Elaine! I was so hoping you would be responding to my query! So nice to hear from you.

OK - good to know - I’ll make my figure in old Chimera. I still know it better anyway, much due to your help.

We are fine here in Iowa. We’ve managed to stay healthy and (largely) sane. I hope you are doing well too!

Miles

On Jul 24, 2020, at 1:35 PM, Elaine Meng meng@cgl.ucsf.edu wrote:

Hi Miles! I remember meeting you at UCSF years ago. I hope you are well.

This unfortunately is one of the features often needed for figures but that is not yet available in ChimeraX, the ability to clip one model (e.g. the surface) without clipping the other (e.g. the ligand atoms).

I've listed it in the Missing Features section of the ChimeraX download page as "per-model clipping." It is one of the things on the To-Do list and is a ticket in our database. I will add your e-mail address to the notification list for that ticket.

For now, you would still need to use Chimera for per-model clipping. Sorry about that, Elaine

---

Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco

...

On Jul 24, 2020, at 10:32 AM, Pufall, Miles A miles-pufall@uiowa.edu wrote:

Hi! I’ve used Chimera for years (though not recently) and am switching to ChimeraX. I’m looking to display the ligand binding pocket with the ligand, and the tutorial you have is great. I generated this picture, which is really close to what I want. It shows the ligand, and the pocket, and I’m able to slice it with the interactive side view tool to get to this point. However, the left side of the ligand is slightly clipped. I’ve played with rotation and with moving the slice plane, but can’t find an orientation that shows the pocket so nicely (without any surface in the foreground) and not ligand clipping. My question is: is there a way to tell ChimeraX to clip the surface but not the ligand? Thanks! Miles

<DAC_binding_pocket.png>

________________________________ Notice: This UI Health Care e-mail (including attachments) is covered by the Electronic Communications Privacy Act, 18 U.S.C. 2510-2521 and is intended only for the use of the individual or entity to which it is addressed, and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If you are not the intended recipient, any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please notify the sender immediately and delete or destroy all copies of the original message and attachments thereto. Email sent to or from UI Health Care may be retained as required by law or regulation. Thank you. ________________________________

Cool - thanks! Downloading now - will let you know if all is well.

Miles

On Jul 24, 2020, at 10:32 PM, Tom Goddard goddard@sonic.net wrote:

Hi Miles,

I added the ability to turn off clipping for specific models, in tonight's ChimeraX builds. It only effects clip planes that rotate with the models, not the near / far camera clip planes:

clip model #!1 off

The molecular surface of atomic model #1 is a submodel #1.1. So I use "#!1" in this command instead of #1 so the command acts on only model #1 and not its child models #1.1, 1.2,... You also will want to turn of surface caps

surface cap false

so that the hole left in the clipped surface is not covered by a cap.

Tom

...

On Jul 24, 2020, at 11:35 AM, Elaine Meng meng@cgl.ucsf.edu wrote:

Hi Miles! I remember meeting you at UCSF years ago. I hope you are well.

This unfortunately is one of the features often needed for figures but that is not yet available in ChimeraX, the ability to clip one model (e.g. the surface) without clipping the other (e.g. the ligand atoms).

I've listed it in the Missing Features section of the ChimeraX download page as "per-model clipping." It is one of the things on the To-Do list and is a ticket in our database. I will add your e-mail address to the notification list for that ticket.

For now, you would still need to use Chimera for per-model clipping. Sorry about that, Elaine

---

Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco

...

On Jul 24, 2020, at 10:32 AM, Pufall, Miles A miles-pufall@uiowa.edu wrote:

Hi! I’ve used Chimera for years (though not recently) and am switching to ChimeraX. I’m looking to display the ligand binding pocket with the ligand, and the tutorial you have is great. I generated this picture, which is really close to what I want. It shows the ligand, and the pocket, and I’m able to slice it with the interactive side view tool to get to this point. However, the left side of the ligand is slightly clipped. I’ve played with rotation and with moving the slice plane, but can’t find an orientation that shows the pocket so nicely (without any surface in the foreground) and not ligand clipping. My question is: is there a way to tell ChimeraX to clip the surface but not the ligand? Thanks! Miles

<DAC_binding_pocket.png>

---

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________________________________ Notice: This UI Health Care e-mail (including attachments) is covered by the Electronic Communications Privacy Act, 18 U.S.C. 2510-2521 and is intended only for the use of the individual or entity to which it is addressed, and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If you are not the intended recipient, any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please notify the sender immediately and delete or destroy all copies of the original message and attachments thereto. Email sent to or from UI Health Care may be retained as required by law or regulation. Thank you. ________________________________

Thanks Elaine! I’ll save the full string of commands you sent.

