Is there any command corresponding to surft (surface transparency) that will modulate the visibility of a sphere representation of a ligand? I want to change it in the course of a morph between substrate-bound and substrate free forms of the same enzyme. I will probably have other questions, but this seems like a good place to start... Thanks, Tom Pochapsky
Hi Tom, The broader command is simply “transparency” … it applies to not only surfaces, but also atomic representations, ribbons, etc. (whichever you specify) and there is a “frames” option for fading in/out over a specified number of frames. So for example with this ligand in 2gbp, the last command would fade it from the initial 0% to 100% transparent over 100 frames: open 2gbp show :bgc repr sphere :bgc transp 100,a :bgc frames 100 … in this case “ligand” could be used instead of “:bgc” but I showed a more general case of specifying by residue name, since “ligand” doesn’t always get what you want. The “,a” means to affect atomic representations, not surfaces, ribbons, etc. See the manpage: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/transparency.html> The “surftransparency” manpage (e.g. shown with command “help surftransparency” refers to this “transparency” command which essentially replaces it, although surftransparency still works too. See also the movie-related commands list, including “coordset” to play through your morph. <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/movies.html#moviecommands> There is also a list of all commands, of course… <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/framecommand.html> … and you can also use "Help… Search Documentation” in the menu to search for specific terms like “transparency" I hope this helps, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jun 12, 2017, at 10:35 AM, Thomas Pochapsky <pochapsk@brandeis.edu> wrote:
Is there any command corresponding to surft (surface transparency) that will modulate the visibility of a sphere representation of a ligand? I want to change it in the course of a morph between substrate-bound and substrate free forms of the same enzyme. I will probably have other questions, but this seems like a good place to start... Thanks, Tom Pochapsky
Thanks, Elaine, This works independently (just applying through the per-frame script in the movie viewer), but I am trying to integrate it with the morph that I generated (120 frames); right now it keeps flashing the structure of the ligand as it appears to fade back and forth on each frame of the morph (at least that is what it looks like to me). Here are the script commands I have tried, again in the per-frame scripting window accessed from the movie viewer: transp 100,a #4:MIV1 transp 0,a #4:MIV frames 60 transp 100,a #4:MIV frames 121 Ideally, the substrate-bound form is reached at frame 60 of the morph, by the time it reaches 121 it has gone back to the substrate-free form. So I would like to have the substrate fade in by frame 60, and back out again by 121. And while we are at it, how would I go about selecting side chains that interact with the substrate on the morph model? If I use *ligand zr<5*, Chimera decides that the heme is the ligand, not the :MIV. Thanks in advance. Sorry, I am brand-new to this, I just found out that PyMOL can't do all the things I need... Tom Pochapsky On 6/12/17 1:50 PM, Elaine Meng wrote:
Hi Tom, The broader command is simply “transparency” … it applies to not only surfaces, but also atomic representations, ribbons, etc. (whichever you specify) and there is a “frames” option for fading in/out over a specified number of frames. So for example with this ligand in 2gbp, the last command would fade it from the initial 0% to 100% transparent over 100 frames:
open 2gbp show :bgc repr sphere :bgc transp 100,a :bgc frames 100
… in this case “ligand” could be used instead of “:bgc” but I showed a more general case of specifying by residue name, since “ligand” doesn’t always get what you want. The “,a” means to affect atomic representations, not surfaces, ribbons, etc. See the manpage: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/transparency.html>
The “surftransparency” manpage (e.g. shown with command “help surftransparency” refers to this “transparency” command which essentially replaces it, although surftransparency still works too. See also the movie-related commands list, including “coordset” to play through your morph. <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/movies.html#moviecommands>
There is also a list of all commands, of course… <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/framecommand.html>
… and you can also use "Help… Search Documentation” in the menu to search for specific terms like “transparency"
I hope this helps, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jun 12, 2017, at 10:35 AM, Thomas Pochapsky <pochapsk@brandeis.edu> wrote:
Is there any command corresponding to surft (surface transparency) that will modulate the visibility of a sphere representation of a ligand? I want to change it in the course of a morph between substrate-bound and substrate free forms of the same enzyme. I will probably have other questions, but this seems like a good place to start... Thanks, Tom Pochapsky
