Display channel as a filled body in Chimera
Hi, Is there a way to display in Chimera a channel identified by CastP as a filled body rather than engulfed by a surface? Thanks, Boaz Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel E-mail: bshaanan@bgu.ac.il Phone: 972-8-647-2220 Fax: 972-8-647-2992 or 972-8-646-1710 ________________________________________ From: Chimera-users <chimera-users-bounces@cgl.ucsf.edu> on behalf of chimera-users-request@cgl.ucsf.edu <chimera-users-request@cgl.ucsf.edu> Sent: Thursday, March 15, 2018 8:41 PM To: chimera-users@cgl.ucsf.edu Subject: Chimera-users Digest, Vol 179, Issue 6 Send Chimera-users mailing list submissions to chimera-users@cgl.ucsf.edu To subscribe or unsubscribe via the World Wide Web, visit http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users or, via email, send a message with subject or body 'help' to chimera-users-request@cgl.ucsf.edu You can reach the person managing the list at chimera-users-owner@cgl.ucsf.edu When replying, please edit your Subject line so it is more specific than "Re: Contents of Chimera-users digest..." Today's Topics: 1. Re: Surface picking (Tom Goddard) 2. Re: Surface picking (Priit Eek) 3. Re: Surface picking (Tom Goddard) 4. Re: Surface picking (Priit Eek) 5. Re: Surface picking (Tom Goddard) ---------------------------------------------------------------------- Message: 1 Date: Thu, 15 Mar 2018 10:34:40 -0700 From: Tom Goddard <goddard@sonic.net> To: Priit Eek <priit.eek@gmail.com> Cc: UCSF Chimera Mailing List <chimera-users@cgl.ucsf.edu> Subject: Re: [Chimera-users] Surface picking Message-ID: <EFAC0902-4CA7-4C28-8EB1-5166495B44C5@sonic.net> Content-Type: text/plain; charset=utf-8 Hi Prit, I can select the split surface pieces of an MSMS surface with ctrl-click using Chimera 1.12. Does ctrl-click work to select atoms, or the original unsplit surface? If not then it is probably a graphics driver problem, since some graphics capabilities are needed to know what object is under the mouse. Another possible graphics driver problem is the green outline is not shown ? but if you select something the magnifying glass icon in the lower right corner of the main Chimera window (select inspector) should turn green. Tom
On Mar 15, 2018, at 4:47 AM, Priit Eek <priit.eek@gmail.com> wrote:
Hi,
I am trying to visualize some specific inner cavities in a structure. I can display the MSMS surface and split it into pieces (accelerator Sc), but then I need to select the extra surfaces to hide/delete them (starting with the main outer surface). For some reason surface picking with mouse (Ctrl + left click) doesn?t work. I checked the surface attributes and ?selectable with mouse? was true.
I recall that this used to work some years ago, but not anymore. I am using the latest daily build (v1.13 build 41684) on macOS v10.12.6. Is this a bug or have some settings changed? I couldn?t find anything referring to this in the docs.
Best regards, Priit _______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
------------------------------ Message: 2 Date: Thu, 15 Mar 2018 20:06:04 +0200 From: Priit Eek <priit.eek@gmail.com> To: Tom Goddard <goddard@sonic.net> Cc: UCSF Chimera Mailing List <chimera-users@cgl.ucsf.edu> Subject: Re: [Chimera-users] Surface picking Message-ID: <A1252D71-C057-4085-83B4-2DC06A198AC8@gmail.com> Content-Type: text/plain; charset=utf-8 Elaine and Tom, Thank you for your replies. Selecting atoms and ribbons works as it should, but ctrl-clicking on surfaces has no effect whatsoever, be it before or after splitting. I could use Sc only because I selected the whole model using the command line. Splitting does work and I get a bunch of pieces, but I have no obvious way to select the distinct surfaces. Also, I?m afraid that using visiblePatches or any other method that involves selecting all residues that define the blobs would be extremely cumbersome in my case. As I said, if I ctrl-click on an atom or a ribbon, it gets selected, is highlighted in green, and the magnifying glass icon turns green as well. However, if I then ctrl-click on a surface, the selection is cleared (status bar displays ?selection cleared?). The graphics driver incompatibility actually seems a likely culprit. I think the previous time I used this feature, I was still on my old laptop. I am currently running Chimera on a 13-inch Early 2015 MacBook Pro (MacBookPro12,1). It has a built-in Intel Iris Graphics 6100 chipset. Could there be an easy hack/workaround on my side or a software patch? If not, then I guess I?ll go and finish that particular figure on another computer :) Cheers, Priit
On 15 Mar 2018, at 19:34, Tom Goddard <goddard@sonic.net> wrote:
Hi Prit,
I can select the split surface pieces of an MSMS surface with ctrl-click using Chimera 1.12. Does ctrl-click work to select atoms, or the original unsplit surface? If not then it is probably a graphics driver problem, since some graphics capabilities are needed to know what object is under the mouse. Another possible graphics driver problem is the green outline is not shown ? but if you select something the magnifying glass icon in the lower right corner of the main Chimera window (select inspector) should turn green.
