Hello,
I wish to generate two images. The first is of protein A which is in session 1. The second is of protein A aligned with protein B using TM-Align which is in session 2. I wish for the alignment of the second image to be in the same orientation as the first with respect to protein A. Is there a feature which lets me do the following:
1) Identify orientation of protein A in session 1 2) Copy that orientation 3) Apply that orientation to protein A in session 2 4) Have protein B in session 2 remain aligned to protein A despite the new orientation
Thank you, Kenneth Sandoval
Dear Kenneth,
Maybe it be best to put both protein A and B in the same cartisen coordinate system by alignment such as matchmaker program, then save the PDB files. Then work on the problem from there on. This seems like a possible direction to try?
Sincerely, David
On Aug 10, 2021, at 6:47 AM, SANDOVAL, KENNETH via Chimera-users chimera-users@cgl.ucsf.edu wrote:
Hello,
I wish to generate two images. The first is of protein A which is in session 1. The second is of protein A aligned with protein B using TM-Align which is in session 2. I wish for the alignment of the second image to be in the same orientation as the first with respect to protein A. Is there a feature which lets me do the following:
- Identify orientation of protein A in session 1
- Copy that orientation
- Apply that orientation to protein A in session 2
- Have protein B in session 2 remain aligned to protein A despite the new orientation
Thank you, Kenneth Sandoval _______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu mailto:Chimera-users@cgl.ucsf.edu Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Hello Kenneth, Similarly to David I was going to say that the better approach would have been to create only a single session with the aligned proteins and simply hide and show model B to make your two figures.
However, given the situation you have now, maybe: (1) in session 1, use "matrixget <file-pathname>" to save file with transformation of protein A. See: https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/matrixset.html
(2) in session 2, use "matrixset <file-pathname>" to apply the transformation from the file you saved in part 1, assuming protein A has the same model number as in session 1. However, that will probably ignore protein B, so you may need step 3.
(3) in session 2, if protein A is model #0 and protein B is model #1, use command "matrixcopy #0 #1" See: https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/matrixcopy.html
I am not completely sure it will work since it depends on how you got the TM-align alignment in there, but it has at least a chance. Also you may need to adjust the command if you have different model numbers.
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Aug 10, 2021, at 9:34 AM, David Gae via Chimera-users chimera-users@cgl.ucsf.edu wrote:
Dear Kenneth,
Maybe it be best to put both protein A and B in the same cartisen coordinate system by alignment such as matchmaker program, then save the PDB files. Then work on the problem from there on. This seems like a possible direction to try?
Sincerely, David
On Aug 10, 2021, at 6:47 AM, SANDOVAL, KENNETH via Chimera-users chimera-users@cgl.ucsf.edu wrote:
Hello,
I wish to generate two images. The first is of protein A which is in session 1. The second is of protein A aligned with protein B using TM-Align which is in session 2. I wish for the alignment of the second image to be in the same orientation as the first with respect to protein A. Is there a feature which lets me do the following:
- Identify orientation of protein A in session 1
- Copy that orientation
- Apply that orientation to protein A in session 2
- Have protein B in session 2 remain aligned to protein A despite the new orientation
Thank you, Kenneth Sandoval _______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Hello,
Thank you for your helpful replies. I apologize for my late response. So following the initial suggestion by David, I have an alignment of protein A with protein B, but with protein B hidden. This is in file prot_A_aligned.png.
However, I am wanting the ribbons of this file to look like those in the image prot_A.png. This is the chimera view for the .pdb file of protein A before alignment with B using TM-align. That is, I want the parts of the protein which are not alpha-helices or beta-sheets to just be in the licorice form. Is this something I can do in chimera? Or is this something that would be integrated into the actual .pdb file which I would have to manually manipulate? I apologize if this is question has an obvious answer.
Thank you, Kenneth ________________________________ From: Elaine Meng meng@cgl.ucsf.edu Sent: Tuesday, August 10, 2021 6:00 PM To: SANDOVAL, KENNETH K.SANDOVAL1@nuigalway.ie Cc: chimera-users@cgl.ucsf.edu chimera-users@cgl.ucsf.edu Subject: Re: [Chimera-users] Copy protein orientation
Hello Kenneth, Similarly to David I was going to say that the better approach would have been to create only a single session with the aligned proteins and simply hide and show model B to make your two figures.
