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