Tom
On Mar 15, 2018, at 4:47 AM, Priit Eek <priit.eek@gmail.com> wrote:
Hi,
I am trying to visualize some specific inner cavities in a structure. I can display the MSMS surface and split it into pieces (accelerator Sc), but then I need to select the extra surfaces to hide/delete them (starting with the main outer surface). For some reason surface picking with mouse (Ctrl + left click) doesn?t work. I checked the surface attributes and ?selectable with mouse? was true.
I recall that this used to work some years ago, but not anymore. I am using the latest daily build (v1.13 build 41684) on macOS v10.12.6. Is this a bug or have some settings changed? I couldn?t find anything referring to this in the docs.
Best regards, Priit _______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
------------------------------ Message: 3 Date: Thu, 15 Mar 2018 11:13:14 -0700 From: Tom Goddard <goddard@sonic.net> To: Priit Eek <priit.eek@gmail.com> Cc: UCSF Chimera Mailing List <chimera-users@cgl.ucsf.edu> Subject: Re: [Chimera-users] Surface picking Message-ID: <AB507F91-8402-4939-8962-B91D8D457836@sonic.net> Content-Type: text/plain; charset=utf-8 Hi Prit, It seems like a graphics driver bug, but I haven?t seen this before where only surfaces cannot be selected. Did you try drag select ? that draws a rectangle and uses a different code path and maybe it would select the surface. If you use "molmap #0 5? to make a density map surface from molecule #0 can you select the resulting surface with ctrl-click? Are you showing your surface in mesh or some other unusual style? Tom
On Mar 15, 2018, at 11:06 AM, Priit Eek <priit.eek@gmail.com> wrote:
Elaine and Tom,
Thank you for your replies. Selecting atoms and ribbons works as it should, but ctrl-clicking on surfaces has no effect whatsoever, be it before or after splitting. I could use Sc only because I selected the whole model using the command line. Splitting does work and I get a bunch of pieces, but I have no obvious way to select the distinct surfaces. Also, I?m afraid that using visiblePatches or any other method that involves selecting all residues that define the blobs would be extremely cumbersome in my case. As I said, if I ctrl-click on an atom or a ribbon, it gets selected, is highlighted in green, and the magnifying glass icon turns green as well. However, if I then ctrl-click on a surface, the selection is cleared (status bar displays ?selection cleared?).
The graphics driver incompatibility actually seems a likely culprit. I think the previous time I used this feature, I was still on my old laptop. I am currently running Chimera on a 13-inch Early 2015 MacBook Pro (MacBookPro12,1). It has a built-in Intel Iris Graphics 6100 chipset. Could there be an easy hack/workaround on my side or a software patch? If not, then I guess I?ll go and finish that particular figure on another computer :)
Cheers, Priit
On 15 Mar 2018, at 19:34, Tom Goddard <goddard@sonic.net> wrote:
Hi Prit,
I can select the split surface pieces of an MSMS surface with ctrl-click using Chimera 1.12. Does ctrl-click work to select atoms, or the original unsplit surface? If not then it is probably a graphics driver problem, since some graphics capabilities are needed to know what object is under the mouse. Another possible graphics driver problem is the green outline is not shown ? but if you select something the magnifying glass icon in the lower right corner of the main Chimera window (select inspector) should turn green.