However, given the situation you have now, maybe: (1) in session 1, use "matrixget <file-pathname>" to save file with transformation of protein A. See: https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/matrixset.html
(2) in session 2, use "matrixset <file-pathname>" to apply the transformation from the file you saved in part 1, assuming protein A has the same model number as in session 1. However, that will probably ignore protein B, so you may need step 3.
(3) in session 2, if protein A is model #0 and protein B is model #1, use command "matrixcopy #0 #1" See: https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/matrixcopy.html
I am not completely sure it will work since it depends on how you got the TM-align alignment in there, but it has at least a chance. Also you may need to adjust the command if you have different model numbers.
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Aug 10, 2021, at 9:34 AM, David Gae via Chimera-users chimera-users@cgl.ucsf.edu wrote:
Dear Kenneth,
Maybe it be best to put both protein A and B in the same cartisen coordinate system by alignment such as matchmaker program, then save the PDB files. Then work on the problem from there on. This seems like a possible direction to try?
Sincerely, David
On Aug 10, 2021, at 6:47 AM, SANDOVAL, KENNETH via Chimera-users chimera-users@cgl.ucsf.edu wrote:
Hello,
I wish to generate two images. The first is of protein A which is in session 1. The second is of protein A aligned with protein B using TM-Align which is in session 2. I wish for the alignment of the second image to be in the same orientation as the first with respect to protein A. Is there a feature which lets me do the following:
- Identify orientation of protein A in session 1
- Copy that orientation
- Apply that orientation to protein A in session 2
- Have protein B in session 2 remain aligned to protein A despite the new orientation
Thank you, Kenneth Sandoval _______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Hello Kenneth, I can't really tell what's going on without having the session file or the atomic coordinates (PDB file) to look at.
Without that information, my only suggestions are: (1) make sure you have a reasonably new version of Chimera, say the last production release (2) try running secondary structure assignment on that model, e.g. if the funny-looking ribbon model is #2, command
ksdssp #2
kdssp help: https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/ksdssp.html
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Sep 3, 2021, at 6:26 AM, SANDOVAL, KENNETH via Chimera-users chimera-users@cgl.ucsf.edu wrote:
Hello,
Thank you for your helpful replies. I apologize for my late response. So following the initial suggestion by David, I have an alignment of protein A with protein B, but with protein B hidden. This is in file prot_A_aligned.png.
However, I am wanting the ribbons of this file to look like those in the image prot_A.png. This is the chimera view for the .pdb file of protein A before alignment with B using TM-align. That is, I want the parts of the protein which are not alpha-helices or beta-sheets to just be in the licorice form. Is this something I can do in chimera? Or is this something that would be integrated into the actual .pdb file which I would have to manually manipulate? I apologize if this is question has an obvious answer.
Thank you, Kenneth From: Elaine Meng meng@cgl.ucsf.edu Sent: Tuesday, August 10, 2021 6:00 PM To: SANDOVAL, KENNETH K.SANDOVAL1@nuigalway.ie Cc: chimera-users@cgl.ucsf.edu chimera-users@cgl.ucsf.edu Subject: Re: [Chimera-users] Copy protein orientation
Hello Kenneth, Similarly to David I was going to say that the better approach would have been to create only a single session with the aligned proteins and simply hide and show model B to make your two figures.
However, given the situation you have now, maybe: (1) in session 1, use "matrixget <file-pathname>" to save file with transformation of protein A. See: https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/matrixset.html
(2) in session 2, use "matrixset <file-pathname>" to apply the transformation from the file you saved in part 1, assuming protein A has the same model number as in session 1. However, that will probably ignore protein B, so you may need step 3.
(3) in session 2, if protein A is model #0 and protein B is model #1, use command "matrixcopy #0 #1" See: https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/matrixcopy.html
I am not completely sure it will work since it depends on how you got the TM-align alignment in there, but it has at least a chance. Also you may need to adjust the command if you have different model numbers.