Tom’s guidance helped a lot - the figure came out just how I wanted it.

[DAC_binding_pocket_cutaway_good.png]

Thanks again -

M

On Jul 27, 2020, at 2:14 PM, Elaine Meng <meng@cgl.ucsf.edumailto:meng@cgl.ucsf.edu> wrote:

Hi Miles, In case it's useful, here's a little example that works in the current daily build. This protein has oleic acid (residue name OLA) in a buried pocket. The example turns off clipping for the parent model #1 (the atomic model, which includes any ribbon and atom/bond displays) but leaves it on for the molecular surface model #1.1.

open 1g74 surface clip front 0 position :ola clip model #!1 false hide ~:ola target ar style :ola ball

Probably you'd want to use the Right Mouse modes to translate and rotate the clipping plane interactively since it's hard to get the position you want with commands only.

Elaine

On Jul 25, 2020, at 7:12 AM, Pufall, Miles A <miles-pufall@uiowa.edumailto:miles-pufall@uiowa.edu> wrote:

Cool - thanks! Downloading now - will let you know if all is well.

Miles

On Jul 24, 2020, at 10:32 PM, Tom Goddard <goddard@sonic.netmailto:goddard@sonic.net> wrote:

Hi Miles,

I added the ability to turn off clipping for specific models, in tonight's ChimeraX builds. It only effects clip planes that rotate with the models, not the near / far camera clip planes:

clip model #!1 off

The molecular surface of atomic model #1 is a submodel #1.1. So I use "#!1" in this command instead of #1 so the command acts on only model #1 and not its child models #1.1, 1.2,... You also will want to turn of surface caps

surface cap false

so that the hole left in the clipped surface is not covered by a cap.

Tom

On Jul 24, 2020, at 11:35 AM, Elaine Meng <meng@cgl.ucsf.edumailto:meng@cgl.ucsf.edu> wrote:

Hi Miles! I remember meeting you at UCSF years ago. I hope you are well.

This unfortunately is one of the features often needed for figures but that is not yet available in ChimeraX, the ability to clip one model (e.g. the surface) without clipping the other (e.g. the ligand atoms).

I've listed it in the Missing Features section of the ChimeraX download page as "per-model clipping." It is one of the things on the To-Do list and is a ticket in our database. I will add your e-mail address to the notification list for that ticket.

For now, you would still need to use Chimera for per-model clipping. Sorry about that, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco

On Jul 24, 2020, at 10:32 AM, Pufall, Miles A <miles-pufall@uiowa.edumailto:miles-pufall@uiowa.edu> wrote:

Hi! I’ve used Chimera for years (though not recently) and am switching to ChimeraX. I’m looking to display the ligand binding pocket with the ligand, and the tutorial you have is great. I generated this picture, which is really close to what I want. It shows the ligand, and the pocket, and I’m able to slice it with the interactive side view tool to get to this point. However, the left side of the ligand is slightly clipped. I’ve played with rotation and with moving the slice plane, but can’t find an orientation that shows the pocket so nicely (without any surface in the foreground) and not ligand clipping. My question is: is there a way to tell ChimeraX to clip the surface but not the ligand? Thanks! Miles

<DAC_binding_pocket.png>

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That is very nice - particularly is you can make the cap translucent (so you can see what the ligand might be interacting with.

