[Chimera-users] Chimera-users Digest, Vol 84, Issue 12
Chinthaka Silva
chinthaka.silva at gmail.com
Tue Apr 13 11:40:32 PDT 2010
Hi,
Is there a way to quantify the electron densities in a unit cell with UCSF?
Thanks,
Chinthaka.
On Tue, Apr 13, 2010 at 2:08 PM, <chimera-users-request at cgl.ucsf.edu> wrote:
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> Today's Topics:
>
> 1. install (Jay Brown)
> 2. Re: Analysis of dihedral angles (Eric Pettersen)
> 3. Re: Analysis of dihedral angles (sette at uniroma2.it)
> 4. Re: Analysis of dihedral angles (Elaine Meng)
> 5. Re: Analysis of dihedral angles (Eric Pettersen)
> 6. Re: Display a spider volume data in a specific orientation
> (Tom Goddard)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Mon, 12 Apr 2010 16:13:27 -0400
> From: "Jay Brown" <jcb2g at virginia.edu>
> To: <chimera-users at cgl.ucsf.edu>
> Subject: [Chimera-users] install
> Message-ID: <009501cada7c$9ccfe2b0$d66fa810$@edu>
> Content-Type: text/plain; charset="us-ascii"
>
> Dear Chimera-Users:
>
> I am trying to install Chimera on a Linux Fedora 12 computer. Download goes
> OK, but when I try to install the program I get an error message saying:
> bad
> ELF interpreter: No such file or directory
>
> Do you know what this means? I can't find anything about ELF interpreter.
>
> -Jay Brown
>
>
>
> Jay C. Brown
>
> Department of Microbiology
>
> University of Virginia School of Medicine
>
> 1300 Jefferson Park Ave.
>
> Charlottesville, VA 22908
>
>
>
> Email: Jcb2g at virginia.edu
>
> Phone: 434-924-1814
>
> http://people.virginia.edu/~jcb2g/index.htm
>
>
>
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> ------------------------------
>
> Message: 2
> Date: Mon, 12 Apr 2010 17:26:01 -0700
> From: Eric Pettersen <pett at cgl.ucsf.edu>
> To: eduardo.troche at uvigo.es
> Cc: chimera-users at cgl.ucsf.edu
> Subject: Re: [Chimera-users] Analysis of dihedral angles
> Message-ID: <7B28F8D4-11F4-4AFE-ABC9-8F93A5770C7D at cgl.ucsf.edu>
> Content-Type: text/plain; charset="us-ascii"; Format="flowed";
> DelSp="yes"
>
> On Apr 12, 2010, at 9:12 AM, eduardo.troche at uvigo.es wrote:
>
> > Hi all,
> >
> > I'm a new Chimera user. I'm performing some molecular dynamics with
> > a more or less simple system with Amber,and now that I have them
> > done, I would like to analyze some specific data,like changes in a
> > dihedral angle during the dynamic process, or distances between
> > pairs of atoms. If I select several dihedral angles in Chimera and I
> > play the dynamic movie, I can see these changes, but is it possible
> > to get a table of results that shows the value of this angle for
> > each step of the dynamic process?
>
> Hi Eduardo,
> You can get this information by defining some actions to perform at
> each frame. To do this use MD Movie's Per Frame->Define Script...
> menu item. This will bring up a dialog that allows you to define
> Chimera commands or Python code to execute at each frame (controlled
> with the "Interpret script as..." menu at the top of the per-frame
> dialog). The Chimera command "angle" can be used to report dihedrals
> to the reply log, so something like:
>
> angle #0:5 at o4',c1',n9,c4
>
> would report the specified dihedral angle to the reply log. Something
> similar can be done with the "distance" command but it's a little
> trickier since the distance command sets up a distance monitor and it
> won't let you set up a duplicate monitor, so you need to clear
> existing distance monitors first (with "~dist"). So something like
> this:
>
> ~dist all
> dist #0:6 at o4',h8
>
> would report the given distance to the reply log. If you are
> reporting many distances/angles you might consider using the "echo"
> command to insert additional text into the reply log to help you keep
> track of things. Also, you can use the "help" command (e.g. "help
> echo") to get more info on any command.