I hope this helps, Elaine
Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Aug 10, 2021, at 9:34 AM, David Gae via Chimera-users chimera-users@cgl.ucsf.edu wrote:
Dear Kenneth,
Maybe it be best to put both protein A and B in the same cartisen coordinate system by alignment such as matchmaker program, then save the PDB files. Then work on the problem from there on. This seems like a possible direction to try?
Sincerely, David
On Aug 10, 2021, at 6:47 AM, SANDOVAL, KENNETH via Chimera-users chimera-users@cgl.ucsf.edu wrote:
Hello,
I wish to generate two images. The first is of protein A which is in session 1. The second is of protein A aligned with protein B using TM-Align which is in session 2. I wish for the alignment of the second image to be in the same orientation as the first with respect to protein A. Is there a feature which lets me do the following:
- Identify orientation of protein A in session 1
- Copy that orientation
- Apply that orientation to protein A in session 2
- Have protein B in session 2 remain aligned to protein A despite the new orientation
Thank you, Kenneth Sandoval _______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
<Prot_A_aligned.png><Prot_A.png>_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Hi Elaine,
Thank you for your answer. I attempted to use the ksdssp command, but it doesn't appear to be doing anything. I have attached the two pdb files. I am wanting the structures of the two proteins in F791140.pdb to be like that of the one in A791140.pdb. Do you have advice on how to do this?
Thank you, Kenneth ________________________________ From: Elaine Meng meng@cgl.ucsf.edu Sent: Friday, September 3, 2021 6:52 PM To: SANDOVAL, KENNETH K.SANDOVAL1@nuigalway.ie Cc: Azad, Roksana via Chimera-users chimera-users@cgl.ucsf.edu Subject: Re: [Chimera-users] Copy protein orientation
EXTERNAL EMAIL: This email originated from outside of NUI Galway. Do not open attachments or click on links in the message unless you recognise the sender's email address and believe the content is safe. RÍOMHPHOST SEACHTRACH: Tháinig an ríomhphost seo as áit éigin taobh amuigh de OÉ Gaillimh. Ná cliceáil ar naisc agus ná hoscail ceangaltáin mura n-aithníonn tú seoladh ríomhphoist an tseoltóra agus mura gcreideann tú go bhfuil an t-ábhar sábháilte.
Hello Kenneth, I can't really tell what's going on without having the session file or the atomic coordinates (PDB file) to look at.
Without that information, my only suggestions are: (1) make sure you have a reasonably new version of Chimera, say the last production release (2) try running secondary structure assignment on that model, e.g. if the funny-looking ribbon model is #2, command
ksdssp #2
kdssp help: https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/ksdssp.html
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Sep 3, 2021, at 6:26 AM, SANDOVAL, KENNETH via Chimera-users chimera-users@cgl.ucsf.edu wrote:
Hello,
Thank you for your helpful replies. I apologize for my late response. So following the initial suggestion by David, I have an alignment of protein A with protein B, but with protein B hidden. This is in file prot_A_aligned.png.
However, I am wanting the ribbons of this file to look like those in the image prot_A.png. This is the chimera view for the .pdb file of protein A before alignment with B using TM-align. That is, I want the parts of the protein which are not alpha-helices or beta-sheets to just be in the licorice form. Is this something I can do in chimera? Or is this something that would be integrated into the actual .pdb file which I would have to manually manipulate? I apologize if this is question has an obvious answer.
Thank you, Kenneth From: Elaine Meng meng@cgl.ucsf.edu Sent: Tuesday, August 10, 2021 6:00 PM To: SANDOVAL, KENNETH K.SANDOVAL1@nuigalway.ie Cc: chimera-users@cgl.ucsf.edu chimera-users@cgl.ucsf.edu Subject: Re: [Chimera-users] Copy protein orientation
Hello Kenneth, Similarly to David I was going to say that the better approach would have been to create only a single session with the aligned proteins and simply hide and show model B to make your two figures.
