precalculated void representation as surface
Hi, I have a precalculated cavity represented as a grid in the pdb format, where “atoms” are spaced by 0.3 A. What would be the option to visualize this as a surface? I can easily show it as point or spheres, but I cannot display it as surface. I appreciate your help, Karolina
Hi Karolina, It is very difficult to answer questions like this without having the input file or a more complete description of what you mean by “cannot” (looks bad? error message? if error message, what does it say??) So I can only make guesses. Maybe it is hard to specify the atoms... at least in my attempt to simulate the problem, even though the model was open as #1, command “surface #1” didn’t work and I had to use this command instead: surface #1@* (without any space between the model number and @*) If that fails to give a surface, another possibility is simulating a density map with “molmap” and then adjusting the isosurface of that density map, for example if you opened the fake PDB file as #3, a command something like: molmap #3@* 1.0 Then you will get the Volume Viewer dialog with a histogram and slider you can drag to adjust the isosurface level. The second number in the example command is an adjustable parameter and I do not know what value will work well with your file. You should try different numbers and also take a look at what other options are available with molmap. <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/molmap.html> 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 Jul 27, 2016, at 2:25 PM, Michalska, Karolina M. <kmichalska@anl.gov> wrote:
Hi,
I have a precalculated cavity represented as a grid in the pdb format, where “atoms” are spaced by 0.3 A. What would be the option to visualize this as a surface? I can easily show it as point or spheres, but I cannot display it as surface.
I appreciate your help, Karolina
Hi Elaine, Thanks a lot, molmap did the trick. With surface I¹m getting error 11, regardless how I specify the model/atoms. Before, I was trying to simply use MSMS surface (from the Action menu), but that would pick only a subset of points. Best, Karolina On 7/27/16, 5:32 PM, "Elaine Meng" <meng@cgl.ucsf.edu> wrote:
Hi Karolina, It is very difficult to answer questions like this without having the input file or a more complete description of what you mean by ³cannot² (looks bad? error message? if error message, what does it say??) So I can only make guesses.
Maybe it is hard to specify the atoms... at least in my attempt to simulate the problem, even though the model was open as #1, command ³surface #1² didn¹t work and I had to use this command instead:
surface #1@*
(without any space between the model number and @*)
If that fails to give a surface, another possibility is simulating a density map with ³molmap² and then adjusting the isosurface of that density map, for example if you opened the fake PDB file as #3, a command something like:
molmap #3@* 1.0
Then you will get the Volume Viewer dialog with a histogram and slider you can drag to adjust the isosurface level. The second number in the example command is an adjustable parameter and I do not know what value will work well with your file. You should try different numbers and also take a look at what other options are available with molmap. <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/molmap.html>
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 Jul 27, 2016, at 2:25 PM, Michalska, Karolina M. <kmichalska@anl.gov> wrote:
Hi,
I have a precalculated cavity represented as a grid in the pdb format, where ³atoms² are spaced by 0.3 A. What would be the option to visualize this as a surface? I can easily show it as point or spheres, but I cannot display it as surface.
I appreciate your help, Karolina
Hello, I have one more question related to the subject. I have currently removed all internal ³atoms² that describe my cavity, leaving only those on the surface as I want to illustrate the interior with the clipping. However, with that my surface has a certain thickness at the clipping plane. Is there a way I could control it? Thanks, Karolina On 7/27/16, 5:32 PM, "Elaine Meng" <meng@cgl.ucsf.edu> wrote:
Hi Karolina, It is very difficult to answer questions like this without having the input file or a more complete description of what you mean by ³cannot² (looks bad? error message? if error message, what does it say??) So I can only make guesses.
Maybe it is hard to specify the atoms... at least in my attempt to simulate the problem, even though the model was open as #1, command ³surface #1² didn¹t work and I had to use this command instead:
surface #1@*
(without any space between the model number and @*)
If that fails to give a surface, another possibility is simulating a density map with ³molmap² and then adjusting the isosurface of that density map, for example if you opened the fake PDB file as #3, a command something like:
molmap #3@* 1.0
Then you will get the Volume Viewer dialog with a histogram and slider you can drag to adjust the isosurface level. The second number in the example command is an adjustable parameter and I do not know what value will work well with your file. You should try different numbers and also take a look at what other options are available with molmap. <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/molmap.html>
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 Jul 27, 2016, at 2:25 PM, Michalska, Karolina M. <kmichalska@anl.gov> wrote:
Hi,
I have a precalculated cavity represented as a grid in the pdb format, where ³atoms² are spaced by 0.3 A. What would be the option to visualize this as a surface? I can easily show it as point or spheres, but I cannot display it as surface.