Tom
On Mar 15, 2018, at 4:47 AM, Priit Eek <priit.eek@gmail.com> wrote:
Hi,
I am trying to visualize some specific inner cavities in a structure. I can display the MSMS surface and split it into pieces (accelerator Sc), but then I need to select the extra surfaces to hide/delete them (starting with the main outer surface). For some reason surface picking with mouse (Ctrl + left click) doesn?t work. I checked the surface attributes and ?selectable with mouse? was true.
I recall that this used to work some years ago, but not anymore. I am using the latest daily build (v1.13 build 41684) on macOS v10.12.6. Is this a bug or have some settings changed? I couldn?t find anything referring to this in the docs.
Best regards, Priit _______________________________________________ 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
------------------------------ Message: 4 Date: Thu, 15 Mar 2018 20:27:15 +0200 From: Priit Eek <priit.eek@gmail.com> To: Tom Goddard <goddard@sonic.net> Cc: UCSF Chimera Mailing List <chimera-users@cgl.ucsf.edu> Subject: Re: [Chimera-users] Surface picking Message-ID: <D8228774-0335-4697-A2B5-4CDF453AF5B6@gmail.com> Content-Type: text/plain; charset=utf-8 Tom, Drag-selecting selects the atoms and ribbons, but not the MSMS surface, even if the atoms are behind the surface. However, I can select the molmap surface with both clicking and dragging. The MSMS surface is a solid. I haven?t done anything to surface display settings to my knowledge, so I should be using the default style. Priit
On 15 Mar 2018, at 20:13, Tom Goddard <goddard@sonic.net> wrote:
Hi Prit,
It seems like a graphics driver bug, but I haven?t seen this before where only surfaces cannot be selected. Did you try drag select ? that draws a rectangle and uses a different code path and maybe it would select the surface. If you use "molmap #0 5? to make a density map surface from molecule #0 can you select the resulting surface with ctrl-click? Are you showing your surface in mesh or some other unusual style?
Tom
On Mar 15, 2018, at 11:06 AM, Priit Eek <priit.eek@gmail.com> wrote:
Elaine and Tom,
Thank you for your replies. Selecting atoms and ribbons works as it should, but ctrl-clicking on surfaces has no effect whatsoever, be it before or after splitting. I could use Sc only because I selected the whole model using the command line. Splitting does work and I get a bunch of pieces, but I have no obvious way to select the distinct surfaces. Also, I?m afraid that using visiblePatches or any other method that involves selecting all residues that define the blobs would be extremely cumbersome in my case. As I said, if I ctrl-click on an atom or a ribbon, it gets selected, is highlighted in green, and the magnifying glass icon turns green as well. However, if I then ctrl-click on a surface, the selection is cleared (status bar displays ?selection cleared?).
The graphics driver incompatibility actually seems a likely culprit. I think the previous time I used this feature, I was still on my old laptop. I am currently running Chimera on a 13-inch Early 2015 MacBook Pro (MacBookPro12,1). It has a built-in Intel Iris Graphics 6100 chipset. Could there be an easy hack/workaround on my side or a software patch? If not, then I guess I?ll go and finish that particular figure on another computer :)
Cheers, Priit
On 15 Mar 2018, at 19:34, Tom Goddard <goddard@sonic.net> wrote:
Hi Prit,
I can select the split surface pieces of an MSMS surface with ctrl-click using Chimera 1.12. Does ctrl-click work to select atoms, or the original unsplit surface? If not then it is probably a graphics driver problem, since some graphics capabilities are needed to know what object is under the mouse. Another possible graphics driver problem is the green outline is not shown ? but if you select something the magnifying glass icon in the lower right corner of the main Chimera window (select inspector) should turn green.
Tom
On Mar 15, 2018, at 4:47 AM, Priit Eek <priit.eek@gmail.com> wrote:
Hi,
I am trying to visualize some specific inner cavities in a structure. I can display the MSMS surface and split it into pieces (accelerator Sc), but then I need to select the extra surfaces to hide/delete them (starting with the main outer surface). For some reason surface picking with mouse (Ctrl + left click) doesn?t work. I checked the surface attributes and ?selectable with mouse? was true.