However, given the situation you have now, maybe: (1) in session 1, use "matrixget <file-pathname>" to save file with transformation of protein A. See: https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/matrixset.html
(2) in session 2, use "matrixset <file-pathname>" to apply the transformation from the file you saved in part 1, assuming protein A has the same model number as in session 1. However, that will probably ignore protein B, so you may need step 3.
(3) in session 2, if protein A is model #0 and protein B is model #1, use command "matrixcopy #0 #1" See: https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/matrixcopy.html
I am not completely sure it will work since it depends on how you got the TM-align alignment in there, but it has at least a chance. Also you may need to adjust the command if you have different model numbers.
I hope this helps, Elaine
Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Aug 10, 2021, at 9:34 AM, David Gae via Chimera-users chimera-users@cgl.ucsf.edu wrote:
Dear Kenneth,
Maybe it be best to put both protein A and B in the same cartisen coordinate system by alignment such as matchmaker program, then save the PDB files. Then work on the problem from there on. This seems like a possible direction to try?
Sincerely, David
On Aug 10, 2021, at 6:47 AM, SANDOVAL, KENNETH via Chimera-users chimera-users@cgl.ucsf.edu wrote:
Hello,
I wish to generate two images. The first is of protein A which is in session 1. The second is of protein A aligned with protein B using TM-Align which is in session 2. I wish for the alignment of the second image to be in the same orientation as the first with respect to protein A. Is there a feature which lets me do the following:
- Identify orientation of protein A in session 1
- Copy that orientation
- Apply that orientation to protein A in session 2
- Have protein B in session 2 remain aligned to protein A despite the new orientation
Thank you, Kenneth Sandoval _______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
<Prot_A_aligned.png><Prot_A.png>_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Hi Kenneth, The problem with F791140.pdb is that you have two proteins right on top of each other that are chains A and B in the same model. This ruins the secondary structure calculation (ksdssp) because it is not physically possible for one structure to have all those atoms nearly on top of each other.
Whichever program wrote the file wrote incorrect PDB format. Although it would still be somewhat incorrect, you can fix the file for purposes of secondary structure calculation by replacing the TER line with ENDMDL (i.e. in your favorite text-editor).
I did that and attached the resulting file. Then the secondary structure can be calculated automatically and looks reasonable when you open it.
I hope this helps, Elaine Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Sep 6, 2021, at 2:48 AM, SANDOVAL, KENNETH via Chimera-users chimera-users@cgl.ucsf.edu wrote:
Hi Elaine,
Thank you for your answer. I attempted to use the ksdssp command, but it doesn't appear to be doing anything. I have attached the two pdb files. I am wanting the structures of the two proteins in F791140.pdb to be like that of the one in A791140.pdb. Do you have advice on how to do this?
Thank you, Kenneth From: Elaine Meng meng@cgl.ucsf.edu Sent: Friday, September 3, 2021 6:52 PM To: SANDOVAL, KENNETH K.SANDOVAL1@nuigalway.ie Cc: Azad, Roksana via Chimera-users chimera-users@cgl.ucsf.edu Subject: Re: [Chimera-users] Copy protein orientation
EXTERNAL EMAIL: This email originated from outside of NUI Galway. Do not open attachments or click on links in the message unless you recognise the sender's email address and believe the content is safe. RÍOMHPHOST SEACHTRACH: Tháinig an ríomhphost seo as áit éigin taobh amuigh de OÉ Gaillimh. Ná cliceáil ar naisc agus ná hoscail ceangaltáin mura n-aithníonn tú seoladh ríomhphoist an tseoltóra agus mura gcreideann tú go bhfuil an t-ábhar sábháilte.
Hello Kenneth, I can't really tell what's going on without having the session file or the atomic coordinates (PDB file) to look at.
Without that information, my only suggestions are: (1) make sure you have a reasonably new version of Chimera, say the last production release (2) try running secondary structure assignment on that model, e.g. if the funny-looking ribbon model is #2, command
ksdssp #2
kdssp help: https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/ksdssp.html
I hope this helps, Elaine
Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Sep 3, 2021, at 6:26 AM, SANDOVAL, KENNETH via Chimera-users chimera-users@cgl.ucsf.edu wrote:
Hello,
Thank you for your helpful replies. I apologize for my late response. So following the initial suggestion by David, I have an alignment of protein A with protein B, but with protein B hidden. This is in file prot_A_aligned.png.