I appreciate your help, Karolina
Hi Karolina, If I understand correctly, you just want to show the “skin” of the pocket but then also what is on the inside. In that case, do you really need the void-volume atoms? Why not just show the surface of the protein and slice that surface with the clipping plane? See first attached image. However, if the protein is completely hidden and you just want the skin of the pocket, a second idea is to keep all the void-volume atoms for calculating the isosurface, but then also hide those fake atoms. When you slice the molmap isosurface, by default it looks solid because there is a “cap”. With Surface Capping (in menu under Tools… Depiction) you can just turn off the cap so that you just see the sliced skin of the pocket, and real atoms inside (if any). See second attached image. <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/per-model/per-model.html> In both cases, if you use a per-model clipping plane instead of the main (global) clipping planes, you can slice at any angle and only the surface, so atoms can stick out beyond the clipping plane. Per-Model Clipping is in the menu under Tools… Depiction. <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/per-model/per-model.html> 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 2, 2016, at 2:35 PM, Michalska, Karolina M. <kmichalska@anl.gov> wrote:
Hello,
I have one more question related to the subject. I have currently removed all internal ³atoms² that describe my cavity, leaving only those on the surface as I want to illustrate the interior with the clipping. However, with that my surface has a certain thickness at the clipping plane. Is there a way I could control it?
Thanks, Karolina
On 7/27/16, 5:32 PM, "Elaine Meng" <meng@cgl.ucsf.edu> wrote:
Hi Karolina, It is very difficult to answer questions like this without having the input file or a more complete description of what you mean by ³cannot² (looks bad? error message? if error message, what does it say??) So I can only make guesses.
Maybe it is hard to specify the atoms... at least in my attempt to simulate the problem, even though the model was open as #1, command ³surface #1² didn¹t work and I had to use this command instead:
surface #1@*
(without any space between the model number and @*)
If that fails to give a surface, another possibility is simulating a density map with ³molmap² and then adjusting the isosurface of that density map, for example if you opened the fake PDB file as #3, a command something like:
molmap #3@* 1.0
Then you will get the Volume Viewer dialog with a histogram and slider you can drag to adjust the isosurface level. The second number in the example command is an adjustable parameter and I do not know what value will work well with your file. You should try different numbers and also take a look at what other options are available with molmap. <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/molmap.html>
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 Jul 27, 2016, at 2:25 PM, Michalska, Karolina M. <kmichalska@anl.gov> wrote:
Hi,
I have a precalculated cavity represented as a grid in the pdb format, where ³atoms² are spaced by 0.3 A. What would be the option to visualize this as a surface? I can easily show it as point or spheres, but I cannot display it as surface.
I appreciate your help, Karolina
_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
On Aug 2, 2016, at 3:07 PM, Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hi Karolina, If I understand correctly, you just want to show the “skin” of the pocket but then also what is on the inside. In that case, do you really need the void-volume atoms? Why not just show the surface of the protein and slice that surface with the clipping plane? See first attached image.
