (which are now separate models) with the chains of the first structure. After each join, you would need to select one atom from the new combined model and then one atom from the next chain of the second structure.
Another way to add bonds is with the Adjust Bonds section of the same tool, but that only works on atoms that are already within the same model. < http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/editing/editing.htm...
Elaine
On Jan 28, 2013, at 10:15 AM, mahad iou muddei addò wrote:
Perfect! now it worked! but if i want to make 4 bonds for for chains how am i suppose to do?
Thank you so much anyway
2013/1/28 Elaine Meng <meng@cgl.ucsf.edu> Hi Mahad, I can't tell what exactly is the problem, but make sure that you have only two atoms selected (not the whole residues), the C at the end of one peptide and the N at the start of the other. Then you should be able to choose the "C-N peptide bond" option, and then apply. You do not need to position the structures before joining them.
Something like the example "select" command I gave in the earlier message should select only two atoms. Or, if you prefer to use the mouse to select from the screen, you would first need to show the atoms... for example:
preset apply int 2
... use Ctrl-click to select the carbonyl C at the end of the first peptide, then Shift-Ctrl-click to select the amino N at the start of the second peptide. Then choose "C-N peptide bond" in the Join Models part of Build Structure, then click Apply.
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 Jan 26, 2013, at 4:06 AM, mahad iou muddei addò wrote:
Dear Elaine, thank you so much because i understand my mistakes, but i'm afraid i have to ask you something again. I've done as you said, so i selected the residues and then used join models function but the apply button cannot be clicked. I don't understand if this happens because:
-of the selected residues -the 2 proteins have to be already in position for the bond -something to be done before using join models
I'm sorry to trouble you so much Sincererly
Mahad
2013/1/25 Elaine Meng <meng@cgl.ucsf.edu> Hi Mahad, If I read your mail correctly, there is no overlap between the two sequences. You would only use "match" to overlap structures, i.e. to try to put one group of atoms on top of another group of atoms (with exactly the same number of atoms). As the error message said,
match #0:422 #1:442 Unequal numbers of atoms chosen for evaluation
... residue 422 in #0 and residue 442 in #1 do not have the same numbers of atoms, which is not surprising if one is an "R" and the other is "D." You could specify using backbone atoms only to get the same numbers, for example:
match #0:422@n,ca,c,o #1:442@n,ca,c,o
HOWEVER: from your description it sounds like you do not really want to match (put 422 on top of 442), but instead you want to join the two peptides (add peptide bond between 422 and 442). In that case you should use the Build Structure tool (in menu under Tools... Structure Editing), Join Models section.
< http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/editing/editing.htm...
< http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/editing/editing.htm...
First select the two atoms you want to bond, maybe something like this:
select #0:422@c #1:442@n
... and then use the C-N peptide bond option in Join Models. 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 Jan 25, 2013, at 6:57 AM, mahad iou muddei addò wrote:
Hi, i'm working with chimera for the first time. I need to patch 2
structures that i have the PDBs. I've already read the user guide and try to follow the instructions for making a controlled superimposition of the two structures.
These are my two sequence:
1)RKYVYSLYWSTLTLTTIGETPPPVRDSEYFFVVADFLIGVLIFATIVGNIGSMISNMNAARAEFQARIDAIKQYMHFR
2)DSSRRQYQEKYKQVEQYMSFHKLPADFRQKIHDYYEHRYQG-KMFDEDSILGELNGPLREKIVNFNCRKLVASMPLFANADPNFVTAMLTKLKFEVFQP
GDYIIREGTIGKKMYFIQHGVVSVLTK-NKEM--KLSDGSYFGEICLLT------RGRRTASVRADTYCRLYSLSVDN
FNEVLEEYPMMRRAFETVAIDRLDR/
I need to create a structure like this:
RKYVYSLYWSTLTLTTIGETPPPVRDSEYFFVVADFLIGVLIFATIVGNIGSMISNMNAARAEFQARIDAIKQYMHFRDSSRRQYQEKYKQVEQYMSFH
KLPADFRQKIHDYYEHRYQG-KMFDEDSILGELNGPLREKIVNFNCRKLVASMPLFANADPNFVTAMLTKLKFEVFQP
GDYIIREGTIGKKMYFIQHGVVSVLTK-NKEM--KLSDGSYFGEICLLT------RGRRTASVRADTYCRLYSLSVDN
FNEVLEEYPMMRRAFETVAIDRLDR/
I know the position of the aa involved but after i launch the command trough command line it gives me errors like
match #0:422 #1:442 Unequal numbers of atoms chosen for evalutation
What am i doing wrong? Thanks, sincererly
Mahad
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Hi Mahad, You can search the manual using the Chimera menu: Help... Search Documentation. For example, if you search for "renumber" it will show there is a Renumber Residues tool, in menu under Tools... Structure Editing. You can also see lists of all the Chimera tools and commands in the User's Guide (also available under the Help menu). You could try minimization, but in my experience it is not very good for improving protein structures if they are tangled up or contain large distortions such as from adding multiple long bonds. That is one reason we added "join models," to make it easy to join peptides without generating such distortions. It always depends on your specific application, however, so you could try minimization... just be sure to save your session or structures before that, in case it does not help or makes everything worse. Regards, Elaine On Jan 30, 2013, at 8:47 AM, mahad iou muddei addò wrote:
Everytime i'm getting closer to what i need and it's all thanks to you! i used the "Adjust Bonds" command (after i manually put the 2 proteins in the position i wanted and combine them in a single structure) because it maintains the structure of my two protein and only adds the bond. Instead using "Join Models" every chain was bonded indipendently and this results in a conformation that is non useful for my work because the various chains moved following the bond but non according to each other (sorry for my bad explanation). Now i'm searching a way to rename every residue of the new model in a sequential way (Example: sequence residues number before 300-351 aa renamed in 1-51 aa) but i don't have the solution right now. There is a function with chimera? And if i use the function "Minimize Structure" it will change the bonds added and make them better?
Regards
Mahad
2013/1/29 Elaine Meng <meng@cgl.ucsf.edu> Not sure I understand the question. You could just repeat the process as many times as you need to. If you meant that you want to join multiple chains from one structure to multiple chains in another structure (for example, A from first structure to A in second structure, B from the same first structure to B in the same second structure, ...) I think you would have to first split the second structure to make each of its chains a separate model.
For example, if the second structure is open as model 1, you could split it with the command:
split #1 <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/split.html>
Then, you could use Join Models several times to combine the chains of the second structure (which are now separate models) with the chains of the first structure. After each join, you would need to select one atom from the new combined model and then one atom from the next chain of the second structure.
Another way to add bonds is with the Adjust Bonds section of the same tool, but that only works on atoms that are already within the same model. <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/editing/editing.html>
Elaine
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mahad iou muddei addò