However, I am wanting the ribbons of this file to look like those in the image prot_A.png. This is the chimera view for the .pdb file of protein A before alignment with B using TM-align. That is, I want the parts of the protein which are not alpha-helices or beta-sheets to just be in the licorice form. Is this something I can do in chimera? Or is this something that would be integrated into the actual .pdb file which I would have to manually manipulate? I apologize if this is question has an obvious answer.
Thank you, Kenneth From: Elaine Meng meng@cgl.ucsf.edu Sent: Tuesday, August 10, 2021 6:00 PM To: SANDOVAL, KENNETH K.SANDOVAL1@nuigalway.ie Cc: chimera-users@cgl.ucsf.edu chimera-users@cgl.ucsf.edu Subject: Re: [Chimera-users] Copy protein orientation
Hello Kenneth, Similarly to David I was going to say that the better approach would have been to create only a single session with the aligned proteins and simply hide and show model B to make your two figures.
However, given the situation you have now, maybe: (1) in session 1, use "matrixget <file-pathname>" to save file with transformation of protein A. See: https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/matrixset.html
(2) in session 2, use "matrixset <file-pathname>" to apply the transformation from the file you saved in part 1, assuming protein A has the same model number as in session 1. However, that will probably ignore protein B, so you may need step 3.
(3) in session 2, if protein A is model #0 and protein B is model #1, use command "matrixcopy #0 #1" See: https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/matrixcopy.html
I am not completely sure it will work since it depends on how you got the TM-align alignment in there, but it has at least a chance. Also you may need to adjust the command if you have different model numbers.
I hope this helps, Elaine
Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Aug 10, 2021, at 9:34 AM, David Gae via Chimera-users chimera-users@cgl.ucsf.edu wrote:
Dear Kenneth,
Maybe it be best to put both protein A and B in the same cartisen coordinate system by alignment such as matchmaker program, then save the PDB files. Then work on the problem from there on. This seems like a possible direction to try?
Sincerely, David
On Aug 10, 2021, at 6:47 AM, SANDOVAL, KENNETH via Chimera-users chimera-users@cgl.ucsf.edu wrote:
Hello,
I wish to generate two images. The first is of protein A which is in session 1. The second is of protein A aligned with protein B using TM-Align which is in session 2. I wish for the alignment of the second image to be in the same orientation as the first with respect to protein A. Is there a feature which lets me do the following:
- Identify orientation of protein A in session 1
- Copy that orientation
- Apply that orientation to protein A in session 2
- Have protein B in session 2 remain aligned to protein A despite the new orientation
Thank you, Kenneth Sandoval _______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
<Prot_A_aligned.png><Prot_A.png>_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
<A791140.pdb><F791140.pdb>_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Hello Elaine,
Thank you very much! I generated that alignment with TM-align so I'm quite surprised that it produced an incorrect PDB format.
https://zhanggroup.org/TM-align/
Anyways I looked at the structure in Chimera and it looks perfect. So I'll be using this in my manuscript now.
Thanks again, Kenneth ________________________________ From: Elaine Meng meng@cgl.ucsf.edu Sent: Monday, September 6, 2021 4:35 PM To: SANDOVAL, KENNETH K.SANDOVAL1@nuigalway.ie Cc: Chimera chimera-users@cgl.ucsf.edu Subject: Re: [Chimera-users] Copy protein orientation
EXTERNAL EMAIL: This email originated from outside of NUI Galway. Do not open attachments or click on links in the message unless you recognise the sender's email address and believe the content is safe. RÍOMHPHOST SEACHTRACH: Tháinig an ríomhphost seo as áit éigin taobh amuigh de OÉ Gaillimh. Ná cliceáil ar naisc agus ná hoscail ceangaltáin mura n-aithníonn tú seoladh ríomhphoist an tseoltóra agus mura gcreideann tú go bhfuil an t-ábhar sábháilte.