However, if the protein is completely hidden and you just want the skin of the pocket, a second idea is to keep all the void-volume atoms for calculating the isosurface, but then also hide those fake atoms. When you slice the molmap isosurface, by default it looks solid because there is a “cap”. With Surface Capping (in menu under Tools… Depiction) you can just turn off the cap so that you just see the sliced skin of the pocket, and real atoms inside (if any). See second attached image. <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/per-model/per-model.html>
oops, the link above was supposed to be: <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/surfcapper/surfcapper.html>
In both cases, if you use a per-model clipping plane instead of the main (global) clipping planes, you can slice at any angle and only the surface, so atoms can stick out beyond the clipping plane. Per-Model Clipping is in the menu under Tools… Depiction. <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/per-model/per-model.html>
I hope this helps, Elaine
Hi Elaine, I did not want to use a surface as with individual pockets ( I have three) I have more control how I want to clip them. I also find such figures less complicated. My mistake was that I removed internal fake atoms from my pocket file so the surface was generated on both sides of the atoms. Consequently, without capping I’m getting two skins. The reason for the removal of these atoms is their number (up to 43000 per pocket) which I thought was the reason for program hanging. But that was happening with the surface command. With molmap it seems to be fine. Thanks, Karolina From: Elaine Meng <meng@cgl.ucsf.edu<mailto:meng@cgl.ucsf.edu>> Reply-To: "chimera-users@cgl.ucsf.edu<mailto:chimera-users@cgl.ucsf.edu> BB" <chimera-users@cgl.ucsf.edu<mailto:chimera-users@cgl.ucsf.edu>> Date: Tuesday, August 2, 2016 at 5:07 PM To: "Michalska, Karolina M." <kmichalska@anl.gov<mailto:kmichalska@anl.gov>> Cc: "chimera-users@cgl.ucsf.edu<mailto:chimera-users@cgl.ucsf.edu> BB" <chimera-users@cgl.ucsf.edu<mailto:chimera-users@cgl.ucsf.edu>> Subject: Re: [Chimera-users] precalculated void representation as surface Hi Karolina, If I understand correctly, you just want to show the “skin” of the pocket but then also what is on the inside. In that case, do you really need the void-volume atoms? Why not just show the surface of the protein and slice that surface with the clipping plane? See first attached image. However, if the protein is completely hidden and you just want the skin of the pocket, a second idea is to keep all the void-volume atoms for calculating the isosurface, but then also hide those fake atoms. When you slice the molmap isosurface, by default it looks solid because there is a “cap”. With Surface Capping (in menu under Tools… Depiction) you can just turn off the cap so that you just see the sliced skin of the pocket, and real atoms inside (if any). See second attached image. <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/per-model/per-model.html> In both cases, if you use a per-model clipping plane instead of the main (global) clipping planes, you can slice at any angle and only the surface, so atoms can stick out beyond the clipping plane. Per-Model Clipping is in the menu under Tools… Depiction. <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/per-model/per-model.html> 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 [cid:4CAA29BF-20BA-4535-B454-83FE044395DA@gateway.sonic.net] [cid:1400A970-09CA-4B92-BB12-9ECA27B9A149@gateway.sonic.net] On Aug 2, 2016, at 2:35 PM, Michalska, Karolina M. <kmichalska@anl.gov<mailto:kmichalska@anl.gov>> wrote: Hello, I have one more question related to the subject. I have currently removed all internal ³atoms² that describe my cavity, leaving only those on the surface as I want to illustrate the interior with the clipping. However, with that my surface has a certain thickness at the clipping plane. Is there a way I could control it? Thanks, Karolina On 7/27/16, 5:32 PM, "Elaine Meng" <meng@cgl.ucsf.edu<mailto:meng@cgl.ucsf.edu>> wrote: Hi Karolina, It is very difficult to answer questions like this without having the input file or a more complete description of what you mean by ³cannot² (looks bad? error message? if error message, what does it say??) So I can only make guesses. Maybe it is hard to specify the atoms... at least in my attempt to simulate the problem, even though the model was open as #1, command ³surface #1² didn¹t work and I had to use this command instead: surface #1@* (without any space between the model number and @*) If that fails to give a surface, another possibility is simulating a density map with ³molmap² and then adjusting the isosurface of that density map, for example if you opened the fake PDB file as #3, a command something like: molmap #3@* 1.0 Then you will get the Volume Viewer dialog with a histogram and slider you can drag to adjust the isosurface level. The second number in the example command is an adjustable parameter and I do not know what value will work well with your file. You should try different numbers and also take a look at what other options are available with molmap. <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/molmap.html> 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 Jul 27, 2016, at 2:25 PM, Michalska, Karolina M. <kmichalska@anl.gov<mailto:kmichalska@anl.gov>> wrote: Hi, I have a precalculated cavity represented as a grid in the pdb format, where ³atoms² are spaced by 0.3 A. What would be the option to visualize this as a surface? I can easily show it as point or spheres, but I cannot display it as surface. I appreciate your help, Karolina _______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu<mailto:Chimera-users@cgl.ucsf.edu> Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
participants (2)
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Elaine Meng -
Michalska, Karolina M.