I recall that this used to work some years ago, but not anymore. I am using the latest daily build (v1.13 build 41684) on macOS v10.12.6. Is this a bug or have some settings changed? I couldn?t find anything referring to this in the docs.
Best regards, Priit _______________________________________________ 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
------------------------------ Message: 5 Date: Thu, 15 Mar 2018 11:41:04 -0700 From: Tom Goddard <goddard@sonic.net> To: Priit Eek <priit.eek@gmail.com> Cc: UCSF Chimera Mailing List <chimera-users@cgl.ucsf.edu> Subject: Re: [Chimera-users] Surface picking Message-ID: <5AB9B1A1-5920-4EF9-B2FD-EC66931D9670@sonic.net> Content-Type: text/plain; charset=utf-8 Hi Priit, That is especially weird that MSMS surfaces cannot be selected by ctrl-click while the molmap surface can be selected. The problem is either your machine?s graphics driver or one other idea it could somehow be some setting in your preferences file. You might try quiting Chimera, renaming your Chimera preferences file ~/.chimera/preferences so Chimera does not find it, and restarting and see if that helps. Tom
On Mar 15, 2018, at 11:27 AM, Priit Eek <priit.eek@gmail.com> wrote:
Tom,
Drag-selecting selects the atoms and ribbons, but not the MSMS surface, even if the atoms are behind the surface. However, I can select the molmap surface with both clicking and dragging. The MSMS surface is a solid. I haven?t done anything to surface display settings to my knowledge, so I should be using the default style.
Priit
On 15 Mar 2018, at 20:13, Tom Goddard <goddard@sonic.net> wrote:
Hi Prit,
It seems like a graphics driver bug, but I haven?t seen this before where only surfaces cannot be selected. Did you try drag select ? that draws a rectangle and uses a different code path and maybe it would select the surface. If you use "molmap #0 5? to make a density map surface from molecule #0 can you select the resulting surface with ctrl-click? Are you showing your surface in mesh or some other unusual style?
Tom
On Mar 15, 2018, at 11:06 AM, Priit Eek <priit.eek@gmail.com> wrote:
Elaine and Tom,
Thank you for your replies. Selecting atoms and ribbons works as it should, but ctrl-clicking on surfaces has no effect whatsoever, be it before or after splitting. I could use Sc only because I selected the whole model using the command line. Splitting does work and I get a bunch of pieces, but I have no obvious way to select the distinct surfaces. Also, I?m afraid that using visiblePatches or any other method that involves selecting all residues that define the blobs would be extremely cumbersome in my case. As I said, if I ctrl-click on an atom or a ribbon, it gets selected, is highlighted in green, and the magnifying glass icon turns green as well. However, if I then ctrl-click on a surface, the selection is cleared (status bar displays ?selection cleared?).
The graphics driver incompatibility actually seems a likely culprit. I think the previous time I used this feature, I was still on my old laptop. I am currently running Chimera on a 13-inch Early 2015 MacBook Pro (MacBookPro12,1). It has a built-in Intel Iris Graphics 6100 chipset. Could there be an easy hack/workaround on my side or a software patch? If not, then I guess I?ll go and finish that particular figure on another computer :)
Cheers, Priit
On 15 Mar 2018, at 19:34, Tom Goddard <goddard@sonic.net> wrote:
Hi Prit,
I can select the split surface pieces of an MSMS surface with ctrl-click using Chimera 1.12. Does ctrl-click work to select atoms, or the original unsplit surface? If not then it is probably a graphics driver problem, since some graphics capabilities are needed to know what object is under the mouse. Another possible graphics driver problem is the green outline is not shown ? but if you select something the magnifying glass icon in the lower right corner of the main Chimera window (select inspector) should turn green.