Hi Tom, Ah, you don’t want this fading to execute at EACH frame of the morph, considering that the fade itself is a multi-frame process...“frames 60” means it changes the transparency to the target value over 60 frames. So it cannot be done within a per-frame script in the playback tool (MD Movie). Instead you would need to generate the morph (I’d recommend saving a session with the morph already calculated) and then in that session or after restoring the session, executing a script that plays the morph trajectory with the “coordset" command and simultaneously fades the ligand. <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/coordset.html> E.g. if your morph trajectory with 121 frames is model #5 and the model with your ligand (residue name MIV) is model #4, the script would contain something like the following to play the first 60 frames before starting the ligand fade: trans 100,a #4:miv coordset #5 1,60; trans 0,a #4:miv frames 60; wait 60 coordset #5 61,121; trans 100,a #4:miv frames 60; wait 60 There are some other example scripts with morph playback in the Animations gallery, see “kinase morph” at the top and “ball-and-socket motion” about halfway down the page: <http://www.rbvi.ucsf.edu/chimera/animations/animations.html> <http://www.rbvi.ucsf.edu/chimera/animations/animations.html#trmovie> For your zone question, instead of using the word “ligand” you’d simply use the residue-name specifier instead, :miv zr<5 I hope this helps, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jun 12, 2017, at 1:12 PM, Thomas Pochapsky <pochapsk@brandeis.edu> wrote:
Thanks, Elaine,
This works independently (just applying through the per-frame script in the movie viewer), but I am trying to integrate it with the morph that I generated (120 frames); right now it keeps flashing the structure of the ligand as it appears to fade back and forth on each frame of the morph (at least that is what it looks like to me). Here are the script commands I have tried, again in the per-frame scripting window accessed from the movie viewer:
transp 100,a #4:MIV1 transp 0,a #4:MIV frames 60 transp 100,a #4:MIV frames 121 Ideally, the substrate-bound form is reached at frame 60 of the morph, by the time it reaches 121 it has gone back to the substrate-free form. So I would like to have the substrate fade in by frame 60, and back out again by 121.
And while we are at it, how would I go about selecting side chains that interact with the substrate on the morph model? If I use ligand zr<5, Chimera decides that the heme is the ligand, not the :MIV.
Thanks in advance. Sorry, I am brand-new to this, I just found out that PyMOL can't do all the things I need...
Tom Pochapsky
On 6/12/17 1:50 PM, Elaine Meng wrote:
Hi Tom, The broader command is simply “transparency” … it applies to not only surfaces, but also atomic representations, ribbons, etc. (whichever you specify) and there is a “frames” option for fading in/out over a specified number of frames. So for example with this ligand in 2gbp, the last command would fade it from the initial 0% to 100% transparent over 100 frames:
open 2gbp show :bgc repr sphere :bgc transp 100,a :bgc frames 100
… in this case “ligand” could be used instead of “:bgc” but I showed a more general case of specifying by residue name, since “ligand” doesn’t always get what you want. The “,a” means to affect atomic representations, not surfaces, ribbons, etc. See the manpage:
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/transparency.html>
The “surftransparency” manpage (e.g. shown with command “help surftransparency” refers to this “transparency” command which essentially replaces it, although surftransparency still works too. See also the movie-related commands list, including “coordset” to play through your morph.
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/movies.html#moviecommands>
There is also a list of all commands, of course…
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/framecommand.html>
… and you can also use "Help… Search Documentation” in the menu to search for specific terms like “transparency"
I hope this helps, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jun 12, 2017, at 10:35 AM, Thomas Pochapsky <pochapsk@brandeis.edu> wrote:
Is there any command corresponding to surft (surface transparency) that will modulate the visibility of a sphere representation of a ligand? I want to change it in the course of a morph between substrate-bound and substrate free forms of the same enzyme. I will probably have other questions, but this seems like a good place to start... Thanks, Tom Pochapsky
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On Jun 12, 2017, at 1:48 PM, Elaine Meng <meng@cgl.ucsf.edu> wrote:
So it cannot be done within a per-frame script in the playback tool (MD Movie).
Correction: It turns out that “cannot” was a little too strong… I’d forgotten that there is a mechanism in per-frame scripts to only execute a command at a particular trajectory frame, by prefixing it with #N:. I had an example morph (2fw0 -> 2gbp -> 2fw0) 121 frames where the middle structure has bound BGC, and in that case I could use this per-frame script #1:trans 0,a :bgc frames 60 #61:trans 100,a :bgc frames 60 However, the other method with “coordset” in a script may still be superior for at least two reasons: (1) If you use the per-frame script method above, you also have to move the MD Movie slider to the far right to ensure a 1-to-1 relationship between trajectory frames and image update frames. If you have the slider somewhat to the left there will be more than one image update frame per trajectory frame and the fade-in and fade-out over 60 frames will occupy a smaller fraction of the trajectory. Yes, you could increase the transparency command frames number from 60 to something bigger, but hard to tell exactly how much bigger to make it. (2) The “coordset” command method has more control. You could choose to insert a pause between the two stages of the morph, for example to linger on the bound state for a while before starting the fade-out and morph to unbound state: trans 100,a :miv coordset #5 1,60; trans 0,a :miv frames 60; wait 60 wait 20 coordset #5 61,121; trans 100,a :miv frames 60; wait 60 I hope this helps, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
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