Hi Kenneth, The problem with F791140.pdb is that you have two proteins right on top of each other that are chains A and B in the same model. This ruins the secondary structure calculation (ksdssp) because it is not physically possible for one structure to have all those atoms nearly on top of each other.
Whichever program wrote the file wrote incorrect PDB format. Although it would still be somewhat incorrect, you can fix the file for purposes of secondary structure calculation by replacing the TER line with ENDMDL (i.e. in your favorite text-editor).
I did that and attached the resulting file. Then the secondary structure can be calculated automatically and looks reasonable when you open it.
I hope this helps, Elaine Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Sep 6, 2021, at 2:48 AM, SANDOVAL, KENNETH via Chimera-users chimera-users@cgl.ucsf.edu wrote:
Hi Elaine,
Thank you for your answer. I attempted to use the ksdssp command, but it doesn't appear to be doing anything. I have attached the two pdb files. I am wanting the structures of the two proteins in F791140.pdb to be like that of the one in A791140.pdb. Do you have advice on how to do this?
Thank you, Kenneth From: Elaine Meng meng@cgl.ucsf.edu Sent: Friday, September 3, 2021 6:52 PM To: SANDOVAL, KENNETH K.SANDOVAL1@nuigalway.ie Cc: Azad, Roksana via Chimera-users chimera-users@cgl.ucsf.edu Subject: Re: [Chimera-users] Copy protein orientation
EXTERNAL EMAIL: This email originated from outside of NUI Galway. Do not open attachments or click on links in the message unless you recognise the sender's email address and believe the content is safe. RÍOMHPHOST SEACHTRACH: Tháinig an ríomhphost seo as áit éigin taobh amuigh de OÉ Gaillimh. Ná cliceáil ar naisc agus ná hoscail ceangaltáin mura n-aithníonn tú seoladh ríomhphoist an tseoltóra agus mura gcreideann tú go bhfuil an t-ábhar sábháilte.
Hello Kenneth, I can't really tell what's going on without having the session file or the atomic coordinates (PDB file) to look at.
Without that information, my only suggestions are: (1) make sure you have a reasonably new version of Chimera, say the last production release (2) try running secondary structure assignment on that model, e.g. if the funny-looking ribbon model is #2, command
ksdssp #2
kdssp help: https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/ksdssp.html
I hope this helps, Elaine
Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Sep 3, 2021, at 6:26 AM, SANDOVAL, KENNETH via Chimera-users chimera-users@cgl.ucsf.edu wrote:
Hello,
Thank you for your helpful replies. I apologize for my late response. So following the initial suggestion by David, I have an alignment of protein A with protein B, but with protein B hidden. This is in file prot_A_aligned.png.
However, I am wanting the ribbons of this file to look like those in the image prot_A.png. This is the chimera view for the .pdb file of protein A before alignment with B using TM-align. That is, I want the parts of the protein which are not alpha-helices or beta-sheets to just be in the licorice form. Is this something I can do in chimera? Or is this something that would be integrated into the actual .pdb file which I would have to manually manipulate? I apologize if this is question has an obvious answer.
Thank you, Kenneth From: Elaine Meng meng@cgl.ucsf.edu Sent: Tuesday, August 10, 2021 6:00 PM To: SANDOVAL, KENNETH K.SANDOVAL1@nuigalway.ie Cc: chimera-users@cgl.ucsf.edu chimera-users@cgl.ucsf.edu Subject: Re: [Chimera-users] Copy protein orientation
Hello Kenneth, Similarly to David I was going to say that the better approach would have been to create only a single session with the aligned proteins and simply hide and show model B to make your two figures.
However, given the situation you have now, maybe: (1) in session 1, use "matrixget <file-pathname>" to save file with transformation of protein A. See: https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/matrixset.html
(2) in session 2, use "matrixset <file-pathname>" to apply the transformation from the file you saved in part 1, assuming protein A has the same model number as in session 1. However, that will probably ignore protein B, so you may need step 3.