> I hope this helps.
>
> --Eric
>
> Eric Pettersen
> UCSF Computer Graphics Lab
> http://www.cgl.ucsf.edu
>
>
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> ------------------------------
>
> Message: 3
> Date: Tue, 13 Apr 2010 11:24:14 +0200
> From: sette at uniroma2.it
> To: chimera-users at cgl.ucsf.edu
> Subject: Re: [Chimera-users] Analysis of dihedral angles
> Message-ID: <20100413112414.5835742ht7fe8f26 at webmail.uniroma2.it>
> Content-Type: text/plain; charset=ISO-8859-1; DelSp="Yes";
> format="flowed"
>
>
> Hi all,
>
> my reply is not really related but similar.
> I work with NMR data and often we need list of distances or dihedral
> angles for the whole molecule, like distances between a NH protons and
> the rest of the molecule, or list of the chi1 dihedral angles. It
> seems that at present there is no way to get this. Scripts are possible?
>
> Thanks,
> Marco
>
>
>
> Def. Quota "Eric Pettersen" <pett at cgl.ucsf.edu>:
>
> > On Apr 12, 2010, at 9:12 AM, eduardo.troche at uvigo.es wrote:
> >
> >> Hi all,
> >>
> >> I'm a new Chimera user. I'm performing some molecular dynamics with
> >> a more or less simple system with Amber,and now that I have them
> >> done, I would like to analyze some specific data,like changes in a
> >> dihedral angle during the dynamic process, or distances between
> >> pairs of atoms. If I select several dihedral angles in Chimera and
> >> I play the dynamic movie, I can see these changes, but is it
> >> possible to get a table of results that shows the value of this
> >> angle for each step of the dynamic process?
> >
> > Hi Eduardo,
> > You can get this information by defining some actions to perform at
> > each frame. To do this use MD Movie's Per Frame->Define Script...
> > menu item. This will bring up a dialog that allows you to define
> > Chimera commands or Python code to execute at each frame (controlled
> > with the "Interpret script as..." menu at the top of the per-frame
> > dialog). The Chimera command "angle" can be used to report
> > dihedrals to the reply log, so something like:
> >
> > angle #0:5 at o4',c1',n9,c4
> >
> > would report the specified dihedral angle to the reply log.
> > Something similar can be done with the "distance" command but it's
> > a little trickier since the distance command sets up a distance
> > monitor and it won't let you set up a duplicate monitor, so you
> > need to clear existing distance monitors first (with "~dist"). So
> > something like this:
> >
> > ~dist all
> > dist #0:6 at o4',h8
> >
> > would report the given distance to the reply log. If you are
> > reporting many distances/angles you might consider using the "echo"
> > command to insert additional text into the reply log to help you
> > keep track of things. Also, you can use the "help" command (e.g.
> > "help echo") to get more info on any command.
> > I hope this helps.
> >
> > --Eric
> >
> > Eric Pettersen
> > UCSF Computer Graphics Lab
> > http://www.cgl.ucsf.edu
> >
> >
> >
>
>
>
> Dr.Marco Sette, Ph.D.
>
> Department of Chemical Sciences and Technology
> University of Rome, "Tor Vergata"
> via della Ricerca Scientifica, 00133, Rome, Italy
> e-mail: sette at uniroma2.it
> e-mail: m77it at yahoo.it
> Tel.: +39-0672594424
> Fax: +39-0672594328
>
>
> ----------------------------------------------------------------
> This message was sent using IMP, the Internet Messaging Program.