Tom
On Mar 15, 2018, at 4:47 AM, Priit Eek <priit.eek@gmail.com> wrote:
Hi,
I am trying to visualize some specific inner cavities in a structure. I can display the MSMS surface and split it into pieces (accelerator Sc), but then I need to select the extra surfaces to hide/delete them (starting with the main outer surface). For some reason surface picking with mouse (Ctrl + left click) doesn?t work. I checked the surface attributes and ?selectable with mouse? was true.
I recall that this used to work some years ago, but not anymore. I am using the latest daily build (v1.13 build 41684) on macOS v10.12.6. Is this a bug or have some settings changed? I couldn?t find anything referring to this in the docs.
Best regards, Priit _______________________________________________ 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
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------------------------------ Subject: Digest Footer _______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users ------------------------------ End of Chimera-users Digest, Vol 179, Issue 6 *********************************************
Hi Boaz, The CastP tool just takes the atoms listed as lining the pocket and then shows their molecular surface patches, so what you get may not be a closed surface unless the molecular surface of those atoms really does form an enclosed bubble. For approaches to get an enclosed surface even when the molecular surface does not form an enclosed bubble, please see the last part of this previous post: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/2015-May/010993.html> It mentions (A) Surfnet tool in Chimera (B) VVV website to calculate a map filling the space. Unfortunately showing a cavity blob in Chimera is not as convenient as using HOLE, HOLLOW, CAVER etc. with Pymol since those tools have Pymol plugins. In this previous post, Oliver Clarke provided a script for visualizing HOLE results in Chimera: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/2015-August/011373.html> … see also <http://plato.cgl.ucsf.edu/pipermail/chimera-users/2015-August/011375.html> Yet another possibility outside of Chimera is MolAxis. At least when I used it a long time ago, it took only minor editing to display in Chimera, as described for this entry in the Image Gallery: <http://www.rbvi.ucsf.edu/chimera/ImageGallery/entries/cavities/cavities.html> MolAxis server: <http://bioinfo3d.cs.tau.ac.il/MolAxis/> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Mar 23, 2018, at 6:57 AM, Boaz Shaanan <bshaanan@bgu.ac.il> wrote:
Hi, Is there a way to display in Chimera a channel identified by CastP as a filled body rather than engulfed by a surface? Thanks, Boaz
Hi Elaine, Your advice about displaying a channel as a filled body was very useful. Using HOLE and Oliver's script I managed to get a satisfactory display of a channel. Now I'd like to do two things using surfcat (if I got right the purpose of this command): 1) The channel display I have is a bunch of little balls that can be treated as atoms. I can select them but can I tell surfcat about this selection? How? I hope to then be able to cover them by a surface or is that too much to ask? 2) I select protein atoms in contact with the channel (using zone) which I'd like to display as a surface. Again, how can I tell surfcat about the selection? Or have I totally misunderstood the surfcat command action? Thanks, Boaz Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel E-mail: bshaanan@bgu.ac.il Phone: 972-8-647-2220 Fax: 972-8-647-2992 or 972-8-646-1710 ________________________________________ From: Elaine Meng <meng@cgl.ucsf.edu> Sent: Friday, March 23, 2018 7:20 PM To: בעז שאנן Cc: chimera-users@cgl.ucsf.edu Subject: Re: [Chimera-users] Display channel as a filled body in Chimera Hi Boaz, The CastP tool just takes the atoms listed as lining the pocket and then shows their molecular surface patches, so what you get may not be a closed surface unless the molecular surface of those atoms really does form an enclosed bubble. For approaches to get an enclosed surface even when the molecular surface does not form an enclosed bubble, please see the last part of this previous