[Chimera-users] Display channel as a filled body in Chimera
Boaz Shaanan
bshaanan at bgu.ac.il
Fri Mar 23 06:57:20 PDT 2018
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 at bgu.ac.il
Phone: 972-8-647-2220
Fax: 972-8-647-2992 or 972-8-646-1710
________________________________________
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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 at sonic.net>
To: Priit Eek <priit.eek at gmail.com>
Cc: UCSF Chimera Mailing List <chimera-users at cgl.ucsf.edu>
Subject: Re: [Chimera-users] Surface picking
Message-ID: <EFAC0902-4CA7-4C28-8EB1-5166495B44C5 at 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 at 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 at 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 at gmail.com>
To: Tom Goddard <goddard at sonic.net>
Cc: UCSF Chimera Mailing List <chimera-users at cgl.ucsf.edu>
Subject: Re: [Chimera-users] Surface picking
Message-ID: <A1252D71-C057-4085-83B4-2DC06A198AC8 at 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 at 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 at 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 at 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 at sonic.net>
To: Priit Eek <priit.eek at gmail.com>
Cc: UCSF Chimera Mailing List <chimera-users at cgl.ucsf.edu>
Subject: Re: [Chimera-users] Surface picking
Message-ID: <AB507F91-8402-4939-8962-B91D8D457836 at 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 at 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 at 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 at 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 at cgl.ucsf.edu
>>> Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
>>>
>>
>
>
> _______________________________________________
> Chimera-users mailing list: Chimera-users at 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 at gmail.com>
To: Tom Goddard <goddard at sonic.net>
Cc: UCSF Chimera Mailing List <chimera-users at cgl.ucsf.edu>
Subject: Re: [Chimera-users] Surface picking
Message-ID: <D8228774-0335-4697-A2B5-4CDF453AF5B6 at 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 at 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 at 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 at 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 at 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 at cgl.ucsf.edu
>>>> Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
>>>>
>>>
>>
>>
>> _______________________________________________
>> Chimera-users mailing list: Chimera-users at 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 at sonic.net>
To: Priit Eek <priit.eek at gmail.com>
Cc: UCSF Chimera Mailing List <chimera-users at cgl.ucsf.edu>
Subject: Re: [Chimera-users] Surface picking
Message-ID: <5AB9B1A1-5920-4EF9-B2FD-EC66931D9670 at 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 at 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 at 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 at 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 at 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 at 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 at cgl.ucsf.edu
>>>>> Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
>>>>>
>>>>
>>>
>>>
>>> _______________________________________________
>>> Chimera-users mailing list: Chimera-users at cgl.ucsf.edu
>>> Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
>>>
>>
>
>
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> Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
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