M

On Jul 27, 2020, at 3:15 PM, Elaine Meng <meng@cgl.ucsf.edumailto:meng@cgl.ucsf.edu> wrote:

Another thing users might not know is that one can also color the planar surface cap by the MLP, e.g. by saving the lipophilicity map and then using a separate command to recolor the surface including the cap. E.g. adding the following commands to my previous example:

mlp map true color sample #1.1 map #2 palette lipophilicity range -20,20

This is not to say it would make a better figure... just giving options. :-)

Best, Elaine

<mlpclip.png>

On Jul 27, 2020, at 12:16 PM, Pufall, Miles A <miles-pufall@uiowa.edumailto:miles-pufall@uiowa.edu> wrote:

Thanks Elaine! I’ll save the full string of commands you sent.

Tom’s guidance helped a lot - the figure came out just how I wanted it.

<699C644F-6A5E-47A1-9559-30329A1B5105.png>

Thanks again -

M

On Jul 27, 2020, at 2:14 PM, Elaine Meng <meng@cgl.ucsf.edumailto:meng@cgl.ucsf.edu> wrote:

Hi Miles, In case it's useful, here's a little example that works in the current daily build. This protein has oleic acid (residue name OLA) in a buried pocket. The example turns off clipping for the parent model #1 (the atomic model, which includes any ribbon and atom/bond displays) but leaves it on for the molecular surface model #1.1.

open 1g74 surface clip front 0 position :ola clip model #!1 false hide ~:ola target ar style :ola ball

Probably you'd want to use the Right Mouse modes to translate and rotate the clipping plane interactively since it's hard to get the position you want with commands only.

Elaine

On Jul 25, 2020, at 7:12 AM, Pufall, Miles A <miles-pufall@uiowa.edumailto:miles-pufall@uiowa.edu> wrote:

Cool - thanks! Downloading now - will let you know if all is well.

Miles

On Jul 24, 2020, at 10:32 PM, Tom Goddard <goddard@sonic.netmailto:goddard@sonic.net> wrote:

Hi Miles,

I added the ability to turn off clipping for specific models, in tonight's ChimeraX builds. It only effects clip planes that rotate with the models, not the near / far camera clip planes:

clip model #!1 off

The molecular surface of atomic model #1 is a submodel #1.1. So I use "#!1" in this command instead of #1 so the command acts on only model #1 and not its child models #1.1, 1.2,... You also will want to turn of surface caps

surface cap false

so that the hole left in the clipped surface is not covered by a cap.

Tom

On Jul 24, 2020, at 11:35 AM, Elaine Meng <meng@cgl.ucsf.edumailto:meng@cgl.ucsf.edu> wrote:

Hi Miles! I remember meeting you at UCSF years ago. I hope you are well.

This unfortunately is one of the features often needed for figures but that is not yet available in ChimeraX, the ability to clip one model (e.g. the surface) without clipping the other (e.g. the ligand atoms).

I've listed it in the Missing Features section of the ChimeraX download page as "per-model clipping." It is one of the things on the To-Do list and is a ticket in our database. I will add your e-mail address to the notification list for that ticket.

For now, you would still need to use Chimera for per-model clipping. Sorry about that, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco

On Jul 24, 2020, at 10:32 AM, Pufall, Miles A <miles-pufall@uiowa.edumailto:miles-pufall@uiowa.edu> wrote:

Hi! I’ve used Chimera for years (though not recently) and am switching to ChimeraX. I’m looking to display the ligand binding pocket with the ligand, and the tutorial you have is great. I generated this picture, which is really close to what I want. It shows the ligand, and the pocket, and I’m able to slice it with the interactive side view tool to get to this point. However, the left side of the ligand is slightly clipped. I’ve played with rotation and with moving the slice plane, but can’t find an orientation that shows the pocket so nicely (without any surface in the foreground) and not ligand clipping. My question is: is there a way to tell ChimeraX to clip the surface but not the ligand? Thanks! Miles

<DAC_binding_pocket.png>

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________________________________ Notice: This UI Health Care e-mail (including attachments) is covered by the Electronic Communications Privacy Act, 18 U.S.C. 2510-2521 and is intended only for the use of the individual or entity to which it is addressed, and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If you are not the intended recipient, any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please notify the sender immediately and delete or destroy all copies of the original message and attachments thereto. Email sent to or from UI Health Care may be retained as required by law or regulation. Thank you. ________________________________