(3) in session 2, if protein A is model #0 and protein B is model #1, use command "matrixcopy #0 #1" See: https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/matrixcopy.html
I am not completely sure it will work since it depends on how you got the TM-align alignment in there, but it has at least a chance. Also you may need to adjust the command if you have different model numbers.
I hope this helps, Elaine
Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Aug 10, 2021, at 9:34 AM, David Gae via Chimera-users chimera-users@cgl.ucsf.edu wrote:
Dear Kenneth,
Maybe it be best to put both protein A and B in the same cartisen coordinate system by alignment such as matchmaker program, then save the PDB files. Then work on the problem from there on. This seems like a possible direction to try?
Sincerely, David
On Aug 10, 2021, at 6:47 AM, SANDOVAL, KENNETH via Chimera-users chimera-users@cgl.ucsf.edu wrote:
Hello,
I wish to generate two images. The first is of protein A which is in session 1. The second is of protein A aligned with protein B using TM-Align which is in session 2. I wish for the alignment of the second image to be in the same orientation as the first with respect to protein A. Is there a feature which lets me do the following:
- Identify orientation of protein A in session 1
- Copy that orientation
- Apply that orientation to protein A in session 2
- Have protein B in session 2 remain aligned to protein A despite the new orientation
Thank you, Kenneth Sandoval _______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
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Great, you're welcome! The file probably looks OK in some other molecular graphics programs. Diffferent programs make different assumptions when calculating secondary structure. However, now that you know what's wrong, it's an easy fix for Chimera to text-edit one line. Best, Elaine
On Sep 6, 2021, at 8:43 AM, SANDOVAL, KENNETH via Chimera-users chimera-users@cgl.ucsf.edu wrote:
Hello Elaine,
Thank you very much! I generated that alignment with TM-align so I'm quite surprised that it produced an incorrect PDB format.
https://zhanggroup.org/TM-align/
Anyways I looked at the structure in Chimera and it looks perfect. So I'll be using this in my manuscript now.
Thanks again, Kenneth From: Elaine Meng meng@cgl.ucsf.edu Sent: Monday, September 6, 2021 4:35 PM To: SANDOVAL, KENNETH K.SANDOVAL1@nuigalway.ie Cc: Chimera chimera-users@cgl.ucsf.edu Subject: Re: [Chimera-users] Copy protein orientation
EXTERNAL EMAIL: This email originated from outside of NUI Galway. Do not open attachments or click on links in the message unless you recognise the sender's email address and believe the content is safe. RÍOMHPHOST SEACHTRACH: Tháinig an ríomhphost seo as áit éigin taobh amuigh de OÉ Gaillimh. Ná cliceáil ar naisc agus ná hoscail ceangaltáin mura n-aithníonn tú seoladh ríomhphoist an tseoltóra agus mura gcreideann tú go bhfuil an t-ábhar sábháilte.
Hi Kenneth, The problem with F791140.pdb is that you have two proteins right on top of each other that are chains A and B in the same model. This ruins the secondary structure calculation (ksdssp) because it is not physically possible for one structure to have all those atoms nearly on top of each other.
Whichever program wrote the file wrote incorrect PDB format. Although it would still be somewhat incorrect, you can fix the file for purposes of secondary structure calculation by replacing the TER line with ENDMDL (i.e. in your favorite text-editor).
I did that and attached the resulting file. Then the secondary structure can be calculated automatically and looks reasonable when you open it.
I hope this helps, Elaine Elaine
Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Sep 6, 2021, at 2:48 AM, SANDOVAL, KENNETH via Chimera-users chimera-users@cgl.ucsf.edu wrote:
Hi Elaine,
Thank you for your answer. I attempted to use the ksdssp command, but it doesn't appear to be doing anything. I have attached the two pdb files. I am wanting the structures of the two proteins in F791140.pdb to be like that of the one in A791140.pdb. Do you have advice on how to do this?
