Hi guys, Trying to show multiple binding protein sites on a large protein. Could successfully make footprints on the protein in different colors on the protein for different binding sites. Was trying to include binding constants as 2dlabels with each model protein. How to associate these labels with models to tile them along with the models? Combining the models (combine on (2dlabel model and structure models did not work.) Trying to use tile command with the 2dlabels to show IC50’s with the individual proteins. What is best way to do this… May be use the label command? Thanks Krish Sent from Mailhttps://go.microsoft.com/fwlink/?LinkId=550986 for Windows
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Hi Krishnan, The 2D labels are completely independent of the 3D models. Just think of them as being pasted onto the rectangular graphics window, like you had already saved the image and were using some other program to put labels on top. I would first tile the models or position/size them exactly as you want for the figure, and then as the last step, create the 2D labels and put them where you want them in teh window. You can move them by click-drag with the "move labels" mouse mode.
https://rbvi.ucsf.edu/chimerax/docs/user/commands/2dlabels.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 Nov 29, 2022, at 9:44 AM, Krishnan Raman via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
Hi guys, Trying to show multiple binding protein sites on a large protein. Could successfully make footprints on the protein in different colors on the protein for different binding sites. Was trying to include binding constants as 2dlabels with each model protein. How to associate these labels with models to tile them along with the models? Combining the models (combine on (2dlabel model and structure models did not work.) Trying to use tile command with the 2dlabels to show IC50’s with the individual proteins. What is best way to do this… May be use the label command? Thanks Krish
Thanks. How do we change the order/renumber the models? Krish.
-----Original Message----- From: Elaine Meng meng@cgl.ucsf.edu Sent: Tuesday, November 29, 2022 1:01 PM To: Krishnan Raman RKrishnan@BIOCRYST.com Cc: chimerax-users@cgl.ucsf.edu Subject: Re: [chimerax-users] tile and 2dlabels
[EXTERNAL]
Hi Krishnan, The 2D labels are completely independent of the 3D models. Just think of them as being pasted onto the rectangular graphics window, like you had already saved the image and were using some other program to put labels on top. I would first tile the models or position/size them exactly as you want for the figure, and then as the last step, create the 2D labels and put them where you want them in teh window. You can move them by click-drag with the "move labels" mouse mode.
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Nov 29, 2022, at 9:44 AM, Krishnan Raman via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
Hi guys, Trying to show multiple binding protein sites on a large protein. Could successfully make footprints on the protein in different colors on the protein for different binding sites. Was trying to include binding constants as 2dlabels with each model protein. How to associate these labels with models to tile them along with the models? Combining the models (combine on (2dlabel model and structure models did not work.) Trying to use tile command with the 2dlabels to show IC50’s with the individual proteins. What is best way to do this… May be use the label command? Thanks Krish
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Hi Krish,
You can change model name and/or number by just double-clicking the respective field in the Model Panel and entering a new value, or you can do it with the "rename" command: https://rbvi.ucsf.edu/chimerax/docs/user/commands/rename.html
You may need to do it in a strategic order to avoid trying to give two models the same number, which would instead make one a submodel of the other.
Elaine
On Nov 29, 2022, at 11:04 AM, Krishnan Raman via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
Thanks. How do we change the order/renumber the models? Krish.
-----Original Message----- From: Elaine Meng meng@cgl.ucsf.edu Sent: Tuesday, November 29, 2022 1:01 PM To: Krishnan Raman RKrishnan@BIOCRYST.com Cc: chimerax-users@cgl.ucsf.edu Subject: Re: [chimerax-users] tile and 2dlabels
[EXTERNAL]
Hi Krishnan, The 2D labels are completely independent of the 3D models. Just think of them as being pasted onto the rectangular graphics window, like you had already saved the image and were using some other program to put labels on top. I would first tile the models or position/size them exactly as you want for the figure, and then as the last step, create the 2D labels and put them where you want them in teh window. You can move them by click-drag with the "move labels" mouse mode.
I hope this helps, Elaine
Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Nov 29, 2022, at 9:44 AM, Krishnan Raman via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
Hi guys, Trying to show multiple binding protein sites on a large protein. Could successfully make footprints on the protein in different colors on the protein for different binding sites. Was trying to include binding constants as 2dlabels with each model protein. How to associate these labels with models to tile them along with the models? Combining the models (combine on (2dlabel model and structure models did not work.) Trying to use tile command with the 2dlabels to show IC50’s with the individual proteins. What is best way to do this… May be use the label command? Thanks Krish
Links contained in this email have been replaced. If you click on a link in the email above, the link will be analyzed for known threats. If a known threat is found, you will not be able to proceed to the destination. If suspicious content is detected, you will see a warning. CONFIDENTIALITY NOTICE
This email, including any attachments, may contain confidential or legally privileged information that is intended only for the individual or entity to whom it is addressed. If you are not the intended recipient, please be advised that any dissemination, distribution or copying of this email and any attachment is strictly prohibited. If you have received this email in error, please reply to the sender so that BioCryst Pharmaceuticals, Inc. can take corrective measures and then permanently delete this email and any attachment, including any printed copies. Thank you.
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participants (2)
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Elaine Meng -
Krishnan Raman