Visualizing specific atoms in autodock-vina output
I am trying to investigate the protein surrounding a docked (autodock-vina, alpha chimera 1.1 build 40505 linux 64) ligand. I am interested in the environment of specific atoms of the ligand. With command sel #1.1@N z<5 I can investigate the protein at 5A from BOTH nitrogen atoms of model 1.1. How to select one of the two existing N atoms in the ligand? Same questions for other ligand atoms (there are many O-atoms) Is that possible without elaborating the vina output? thanks francesco pietra
Hi Francesco, Although each atom in a residue should have a different name, I guess your model #1.1 has more than one residue. If you hover the mouse over the atom you are interested in, the pop-up information should include both the residue number and the atom name, which you can include in the command to narrow it down, for example: sel #1.1:2@N z<5 (atom named N in residue 2 of model 1.1). Or, if you don’t mind doing it interactively, you could Ctrl-click to select the atom you want and then use “sel” to specify it, for example: sel sel z<5 Although you might think that wouldn’t work, it does! 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 May 12, 2017, at 10:26 AM, Francesco Pietra <chiendarret@gmail.com> wrote:
I am trying to investigate the protein surrounding a docked (autodock-vina, alpha chimera 1.1 build 40505 linux 64) ligand. I am interested in the environment of specific atoms of the ligand.
With command
sel #1.1@N z<5
I can investigate the protein at 5A from BOTH nitrogen atoms of model 1.1.
How to select one of the two existing N atoms in the ligand? Same questions for other ligand atoms (there are many O-atoms) Is that possible without elaborating the vina output? thanks francesco pietra
Hi Elaine: That fantastic 'sel sel z<5'! Thanks a lot francesco On Fri, May 12, 2017 at 7:36 PM, Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hi Francesco, Although each atom in a residue should have a different name, I guess your model #1.1 has more than one residue. If you hover the mouse over the atom you are interested in, the pop-up information should include both the residue number and the atom name, which you can include in the command to narrow it down, for example:
sel #1.1:2@N z<5
(atom named N in residue 2 of model 1.1). Or, if you don’t mind doing it interactively, you could Ctrl-click to select the atom you want and then use “sel” to specify it, for example:
sel sel z<5
Although you might think that wouldn’t work, it does! 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 May 12, 2017, at 10:26 AM, Francesco Pietra <chiendarret@gmail.com> wrote:
I am trying to investigate the protein surrounding a docked (autodock-vina, alpha chimera 1.1 build 40505 linux 64) ligand. I am interested in the environment of specific atoms of the ligand.
With command
sel #1.1@N z<5
I can investigate the protein at 5A from BOTH nitrogen atoms of model 1.1.
How to select one of the two existing N atoms in the ligand? Same questions for other ligand atoms (there are many O-atoms) Is that possible without elaborating the vina output? thanks francesco pietra
Hi all, If I select multiple models of a protein-DNA complex select #0:1-40.B #1:1-40.B #2:1-40.B #3:1-40.B #4:1-40.B #5:1-40.B #6:1-40.B #7:1-40.B where B is the DNA and then match match #0 #1 #2 #3 #4 #5 #6 #7 I obtain a message about the RMSD so it is working, but no superposition on the monitor... Also, selection of part of the models select #5:1-40.B #6:1-40.B #7:1-40.B followed by match #5 #6 #7 Report an error like "an even number of space-separated atom specs are required" Why? All atoms were selected. And in the previous case, where 8 models were selected using the same procedure, this message does not appear. In both cases selection is done properly (as judged from the monitor) but the match command gives a not clear response. All DNA models have the same sequence. I miss something... I'm using version 1.11 of Chimera on Linux Ubuntu. Thanks for your help, Marco
Hi Marco, A single “match” command only does a pairwise match… so if you wanted to match #1 to #0, #2 to #0, etc. it would need to be done in separate commands. I believe your first example”match" command would superimpose #0-3 onto #4-7 (pairing #0 and #4, #1 and #5, etc. Maybe it is hard to see that that is what happened. <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/match.html> The select commands are unnecessary. The “match” command doesn’t care about the selection unless you use “sel” in the atom specification. Assuming the models have tthe same atoms, your second “match” command example has an odd number of atoms ( models #5-7) and so it cannot do anything. I hope this clarifies the situation, 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 May 15, 2017, at 3:30 AM, Marco Sette <sette@uniroma2.it> wrote:
Hi all,
If I select multiple models of a protein-DNA complex select #0:1-40.B #1:1-40.B #2:1-40.B #3:1-40.B #4:1-40.B #5:1-40.B #6:1-40.B #7:1-40.B where B is the DNA and then match match #0 #1 #2 #3 #4 #5 #6 #7 I obtain a message about the RMSD so it is working, but no superposition on the monitor...
Also, selection of part of the models select #5:1-40.B #6:1-40.B #7:1-40.B followed by match #5 #6 #7 Report an error like "an even number of space-separated atom specs are required" Why? All atoms were selected. And in the previous case, where 8 models were selected using the same procedure, this message does not appear.