Thank you, Kenneth From: Elaine Meng meng@cgl.ucsf.edu Sent: Friday, September 3, 2021 6:52 PM To: SANDOVAL, KENNETH K.SANDOVAL1@nuigalway.ie Cc: Azad, Roksana via Chimera-users chimera-users@cgl.ucsf.edu Subject: Re: [Chimera-users] Copy protein orientation
EXTERNAL EMAIL: This email originated from outside of NUI Galway. Do not open attachments or click on links in the message unless you recognise the sender's email address and believe the content is safe. RÍOMHPHOST SEACHTRACH: Tháinig an ríomhphost seo as áit éigin taobh amuigh de OÉ Gaillimh. Ná cliceáil ar naisc agus ná hoscail ceangaltáin mura n-aithníonn tú seoladh ríomhphoist an tseoltóra agus mura gcreideann tú go bhfuil an t-ábhar sábháilte.
Hello Kenneth, I can't really tell what's going on without having the session file or the atomic coordinates (PDB file) to look at.
Without that information, my only suggestions are: (1) make sure you have a reasonably new version of Chimera, say the last production release (2) try running secondary structure assignment on that model, e.g. if the funny-looking ribbon model is #2, command
ksdssp #2
kdssp help: https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/ksdssp.html
I hope this helps, Elaine
Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Sep 3, 2021, at 6:26 AM, SANDOVAL, KENNETH via Chimera-users chimera-users@cgl.ucsf.edu wrote:
Hello,
Thank you for your helpful replies. I apologize for my late response. So following the initial suggestion by David, I have an alignment of protein A with protein B, but with protein B hidden. This is in file prot_A_aligned.png.
However, I am wanting the ribbons of this file to look like those in the image prot_A.png. This is the chimera view for the .pdb file of protein A before alignment with B using TM-align. That is, I want the parts of the protein which are not alpha-helices or beta-sheets to just be in the licorice form. Is this something I can do in chimera? Or is this something that would be integrated into the actual .pdb file which I would have to manually manipulate? I apologize if this is question has an obvious answer.
Thank you, Kenneth From: Elaine Meng meng@cgl.ucsf.edu Sent: Tuesday, August 10, 2021 6:00 PM To: SANDOVAL, KENNETH K.SANDOVAL1@nuigalway.ie Cc: chimera-users@cgl.ucsf.edu chimera-users@cgl.ucsf.edu Subject: Re: [Chimera-users] Copy protein orientation
Hello Kenneth, Similarly to David I was going to say that the better approach would have been to create only a single session with the aligned proteins and simply hide and show model B to make your two figures.
However, given the situation you have now, maybe: (1) in session 1, use "matrixget <file-pathname>" to save file with transformation of protein A. See: https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/matrixset.html
(2) in session 2, use "matrixset <file-pathname>" to apply the transformation from the file you saved in part 1, assuming protein A has the same model number as in session 1. However, that will probably ignore protein B, so you may need step 3.
(3) in session 2, if protein A is model #0 and protein B is model #1, use command "matrixcopy #0 #1" See: https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/matrixcopy.html
I am not completely sure it will work since it depends on how you got the TM-align alignment in there, but it has at least a chance. Also you may need to adjust the command if you have different model numbers.
I hope this helps, Elaine
Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Aug 10, 2021, at 9:34 AM, David Gae via Chimera-users chimera-users@cgl.ucsf.edu wrote:
Dear Kenneth,
Maybe it be best to put both protein A and B in the same cartisen coordinate system by alignment such as matchmaker program, then save the PDB files. Then work on the problem from there on. This seems like a possible direction to try?
Sincerely, David
On Aug 10, 2021, at 6:47 AM, SANDOVAL, KENNETH via Chimera-users chimera-users@cgl.ucsf.edu wrote:
Hello,
I wish to generate two images. The first is of protein A which is in session 1. The second is of protein A aligned with protein B using TM-Align which is in session 2. I wish for the alignment of the second image to be in the same orientation as the first with respect to protein A. Is there a feature which lets me do the following:
- Identify orientation of protein A in session 1
- Copy that orientation
- Apply that orientation to protein A in session 2
- Have protein B in session 2 remain aligned to protein A despite the new orientation
Thank you, Kenneth Sandoval _______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
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participants (3)
-
David Gae -
Elaine Meng -
SANDOVAL, KENNETH