>
>
>
> ------------------------------
>
> Message: 4
> Date: Tue, 13 Apr 2010 08:58:55 -0700
> From: Elaine Meng <meng at cgl.ucsf.edu>
> To: sette at uniroma2.it
> Cc: chimera-users at cgl.ucsf.edu
> Subject: Re: [Chimera-users] Analysis of dihedral angles
> Message-ID: <FAB12AC4-ECDF-402C-9C0C-3C964404E94A at cgl.ucsf.edu>
> Content-Type: text/plain; charset=US-ASCII; format=flowed; delsp=yes
>
> Hi Marco,
>
> (a) distances. If you have Chimera 1.5 (daily build) you can use the
> findclash command to find all distances between two sets of atoms.
> The two sets can contain the same or different atoms. For example,
> you could find all distances among NH protons or between NH protons
> and other protons. See these previous replies:
> <http://www.cgl.ucsf.edu/pipermail/chimera-users/2010-February/004826.html
> >
> <http://www.cgl.ucsf.edu/pipermail/chimera-users/2010-March/004887.html>
> (except note that the mail program has expanded "@" to " at "!)
>
> (b) peptide dihedrals. The phi,psi,chiN values for amino acid
> residues are automatically assigned as attributes. You can save an
> attribute (list of values) to a file from the Render by Attribute tool.
> <
> http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/render/render.html#saving
> >
>
> Currently there is no Chimera command to save attributes, however.
>
> 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 Apr 13, 2010, at 2:24 AM, sette at uniroma2.it wrote:
>
> > Hi all,
> > my reply is not really related but similar.
> > I work with NMR data and often we need list of distances or dihedral
> > angles for the whole molecule, like distances between a NH protons
> > and the rest of the molecule, or list of the chi1 dihedral angles.
> > It seems that at present there is no way to get this. Scripts are
> > possible?
> > Thanks,
> > Marco
>
>
> ------------------------------
>
> Message: 5
> Date: Tue, 13 Apr 2010 10:03:35 -0700
> From: Eric Pettersen <pett at cgl.ucsf.edu>
> To: "chimera-users at cgl.ucsf.edu BB" <chimera-users at cgl.ucsf.edu>
> Subject: Re: [Chimera-users] Analysis of dihedral angles
> Message-ID: <37EE9CFA-AA27-45C2-843B-EF516634707F at cgl.ucsf.edu>
> Content-Type: text/plain; charset="us-ascii"; Format="flowed";
> DelSp="yes"
>
> On Apr 13, 2010, at 8:58 AM, Elaine Meng wrote:
>
> > (b) peptide dihedrals. The phi,psi,chiN values for amino acid
> > residues are automatically assigned as attributes. You can save an
> > attribute (list of values) to a file from the Render by Attribute
> > tool.
> > <
> http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/render/render.html#saving
> > >
>
> Also, a short Python script could be used for this:
>
> from chimera import openModels, Molecule
> for m in openModels.list(modelTypes=[Molecule]):
> for r in m.residues:
> print r, r.chi1
>
> If you save the above in a file ending in .py and open it in Chimera
> (e.g. File...Open, or the "open" command) then the chi1 angles of all
> residues will be printed to the reply log.
>
> --Eric
>
>
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> ------------------------------
>
> Message: 6
> Date: Tue, 13 Apr 2010 11:08:01 -0700
> From: Tom Goddard <goddard at cgl.ucsf.edu>
> To: "Li, Zongli" <Zongli_Li at hms.harvard.edu>
> Cc: Chimera BB <chimera-users at cgl.ucsf.edu>
> Subject: Re: [Chimera-users] Display a spider volume data in a
> specific orientation
> Message-ID: <4BC4B301.7020709 at cgl.ucsf.edu>
> Content-Type: text/plain; charset="iso-8859-1"; Format="flowed"
>
> Hi Zongli,
>
> I've improved the Chimera Transform Molecule Coordinates dialog to
> allow using Euler angles to reorient volume data and other non-molecule
> models. The dialog has been renamed to "Transform Coordinates" and is
> under the Tools / Movement menu. You can get this improved version in
> tomorrow's Chimera daily build.
