[Chimera-users] selection of different part of the protein through the sequence prompt
Jean Didier Pie Marechal
JeanDidier.Marechal at uab.cat
Sat Feb 16 01:10:33 PST 2008
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 at uab.es
----- Missatge original -----
De: chimera-users-request at 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)
>
>
> --------------------------------------------------------------------
> --
>
> Message: 1
> Date: Tue, 12 Feb 2008 17:51:30 -0600
> From: "Sadler, Evan" <ESADLER at dom.wustl.edu>
> Subject: [Chimera-users] Split into models
> To: "chimera-users at cgl.ucsf.edu" <chimera-users at cgl.ucsf.edu>
> Message-ID: <C3D78D22.18B15%esadler at 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 at im.wustl.edu
>
>
>
>
> ------------------------------
>
> Message: 2
> Date: Tue, 12 Feb 2008 16:09:22 -0800
> From: Elaine Meng <meng at cgl.ucsf.edu>
> Subject: Re: [Chimera-users] Split into models
> To: "Sadler, Evan" <ESADLER at dom.wustl.edu>
> Cc: chimera BB <chimera-users at cgl.ucsf.edu>
> Message-ID: <84C5F9DD-BED6-4476-B29C-F39C322D4BEB at 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 at 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 at im.wustl.edu
> >
> >
> > _______________________________________________
> > Chimera-users mailing list
> > Chimera-users at cgl.ucsf.edu
> > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users
>
>
>
> ------------------------------
>
> Message: 3
> Date: Tue, 12 Feb 2008 17:41:06 -0800
> From: Tom Goddard <goddard at cgl.ucsf.edu>
> Subject: [Chimera-users] Opaque volume planes
> To: William Jeffrey Triffo <triffo at rice.edu>, "'Chimera BB'"
> <chimera-users at cgl.ucsf.edu>
> Message-ID: <47B24AB2.3060501 at 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?
>
>
>
> ------------------------------
>
> Message: 4
> Date: Tue, 12 Feb 2008 17:47:37 -0800
> From: William Jeffrey Triffo <triffo at rice.edu>
> Subject: Re: [Chimera-users] Opaque volume planes
> To: "'Chimera BB'" <chimera-users at cgl.ucsf.edu>
> Message-ID: <47B24C39.10306 at 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
>
>
>
> ------------------------------
>
> Message: 5
> Date: Tue, 12 Feb 2008 18:10:01 -0800
> From: Tom Goddard <goddard at cgl.ucsf.edu>
> Subject: Re: [Chimera-users] Opaque volume planes
> To: William Jeffrey Triffo <triffo at rice.edu>
> Cc: 'Chimera BB' <chimera-users at cgl.ucsf.edu>
> Message-ID: <47B25179.5050005 at 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
>
>
>
> ------------------------------
>
> _______________________________________________
> Chimera-users mailing list
> Chimera-users at cgl.ucsf.edu
> http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users
>
>
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