In both cases selection is done properly (as judged from the monitor) but the match command gives a not clear response. All DNA models have the same sequence. I miss something... I'm using version 1.11 of Chimera on Linux Ubuntu.
Thanks for your help, Marco
Hi Elaine, thanks for your help. I would like to match only the DNA part of the complex (chain B in my case), and watch the different protein (chain A) orientation between the models. If my command is match #0 #1 I do not specify that the match should concern chains B. Thanks again, Marco Il 15/05/2017 18.30, Elaine Meng ha scritto:
Hi Marco, A single “match” command only does a pairwise match… so if you wanted to match #1 to #0, #2 to #0, etc. it would need to be done in separate commands. I believe your first example”match" command would superimpose #0-3 onto #4-7 (pairing #0 and #4, #1 and #5, etc. Maybe it is hard to see that that is what happened.
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/match.html>
The select commands are unnecessary. The “match” command doesn’t care about the selection unless you use “sel” in the atom specification.
Assuming the models have tthe same atoms, your second “match” command example has an odd number of atoms ( models #5-7) and so it cannot do anything.
I hope this clarifies the situation, 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 May 15, 2017, at 3:30 AM, Marco Sette <sette@uniroma2.it> wrote:
Hi all,
If I select multiple models of a protein-DNA complex select #0:1-40.B #1:1-40.B #2:1-40.B #3:1-40.B #4:1-40.B #5:1-40.B #6:1-40.B #7:1-40.B where B is the DNA and then match match #0 #1 #2 #3 #4 #5 #6 #7 I obtain a message about the RMSD so it is working, but no superposition on the monitor...
Also, selection of part of the models select #5:1-40.B #6:1-40.B #7:1-40.B followed by match #5 #6 #7 Report an error like "an even number of space-separated atom specs are required" Why? All atoms were selected. And in the previous case, where 8 models were selected using the same procedure, this message does not appear.
In both cases selection is done properly (as judged from the monitor) but the match command gives a not clear response. All DNA models have the same sequence. I miss something... I'm using version 1.11 of Chimera on Linux Ubuntu.
Thanks for your help, Marco
--- Questa e-mail è stata controllata per individuare virus con Avast antivirus. https://www.avast.com/antivirus
Hi Marco, Does that command do what you want? To be safe, you should specify the atoms you want to use in the fit… maybe match #0:.B #1:.B (if the B chains have exactly the same atoms… otherwise you may need to specify residue number ranges, or P atoms only, or some other specification that is narrower than the whole chains.) Elaine
On May 15, 2017, at 9:47 AM, MarcoSette <sette@uniroma2.it> wrote:
Hi Elaine,
thanks for your help. I would like to match only the DNA part of the complex (chain B in my case), and watch the different protein (chain A) orientation between the models. If my command is match #0 #1 I do not specify that the match should concern chains B.
Thanks again, Marco
Il 15/05/2017 18.30, Elaine Meng ha scritto:
Hi Marco, A single “match” command only does a pairwise match… so if you wanted to match #1 to #0, #2 to #0, etc. it would need to be done in separate commands. I believe your first example”match" command would superimpose #0-3 onto #4-7 (pairing #0 and #4, #1 and #5, etc. Maybe it is hard to see that that is what happened.
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/match.html>
The select commands are unnecessary. The “match” command doesn’t care about the selection unless you use “sel” in the atom specification.
Assuming the models have tthe same atoms, your second “match” command example has an odd number of atoms ( models #5-7) and so it cannot do anything.
I hope this clarifies the situation, 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 May 15, 2017, at 3:30 AM, Marco Sette <sette@uniroma2.it> wrote:
Hi all,
If I select multiple models of a protein-DNA complex select #0:1-40.B #1:1-40.B #2:1-40.B #3:1-40.B #4:1-40.B #5:1-40.B #6:1-40.B #7:1-40.B where B is the DNA and then match match #0 #1 #2 #3 #4 #5 #6 #7 I obtain a message about the RMSD so it is working, but no superposition on the monitor...
Also, selection of part of the models select #5:1-40.B #6:1-40.B #7:1-40.B followed by match #5 #6 #7 Report an error like "an even number of space-separated atom specs are required" Why? All atoms were selected. And in the previous case, where 8 models were selected using the same procedure, this message does not appear.
In both cases selection is done properly (as judged from the monitor) but the match command gives a not clear response. All DNA models have the same sequence. I miss something... I'm using version 1.11 of Chimera on Linux Ubuntu.
Thanks for your help, Marco
--- Questa e-mail è stata controllata per individuare virus con Avast antivirus. https://www.avast.com/antivirus
_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Hi Marco, Another possibility is to use “matchmaker” instead of “match” and let it figure out the pairing if the DNA has the same or similar sequence, for example something like: matchmaker #0:.B #1:.B pair ss matrix Nucleic show true … where “show true” will show the sequence alignment used for the pairing. See also the “iterate” option; some iteration will occur unless you specify “iterate false” <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/mmaker.html> Elaine
On May 15, 2017, at 9:59 AM, Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hi Marco, Does that command do what you want? To be safe, you should specify the atoms you want to use in the fit… maybe
match #0:.B #1:.B
(if the B chains have exactly the same atoms… otherwise you may need to specify residue number ranges, or P atoms only, or some other specification that is narrower than the whole chains.)
