On Tue, Apr 13, 2010 at 2:08 PM, <chimera-users-request@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@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)

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Message: 1
Date: Mon, 12 Apr 2010 16:13:27 -0400
From: "Jay Brown" <jcb2g@virginia.edu>
To: <chimera-users@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@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@cgl.ucsf.edu>
To: eduardo.troche@uvigo.es
Cc: chimera-users@cgl.ucsf.edu
Subject: Re: [Chimera-users] Analysis of dihedral angles
Message-ID: <7B28F8D4-11F4-4AFE-ABC9-8F93A5770C7D@cgl.ucsf.edu>
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On Apr 12, 2010, at 9:12 AM, eduardo.troche@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@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@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@uniroma2.it
To: chimera-users@cgl.ucsf.edu
Subject: Re: [Chimera-users] Analysis of dihedral angles
Message-ID: <20100413112414.5835742ht7fe8f26@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@cgl.ucsf.edu>:

> On Apr 12, 2010, at 9:12 AM, eduardo.troche@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@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@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@uniroma2.it
e-mail: m77it@yahoo.it
Tel.: +39-0672594424
Fax: +39-0672594328

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------------------------------

Message: 4
Date: Tue, 13 Apr 2010 08:58:55 -0700
From: Elaine Meng <meng@cgl.ucsf.edu>
To: sette@uniroma2.it
Cc: chimera-users@cgl.ucsf.edu
Subject: Re: [Chimera-users] Analysis of dihedral angles
Message-ID: <FAB12AC4-ECDF-402C-9C0C-3C964404E94A@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@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@cgl.ucsf.edu>
To: "chimera-users@cgl.ucsf.edu BB" <chimera-users@cgl.ucsf.edu>
Subject: Re: [Chimera-users] Analysis of dihedral angles
Message-ID: <37EE9CFA-AA27-45C2-843B-EF516634707F@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@cgl.ucsf.edu>
To: "Li, Zongli" <Zongli_Li@hms.harvard.edu>
Cc: Chimera BB <chimera-users@cgl.ucsf.edu>
Subject: Re: [Chimera-users] Display a spider volume data in a
specific orientation
Message-ID: <4BC4B301.7020709@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@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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