Hi all, Is there a way in chimera to fix the position of one model when creating a peptide bond between two models? I selected 'move atoms on C side' but the N side chain still moves. Thanks in advance! Jing
Hi Jing, Just choose the other option, move on N side. We need to change the wording in the dialog to make it more clear. By “C side” we really meant the side with the selected C atom, even though that becomes the N side of the final joined protein. 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 Aug 12, 2016, at 6:15 PM, Jie, Jing <jiej@oregonstate.edu> wrote:
Hi all, Is there a way in chimera to fix the position of one model when creating a peptide bond between two models? I selected 'move atoms on C side' but the N side chain still moves. Thanks in advance! Jing
Hi Elaine, I tried both selections but the side with the selected N atom (N side) moves in either one. The N side has a ligand bound to it. Is there a way to treat the N side and its ligand as a single object so that even it moves the ligand moves with it? Thank you. Jing On Sat, Aug 13, 2016 at 8:48 AM, Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hi Jing, Just choose the other option, move on N side.
We need to change the wording in the dialog to make it more clear. By “C side” we really meant the side with the selected C atom, even though that becomes the N side of the final joined protein.
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 Aug 12, 2016, at 6:15 PM, Jie, Jing <jiej@oregonstate.edu> wrote:
Hi all, Is there a way in chimera to fix the position of one model when creating a peptide bond between two models? I selected 'move atoms on C side' but the N side chain still moves. Thanks in advance! Jing
Hi Jing, I was not able to reproduce the problem. When I chose “N side” the side with the N atom selected moved, and when I chose “C side” the side with the C atom selected moved. If the ligand is in the same model as the part it is bound to, they should move together. In general when you have data-specific issues you should include your data, or else we cannot suggest any specific solution. If you think it is a bug, you should use menu: Help.. Report a Bug and attach any data (such as a Chimera session of the models before the joining) that is needed to reproduce the problem. Best, Elaine On Aug 13, 2016, at 10:42 AM, Jie, Jing <jiej@oregonstate.edu> wrote:
Hi Elaine, I tried both selections but the side with the selected N atom (N side) moves in either one. The N side has a ligand bound to it. Is there a way to treat the N side and its ligand as a single object so that even it moves the ligand moves with it? Thank you. Jing
On Sat, Aug 13, 2016 at 8:48 AM, Elaine Meng <meng@cgl.ucsf.edu> wrote: Hi Jing, Just choose the other option, move on N side.
We need to change the wording in the dialog to make it more clear. By “C side” we really meant the side with the selected C atom, even though that becomes the N side of the final joined protein.
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 Aug 12, 2016, at 6:15 PM, Jie, Jing <jiej@oregonstate.edu> wrote:
Hi all, Is there a way in chimera to fix the position of one model when creating a peptide bond between two models? I selected 'move atoms on C side' but the N side chain still moves. Thanks in advance! Jing
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Hi Jing, I was, eventually, able to reproduce the problem. It was due to the setting of the phi angle possibly causing the “non-moving” side to move. It’s fixed now and the fix will be in tomorrow’s daily build, so try that and see if it helps. —Eric Eric Pettersen UCSF Computer Graphics Lab
On Aug 13, 2016, at 10:56 AM, Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hi Jing, I was not able to reproduce the problem. When I chose “N side” the side with the N atom selected moved, and when I chose “C side” the side with the C atom selected moved.
If the ligand is in the same model as the part it is bound to, they should move together.
In general when you have data-specific issues you should include your data, or else we cannot suggest any specific solution. If you think it is a bug, you should use menu: Help.. Report a Bug and attach any data (such as a Chimera session of the models before the joining) that is needed to reproduce the problem. Best, Elaine
On Aug 13, 2016, at 10:42 AM, Jie, Jing <jiej@oregonstate.edu> wrote:
Hi Elaine, I tried both selections but the side with the selected N atom (N side) moves in either one. The N side has a ligand bound to it. Is there a way to treat the N side and its ligand as a single object so that even it moves the ligand moves with it? Thank you. Jing
On Sat, Aug 13, 2016 at 8:48 AM, Elaine Meng <meng@cgl.ucsf.edu> wrote: Hi Jing, Just choose the other option, move on N side.
We need to change the wording in the dialog to make it more clear. By “C side” we really meant the side with the selected C atom, even though that becomes the N side of the final joined protein.
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 Aug 12, 2016, at 6:15 PM, Jie, Jing <jiej@oregonstate.edu> wrote:
Hi all, Is there a way in chimera to fix the position of one model when creating a peptide bond between two models? I selected 'move atoms on C side' but the N side chain still moves. Thanks in advance! Jing
_______________________________________________ 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
participants (3)
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Elaine Meng -
Eric Pettersen -
Jie, Jing