post: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/2015-May/010993.html> It mentions (A) Surfnet tool in Chimera (B) VVV website to calculate a map filling the space. Unfortunately showing a cavity blob in Chimera is not as convenient as using HOLE, HOLLOW, CAVER etc. with Pymol since those tools have Pymol plugins. In this previous post, Oliver Clarke provided a script for visualizing HOLE results in Chimera: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/2015-August/011373.html> … see also <http://plato.cgl.ucsf.edu/pipermail/chimera-users/2015-August/011375.html> Yet another possibility outside of Chimera is MolAxis. At least when I used it a long time ago, it took only minor editing to display in Chimera, as described for this entry in the Image Gallery: <http://www.rbvi.ucsf.edu/chimera/ImageGallery/entries/cavities/cavities.html> MolAxis server: <http://bioinfo3d.cs.tau.ac.il/MolAxis/> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Mar 23, 2018, at 6:57 AM, Boaz Shaanan <bshaanan@bgu.ac.il> wrote:
Hi, Is there a way to display in Chimera a channel identified by CastP as a filled body rather than engulfed by a surface? Thanks, Boaz
Hi Boaz, Glad you made some headway. surfcat command specifies groups of atoms to enclose in a surface, e.g. myglobin could be enclosed without the heme, or myoglobin + heme could be enclosed in one “blob” together. It does not specify which atoms’ surface is shown, only how they are grouped for surface-calculation purposes. Surfcat categories are mutually exclusive (an atom only belongs to one category), and most people just use the ones calculated automatically, without using the surfcat command explicitly. <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/msms.html> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/surface.html#surfcats> surface command specifies which atoms’ surface patches are shown, after the surface is calculated enclosing the set of atoms in a surface category Both commands can take “sel” as an atomspec, meaning the currently selected atoms. I haven’t tried this with HOLE plus Oliver’s script, so can’t be absolutely certain how it would turn out, but “in theory” it sounds reasonable. E.g. I have no idea what radii the dots are assigned, you may have to fiddle with that using the vdwdef command.s <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/vdwdefine.html> Another possibility is to just use “molmap” command (simulate density for those atoms, show isosurface that can be adjusted in Volume Viewer). <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/molmap.html> Best Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Mar 27, 2018, at 1:45 PM, Boaz Shaanan <bshaanan@bgu.ac.il> wrote:
Hi Elaine,
Your advice about displaying a channel as a filled body was very useful. Using HOLE and Oliver's script I managed to get a satisfactory display of a channel. Now I'd like to do two things using surfcat (if I got right the purpose of this command): 1) The channel display I have is a bunch of little balls that can be treated as atoms. I can select them but can I tell surfcat about this selection? How? I hope to then be able to cover them by a surface or is that too much to ask?
2) I select protein atoms in contact with the channel (using zone) which I'd like to display as a surface. Again, how can I tell surfcat about the selection?
Or have I totally misunderstood the surfcat command action?
Thanks,
Boaz
________________________________________ From: Elaine Meng <meng@cgl.ucsf.edu> Sent: Friday, March 23, 2018 7:20 PM To: בעז שאנן Cc: chimera-users@cgl.ucsf.edu Subject: Re: [Chimera-users] Display channel as a filled body in Chimera
Hi Boaz, The CastP tool just takes the atoms listed as lining the pocket and then shows their molecular surface patches, so what you get may not be a closed surface unless the molecular surface of those atoms really does form an enclosed bubble.
For approaches to get an enclosed surface even when the molecular surface does not form an enclosed bubble, please see the last part of this previous post: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/2015-May/010993.html>
It mentions (A) Surfnet tool in Chimera (B) VVV website to calculate a map filling the space.