>
> There are alternate Euler angle conventions. Chimera only uses the
> chi-convention as described in the Chimera manual:
>
>
> http://www.cgl.ucsf.edu/chimera/current/docs/ContributedSoftware/transform/transform.html
>
> "Euler angles [? ? ?] - rotations defined by the ?-convention, where the
> first rotation is by an angle ? about the Z-axis, the second is by an
> angle ? (potentially ranging from 0 to ?) about the new X-axis, and the
> third is by an angle ? about the new Z-axis."
>
> Hope this is the Euler angle convention you are using.
>
> Tom
>
>
>
>
> > Thanks a lot, Elaine. I'll try it your way before I got other
> suggestions.
> >
> > Best,
> >
> > Zongli
> >
> > ________________________________________
> > From: Elaine Meng
> > Sent: Wednesday, April 07, 2010 3:30 PM
> > To: Li, Zongli
> > Cc: Chimera BB
> > Subject: Re: Display a spider volume data in a specific orientation
> >
> > Hi Zongli,
> > This is not my area of expertise (our expert is currently out of town)
> > -- at first I thought you could use "Transform Molecule
> > Coordinates" (under Tools... Movement), but now I see that it works
> > only on atomic structures rather than maps:
> > <
> http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/transform/transform.html
> > >
> >
> > It only works on molecular structures because it actually changes the
> > atomic coordinates, without changing the model transformation.
> >
> > I've figured out one workaround, but it is both crazy and slightly
> > tedious:
> > (1) open your map (say as model 0).
> > (2) open any atomic-resolution structure, it doesn't matter what, and
> > open it twice -- now you have three models. Don't move them
> > separately from the map (yet). Let's say the atomic structures are
> > models 1 and 2.
> > (3) use "Transform Molecule Coordinates" with desired Euler angles and
> > shift on one copy of the atomic structure (say model 1).
> > (4) use the match command to superimpose the other copy of the atomic
> > structure on the one that was transformed:
> > match #2 #1
> > (the command can use the whole models since they should have exactly
> > the same atoms)
> > (5) use the matrixcopy command to apply the transformation matrix of
> > the second copy of the atomic structure to the map:
> > matrixcopy 2 0
> >
> > You might think "why do I need two copies of the atomic structure?
> > can't I just transform one copy and then use matrixcopy?" ... in fact
> > that's what I tried first, but after it didn't work, I realized it was
> > because the Transform tool works by changing the coordinate values and
> > not the stored matrix of the model. It is necessary to match the
> > second copy to generate a corresponding matrix, and then matrixcopy
> > can be used.
> >
> > I'm CC-ing the chimera-users at cgl.ucsf.edu list in case other Chimera
> > users have suggestions. Our expert Tom G should be back next week and
> > he might also have ideas. In general, it's better to send Chimera
> > questions to that mailing list instead of just me, because I could be
> > away from work or (like now) lacking a good answer!
> >
> > 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 Apr 7, 2010, at 11:51 AM, Li, Zongli wrote:
> >
> >
> >> Hi Elaine,
> >> I have a spider volume data (or mrc density map) from which I got a
> >> serious 2D projections. I have the Euler angles for each projection.
> >> Is there a way in Chimera that I can use those Euler angles to
> >> display the 3D spider volume data (or mrc density map) in a specific
> >> orientation that corresponding to that 2D projection?
> >> Thank you very much in advance.
> >> Best,
> >> Zongli
> >>
> >> ****************************************
> >> Zongli Li, Ph.D.
> >>
> >> Howard Hughes Medical Institute
> >> Department of Cell Biology
> >> Harvard Medical School
> >> C Building, Room 420B
> >> 240 Longwood Avenue
> >> Boston, MA 02115
> >>
> >> ***************************************
> >>
> >>
>
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