Hello,
I am trying to join the two models attached to this sequence.
I have used the sequence selection code in atom specifier: #1:559.a@C #0:2.a@N
Where model #0 is YFP and #1 is PcPs.
When I go to join models, the Apply button is not accessible.
Can you indicate if I am doing something incorrect in the selection of the C and N atoms?
Thank you for your time.
Kyle
Dr. Kyle J. Lauersen Algae Biotechnology & Bioenergy Center for Biotechnology Bielefeld University p: +49 (0) 521 106 12289 e: kyle.lauersen@uni-bielefeld.de mailto:kyle.lauersen@uni-bielefeld.de
Hi Kyle, The following works for me:
I opened YFP and PcPs in that order, then:
commands: ~ribbon disp @n,ca,c sel #1:559.a@C #0:2.a@N
menu: Tools….Structure Editing… Build Structure, change to Join Models section of the resulting dialog.
Then I chose the “C-N peptide bond” option and clicked Apply, and the join appears to take place successfully.
However, I see your point that something weird is going on: I repeated the process several times, and sometimes (but not always!!) if I didn’t change from ribbon to atom display, the Apply button was grayed out. We should look into why that is happening.
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 29, 2016, at 5:33 AM, Kyle J. Lauersen kyle.lauersen@uni-bielefeld.de wrote:
Hello,
I am trying to join the two models attached to this sequence.
I have used the sequence selection code in atom specifier: #1:559.a@C #0:2.a@N
Where model #0 is YFP and #1 is PcPs.
When I go to join models, the Apply button is not accessible.
Can you indicate if I am doing something incorrect in the selection of the C and N atoms?
Thank you for your time.
Kyle
<YFP.pdb> <PcPs.pdb>
Dr. Kyle J. Lauersen Algae Biotechnology & Bioenergy Center for Biotechnology Bielefeld University p: +49 (0) 521 106 12289 e: kyle.lauersen@uni-bielefeld.de
Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Thanks Elaine.
I was omitting the .A. Since they only had one chain I didn't think it was required. But it's working now.
Best,
Kyle
Dr. Kyle J. Lauersen Algae Biotechnology & Bioenergy Center for Biotechnology Bielefeld University p: +49 (0) 521 106 12261 e: kyle.lauersen@uni-bielefeld.de
On 29.01.2016, at 20:43, Elaine Meng meng@cgl.ucsf.edu wrote:
Hi Kyle, The following works for me:
I opened YFP and PcPs in that order, then:
commands: ~ribbon disp @n,ca,c sel #1:559.a@C #0:2.a@N
menu: Tools….Structure Editing… Build Structure, change to Join Models section of the resulting dialog.
Then I chose the “C-N peptide bond” option and clicked Apply, and the join appears to take place successfully.
However, I see your point that something weird is going on: I repeated the process several times, and sometimes (but not always!!) if I didn’t change from ribbon to atom display, the Apply button was grayed out. We should look into why that is happening.
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 29, 2016, at 5:33 AM, Kyle J. Lauersen kyle.lauersen@uni-bielefeld.de wrote:
Hello,
I am trying to join the two models attached to this sequence.
I have used the sequence selection code in atom specifier: #1:559.a@C #0:2.a@N
Where model #0 is YFP and #1 is PcPs.
When I go to join models, the Apply button is not accessible.
Can you indicate if I am doing something incorrect in the selection of the C and N atoms?
Thank you for your time.
Kyle
<YFP.pdb> <PcPs.pdb>
Dr. Kyle J. Lauersen Algae Biotechnology & Bioenergy Center for Biotechnology Bielefeld University p: +49 (0) 521 106 12289 e: kyle.lauersen@uni-bielefeld.de
Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Hi Kyle, I don’t think that was the problem, since I could repeat the same except omitting the “.a” from both places in the select command. It still selected just 2 atoms. If there is only one residue with that number in that structure, it should not matter. Elaine
On Jan 29, 2016, at 11:56 AM, Kyle J. Lauersen kyle.lauersen@uni-bielefeld.de wrote:
Thanks Elaine.
I was omitting the .A. Since they only had one chain I didn't think it was required. But it's working now.
Best,
Kyle
Dr. Kyle J. Lauersen Algae Biotechnology & Bioenergy Center for Biotechnology Bielefeld University p: +49 (0) 521 106 12261 e: kyle.lauersen@uni-bielefeld.de
On 29.01.2016, at 20:43, Elaine Meng meng@cgl.ucsf.edu wrote:
Hi Kyle, The following works for me:
I opened YFP and PcPs in that order, then:
commands: ~ribbon disp @n,ca,c sel #1:559.a@C #0:2.a@N
menu: Tools….Structure Editing… Build Structure, change to Join Models section of the resulting dialog.
Then I chose the “C-N peptide bond” option and clicked Apply, and the join appears to take place successfully.
However, I see your point that something weird is going on: I repeated the process several times, and sometimes (but not always!!) if I didn’t change from ribbon to atom display, the Apply button was grayed out. We should look into why that is happening.
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 29, 2016, at 5:33 AM, Kyle J. Lauersen kyle.lauersen@uni-bielefeld.de wrote:
Hello,
I am trying to join the two models attached to this sequence.
I have used the sequence selection code in atom specifier: #1:559.a@C #0:2.a@N
Where model #0 is YFP and #1 is PcPs.
When I go to join models, the Apply button is not accessible.
Can you indicate if I am doing something incorrect in the selection of the C and N atoms?
Thank you for your time.
Kyle
<YFP.pdb> <PcPs.pdb>
Dr. Kyle J. Lauersen Algae Biotechnology & Bioenergy Center for Biotechnology Bielefeld University p: +49 (0) 521 106 12289 e: kyle.lauersen@uni-bielefeld.de
Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
participants (2)
-
Elaine Meng
-
Kyle J. Lauersen