Elaine
On May 15, 2017, at 9:47 AM, MarcoSette <sette@uniroma2.it> wrote:
Hi Elaine,
thanks for your help. I would like to match only the DNA part of the complex (chain B in my case), and watch the different protein (chain A) orientation between the models. If my command is match #0 #1 I do not specify that the match should concern chains B.
Thanks again, Marco
Il 15/05/2017 18.30, Elaine Meng ha scritto:
Hi Marco, A single “match” command only does a pairwise match… so if you wanted to match #1 to #0, #2 to #0, etc. it would need to be done in separate commands. I believe your first example”match" command would superimpose #0-3 onto #4-7 (pairing #0 and #4, #1 and #5, etc. Maybe it is hard to see that that is what happened.
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/match.html>
The select commands are unnecessary. The “match” command doesn’t care about the selection unless you use “sel” in the atom specification.
Assuming the models have tthe same atoms, your second “match” command example has an odd number of atoms ( models #5-7) and so it cannot do anything.
I hope this clarifies the situation, 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 May 15, 2017, at 3:30 AM, Marco Sette <sette@uniroma2.it> wrote:
Hi all,
If I select multiple models of a protein-DNA complex select #0:1-40.B #1:1-40.B #2:1-40.B #3:1-40.B #4:1-40.B #5:1-40.B #6:1-40.B #7:1-40.B where B is the DNA and then match match #0 #1 #2 #3 #4 #5 #6 #7 I obtain a message about the RMSD so it is working, but no superposition on the monitor...
Also, selection of part of the models select #5:1-40.B #6:1-40.B #7:1-40.B followed by match #5 #6 #7 Report an error like "an even number of space-separated atom specs are required" Why? All atoms were selected. And in the previous case, where 8 models were selected using the same procedure, this message does not appear.
In both cases selection is done properly (as judged from the monitor) but the match command gives a not clear response. All DNA models have the same sequence. I miss something... I'm using version 1.11 of Chimera on Linux Ubuntu.
Thanks for your help, Marco
--- Questa e-mail è stata controllata per individuare virus con Avast antivirus. https://www.avast.com/antivirus
_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Yes :) match #0:.B #1:.B works fine. Thanks a lot, Marco Il 15/05/2017 18.59, Elaine Meng ha scritto:
Hi Marco, Does that command do what you want? To be safe, you should specify the atoms you want to use in the fit… maybe
match #0:.B #1:.B
(if the B chains have exactly the same atoms… otherwise you may need to specify residue number ranges, or P atoms only, or some other specification that is narrower than the whole chains.)
Elaine
On May 15, 2017, at 9:47 AM, MarcoSette <sette@uniroma2.it> wrote:
Hi Elaine,
thanks for your help. I would like to match only the DNA part of the complex (chain B in my case), and watch the different protein (chain A) orientation between the models. If my command is match #0 #1 I do not specify that the match should concern chains B.
Thanks again, Marco
Il 15/05/2017 18.30, Elaine Meng ha scritto:
Hi Marco, A single “match” command only does a pairwise match… so if you wanted to match #1 to #0, #2 to #0, etc. it would need to be done in separate commands. I believe your first example”match" command would superimpose #0-3 onto #4-7 (pairing #0 and #4, #1 and #5, etc. Maybe it is hard to see that that is what happened.
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/match.html>
The select commands are unnecessary. The “match” command doesn’t care about the selection unless you use “sel” in the atom specification.
Assuming the models have tthe same atoms, your second “match” command example has an odd number of atoms ( models #5-7) and so it cannot do anything.
I hope this clarifies the situation, 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 May 15, 2017, at 3:30 AM, Marco Sette <sette@uniroma2.it> wrote:
Hi all,
If I select multiple models of a protein-DNA complex select #0:1-40.B #1:1-40.B #2:1-40.B #3:1-40.B #4:1-40.B #5:1-40.B #6:1-40.B #7:1-40.B where B is the DNA and then match match #0 #1 #2 #3 #4 #5 #6 #7 I obtain a message about the RMSD so it is working, but no superposition on the monitor...
Also, selection of part of the models select #5:1-40.B #6:1-40.B #7:1-40.B followed by match #5 #6 #7 Report an error like "an even number of space-separated atom specs are required" Why? All atoms were selected. And in the previous case, where 8 models were selected using the same procedure, this message does not appear.
In both cases selection is done properly (as judged from the monitor) but the match command gives a not clear response. All DNA models have the same sequence. I miss something... I'm using version 1.11 of Chimera on Linux Ubuntu.
Thanks for your help, Marco
--- Questa e-mail è stata controllata per individuare virus con Avast antivirus. https://www.avast.com/antivirus
_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
participants (4)
-
Elaine Meng -
Francesco Pietra -
Marco Sette -
MarcoSette