selection of different part of the protein through the sequence prompt
Hi guys, I'd like to select two precise beta strands of my prot and I thought it would be easier to do so from the sequence editor. Unfortunately, I can't find a way to select different parts of the same protein in the sequence editor; I alwys select the full length between first and last selected residues whatever combo I use (shift, ctrl and so on). Is it possible to do this in the sequence editor? Cheers, JD Dr. Jean-Didier Maréchal Professor Lector Unitat de Química Física Departament de Química Universitat Autònoma de Barcelona Edifici C.n. 08193 Cerdanyola (Barcelona) Tel: +34.935814936 e-mail: JeanDidier.Marechal@uab.es ----- Missatge original ----- De: chimera-users-request@cgl.ucsf.edu Data: Dimecres, Febrer 13, 2008 9:00 pm Assumpte: Chimera-users Digest, Vol 58, Issue 15
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Today's Topics:
1. Split into models (Sadler, Evan) 2. Re: Split into models (Elaine Meng) 3. Opaque volume planes (Tom Goddard) 4. Re: Opaque volume planes (William Jeffrey Triffo) 5. Re: Opaque volume planes (Tom Goddard)
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Message: 1 Date: Tue, 12 Feb 2008 17:51:30 -0600 From: "Sadler, Evan" <ESADLER@dom.wustl.edu> Subject: [Chimera-users] Split into models To: "chimera-users@cgl.ucsf.edu" <chimera-users@cgl.ucsf.edu> Message-ID: <C3D78D22.18B15%esadler@dom.wustl.edu> Content-Type: text/plain; charset="iso-8859-1"
Recent email address change caused the first try to bounce, so I resent it.
I've loaded a file (2rjp.pdb) with 4 chains and want to split it into 4 models so I can align them. But "split" returns:
unrecognized command: "split"
What am I doing wrong?
Evan
-- J. Evan Sadler, M.D., Ph.D. Howard Hughes Medical Institute Washington University 660 S. Euclid Ave., Box 8022 St. Louis, MO 63110 Tel: 314-362-9067 FAX: 314-454-3012 email: esadler@im.wustl.edu
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Message: 2 Date: Tue, 12 Feb 2008 16:09:22 -0800 From: Elaine Meng <meng@cgl.ucsf.edu> Subject: Re: [Chimera-users] Split into models To: "Sadler, Evan" <ESADLER@dom.wustl.edu> Cc: chimera BB <chimera-users@cgl.ucsf.edu> Message-ID: <84C5F9DD-BED6-4476-B29C-F39C322D4BEB@cgl.ucsf.edu> Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed
Hi Evan, You must be using a version of Chimera older than the "split" command. If you use the documentation that came with your download
(opened from the Help menu) it should be fairly synchronized with your software and you won't get confused by features you don't have! However, in this case, just get a newer version.
The pages at our web site under http://www.cgl.ucsf.edu/chimera/ docs/UsersGuide/
are "development documentation," which I am constantly changing as Chimera changes. It will generally have newer things than your downloaded software.
The pages under http://www.cgl.ucsf.edu/chimera/current/docs/ UsersGuide/
are documentation for the most recent production release (currently
Nov 2007) and I see it also lists "split". So to use that feature you can get that production release: http://www.cgl.ucsf.edu/chimera/download.html#production
There are also much newer "daily builds" although they are essentially untested and exist mainly to provide access to the very
latest developments. http://www.cgl.ucsf.edu/chimera/download.html#production
I just tried your structure in the production release and last night's daily build; "split" worked in both, so you should be all set! Elaine ----- Elaine C. Meng, Ph.D. meng@cgl.ucsf.edu UCSF Computer Graphics Lab and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html
On Feb 12, 2008, at 3:51 PM, Sadler, Evan wrote:
Recent email address change caused the first try to bounce, so I resent it.
I've loaded a file (2rjp.pdb) with 4 chains and want to split it into 4 models so I can align them. But "split" returns:
unrecognized command: "split"
What am I doing wrong?
Evan
-- J. Evan Sadler, M.D., Ph.D. Howard Hughes Medical Institute Washington University 660 S. Euclid Ave., Box 8022 St. Louis, MO 63110 Tel: 314-362-9067 FAX: 314-454-3012 email: esadler@im.wustl.edu
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Message: 3 Date: Tue, 12 Feb 2008 17:41:06 -0800 From: Tom Goddard <goddard@cgl.ucsf.edu> Subject: [Chimera-users] Opaque volume planes To: William Jeffrey Triffo <triffo@rice.edu>, "'Chimera BB'" <chimera-users@cgl.ucsf.edu> Message-ID: <47B24AB2.3060501@cgl.ucsf.edu> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
Hi Jeff,
The trouble obtaining opaque volume planes is not related to volume plane display being built into the volume dialog. It is related to a change I made in how transparency is handled in solid mode back in Aug 2007.