Unfortunately showing a cavity blob in Chimera is not as convenient as using HOLE, HOLLOW, CAVER etc. with Pymol since those tools have Pymol plugins. In this previous post, Oliver Clarke provided a script for visualizing HOLE results in Chimera: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/2015-August/011373.html> … see also <http://plato.cgl.ucsf.edu/pipermail/chimera-users/2015-August/011375.html>
Yet another possibility outside of Chimera is MolAxis. At least when I used it a long time ago, it took only minor editing to display in Chimera, as described for this entry in the Image Gallery: <http://www.rbvi.ucsf.edu/chimera/ImageGallery/entries/cavities/cavities.html>
MolAxis server: <http://bioinfo3d.cs.tau.ac.il/MolAxis/>
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Mar 23, 2018, at 6:57 AM, Boaz Shaanan <bshaanan@bgu.ac.il> wrote:
Hi, Is there a way to display in Chimera a channel identified by CastP as a filled body rather than engulfed by a surface? Thanks, Boaz
Hi Elaine, As usual, wonderful suggestions. I'll try them. As for the radii of these balls in the channel from HOLE, I can change those after selecting them using the little green square on bottom right. Again, thanks a lot for your help. Boaz Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel E-mail: bshaanan@bgu.ac.il Phone: 972-8-647-2220 Fax: 972-8-647-2992 or 972-8-646-1710 ________________________________________ From: Elaine Meng <meng@cgl.ucsf.edu> Sent: Wednesday, March 28, 2018 12:22 AM To: בעז שאנן Cc: chimera-users@cgl.ucsf.edu Mailing List Subject: Re: [Chimera-users] Display channel as a filled body in Chimera Hi Boaz, Glad you made some headway. surfcat command specifies groups of atoms to enclose in a surface, e.g. myglobin could be enclosed without the heme, or myoglobin + heme could be enclosed in one “blob” together. It does not specify which atoms’ surface is shown, only how they are grouped for surface-calculation purposes. Surfcat categories are mutually exclusive (an atom only belongs to one category), and most people just use the ones calculated automatically, without using the surfcat command explicitly. <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/msms.html> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/surface.html#surfcats> surface command specifies which atoms’ surface patches are shown, after the surface is calculated enclosing the set of atoms in a surface category Both commands can take “sel” as an atomspec, meaning the currently selected atoms. I haven’t tried this with HOLE plus Oliver’s script, so can’t be absolutely certain how it would turn out, but “in theory” it sounds reasonable. E.g. I have no idea what radii the dots are assigned, you may have to fiddle with that using the vdwdef command.s <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/vdwdefine.html> Another possibility is to just use “molmap” command (simulate density for those atoms, show isosurface that can be adjusted in Volume Viewer). <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/molmap.html> Best Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Mar 27, 2018, at 1:45 PM, Boaz Shaanan <bshaanan@bgu.ac.il> wrote:
Hi Elaine,
Your advice about displaying a channel as a filled body was very useful. Using HOLE and Oliver's script I managed to get a satisfactory display of a channel. Now I'd like to do two things using surfcat (if I got right the purpose of this command): 1) The channel display I have is a bunch of little balls that can be treated as atoms. I can select them but can I tell surfcat about this selection? How? I hope to then be able to cover them by a surface or is that too much to ask?
2) I select protein atoms in contact with the channel (using zone) which I'd like to display as a surface. Again, how can I tell surfcat about the selection?
Or have I totally misunderstood the surfcat command action?
Thanks,
Boaz
________________________________________ From: Elaine Meng <meng@cgl.ucsf.edu> Sent: Friday, March 23, 2018 7:20 PM To: בעז שאנן Cc: chimera-users@cgl.ucsf.edu Subject: Re: [Chimera-users] Display channel as a filled body in Chimera
Hi Boaz, The CastP tool just takes the atoms listed as lining the pocket and then shows their molecular surface patches, so what you get may not be a closed surface unless the molecular surface of those atoms really does form an enclosed bubble.
For approaches to get an enclosed surface even when the molecular surface does not form an enclosed bubble, please see the last part of this previous post: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/2015-May/010993.html>
It mentions (A) Surfnet tool in Chimera (B) VVV website to calculate a map filling the space.
Unfortunately showing a cavity blob in Chimera is not as convenient as using HOLE, HOLLOW, CAVER etc. with Pymol since those tools have Pymol plugins. In this previous post, Oliver Clarke provided a script for visualizing HOLE results in Chimera: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/2015-August/011373.html> … see also <http://plato.cgl.ucsf.edu/pipermail/chimera-users/2015-August/011375.html>
Yet another possibility outside of Chimera is MolAxis. At least when I used it a long time ago, it took only minor editing to display in Chimera, as described for this entry in the Image Gallery: <http://www.rbvi.ucsf.edu/chimera/ImageGallery/entries/cavities/cavities.html>
MolAxis server: <http://bioinfo3d.cs.tau.ac.il/MolAxis/>
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Mar 23, 2018, at 6:57 AM, Boaz Shaanan <bshaanan@bgu.ac.il> wrote:
Hi, Is there a way to display in Chimera a channel identified by CastP as a filled body rather than engulfed by a surface? Thanks, Boaz
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Elaine Meng