Today I changed transparency in "solid" style volume rendering so it is easier to obtain completely opaque data planes. In tonight's builds (if they succeed, may not since we are switching to Python 2.5 today) you can obtain completely opaque volume planes by using the "Brightness and Transparency" panel of the volume dialog to set transparency to 0. This transparency value represents the fraction (0-1) of the depth of the volume required to produce opacity to the degree indicated by the height of the yellow curve on the histogram. In other words it modulates the overall transparency. But until today it was arbitrarily deciding not to modulate the transparency if this depth was less than one grid spacing. This meaning of the transparency factor was introduced in August 2007, and prior to that the transparency factor just scaled the opacity given by the yellow curve.
Tom
Jeff wrote:
hi Tom,
in the older (plug-in) volume planes tool, I was able to generate images that were opaque planes. I don't seem to be able to do this anymore, even with transparency = 0. is there a way for me to do this in the current Chimera?
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Message: 4 Date: Tue, 12 Feb 2008 17:47:37 -0800 From: William Jeffrey Triffo <triffo@rice.edu> Subject: Re: [Chimera-users] Opaque volume planes To: "'Chimera BB'" <chimera-users@cgl.ucsf.edu> Message-ID: <47B24C39.10306@rice.edu> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
thanks,
do you know when tonight's builds will go through, I will test it at that point to see if the functionality made it in
-Jeff
Tom Goddard wrote:
Hi Jeff,
The trouble obtaining opaque volume planes is not related to volume plane display being built into the volume dialog. It is related to a change I made in how transparency is handled in solid mode back in Aug 2007.
Today I changed transparency in "solid" style volume rendering so it is easier to obtain completely opaque data planes. In tonight's builds (if they succeed, may not since we are switching to Python 2.5 today) you can obtain completely opaque volume planes by using the "Brightness and Transparency" panel of the volume dialog to set transparency to 0. This transparency value represents the fraction (0-1) of the depth of the volume required to produce opacity to the degree indicated by the height of the yellow curve on the histogram. In other words it modulates the overall transparency. But until today it was arbitrarily deciding not to modulate the transparency if this depth was less than one grid spacing. This meaning of the transparency factor was introduced in August 2007, and prior to that the transparency factor just scaled the opacity given by the yellow curve.
Tom
Jeff wrote:
hi Tom,
in the older (plug-in) volume planes tool, I was able to generate images that were opaque planes. I don't seem to be able to do this anymore, even with transparency = 0. is there a way for me to do this in the current Chimera?
-- ------------------------------------------------------------- Jeff Triffo Auer Group, Donner Lab, Lawrence Berkeley National Laboratory Raphael Group, Bioengineering Department, Rice University Medical Scientist Training Program (MSTP), Baylor College of Medicine phone (Berkeley): 510-486-7940 fax (Berkeley): 510-486-6488
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Message: 5 Date: Tue, 12 Feb 2008 18:10:01 -0800 From: Tom Goddard <goddard@cgl.ucsf.edu> Subject: Re: [Chimera-users] Opaque volume planes To: William Jeffrey Triffo <triffo@rice.edu> Cc: 'Chimera BB' <chimera-users@cgl.ucsf.edu> Message-ID: <47B25179.5050005@cgl.ucsf.edu> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
The Chimera nightly builds usually run around 9 pm pacific standard time (california). The nightly build download web page has the date for each build, and that will not be updated if code checked in during the day does not compile. Code changes checked in before about 8 pm makes it into that night's build.
http://www.cgl.ucsf.edu/chimera/alpha-downloads.html
Tom
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End of Chimera-users Digest, Vol 58, Issue 15 *********************************************
On Feb 16, 2008, at 1:10 AM, Jean Didier Pie Marechal wrote:
Hi guys, I'd like to select two precise beta strands of my prot and I thought it would be easier to do so from the sequence editor. Unfortunately, I can't find a way to select different parts of the same protein in the sequence editor; I alwys select the full length between first and last selected residues whatever combo I use (shift, ctrl and so on). Is it possible to do this in the sequence editor? Cheers, JD
Hi JD, Yes, if you change the selection mode to "append" (in the main menu: Select... Selection Mode... append). Then in the Sequence panel, each segment you drag out adds to the existing selection, so eventually you can have multiple segments selected. The highlighting in sequence blinks off while you are dragging a new segment, but when you let up, they will all be selected. You probably want to turn the selection mode back to the default "replace" afterward to avoid confusion. As a command-line person, I'd probably instead just mouse over the sequence to find out the sequence numbers and then use the numbers in various commands (which could include selecting them: select : 32-38,44-50) However, there are many different ways to accomplish the same result in Chimera, so use the one that you like! I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. meng@cgl.ucsf.edu UCSF Computer Graphics Lab and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html
participants (2)
-
Elaine Meng -
Jean Didier Pie Marechal