<div>Hi,</div>
<div> </div>
<div>Is there a way to quantify the electron densities in a unit cell with UCSF?</div>
<div> </div>
<div>Thanks,</div>
<div>Chinthaka. <br><br></div>
<div class="gmail_quote">On Tue, Apr 13, 2010 at 2:08 PM, <span dir="ltr"><<a href="mailto:chimera-users-request@cgl.ucsf.edu">chimera-users-request@cgl.ucsf.edu</a>></span> wrote:<br>
<blockquote style="BORDER-LEFT: #ccc 1px solid; MARGIN: 0px 0px 0px 0.8ex; PADDING-LEFT: 1ex" class="gmail_quote">Send Chimera-users mailing list submissions to<br> <a href="mailto:chimera-users@cgl.ucsf.edu">chimera-users@cgl.ucsf.edu</a><br>
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<br>When replying, please edit your Subject line so it is more specific<br>than "Re: Contents of Chimera-users digest..."<br><br><br>Today's Topics:<br><br> 1. install (Jay Brown)<br> 2. Re: Analysis of dihedral angles (Eric Pettersen)<br>
3. Re: Analysis of dihedral angles (<a href="mailto:sette@uniroma2.it">sette@uniroma2.it</a>)<br> 4. Re: Analysis of dihedral angles (Elaine Meng)<br> 5. Re: Analysis of dihedral angles (Eric Pettersen)<br> 6. Re: Display a spider volume data in a specific orientation<br>
(Tom Goddard)<br><br><br>----------------------------------------------------------------------<br><br>Message: 1<br>Date: Mon, 12 Apr 2010 16:13:27 -0400<br>From: "Jay Brown" <<a href="mailto:jcb2g@virginia.edu">jcb2g@virginia.edu</a>><br>
To: <<a href="mailto:chimera-users@cgl.ucsf.edu">chimera-users@cgl.ucsf.edu</a>><br>Subject: [Chimera-users] install<br>Message-ID: <009501cada7c$9ccfe2b0$d66fa810$@edu><br>Content-Type: text/plain; charset="us-ascii"<br>
<br>Dear Chimera-Users:<br><br>I am trying to install Chimera on a Linux Fedora 12 computer. Download goes<br>OK, but when I try to install the program I get an error message saying: bad<br>ELF interpreter: No such file or directory<br>
<br>Do you know what this means? I can't find anything about ELF interpreter.<br><br> -Jay Brown<br><br><br><br>Jay C. Brown<br><br>Department of Microbiology<br><br>University of Virginia School of Medicine<br><br>1300 Jefferson Park Ave.<br>
<br>Charlottesville, VA 22908<br><br><br><br>Email: <a href="mailto:Jcb2g@virginia.edu">Jcb2g@virginia.edu</a><br><br>Phone: 434-924-1814<br><br><a href="http://people.virginia.edu/~jcb2g/index.htm" target="_blank">http://people.virginia.edu/~jcb2g/index.htm</a><br>
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<br>------------------------------<br><br>Message: 2<br>Date: Mon, 12 Apr 2010 17:26:01 -0700<br>From: Eric Pettersen <<a href="mailto:pett@cgl.ucsf.edu">pett@cgl.ucsf.edu</a>><br>To: <a href="mailto:eduardo.troche@uvigo.es">eduardo.troche@uvigo.es</a><br>
Cc: <a href="mailto:chimera-users@cgl.ucsf.edu">chimera-users@cgl.ucsf.edu</a><br>Subject: Re: [Chimera-users] Analysis of dihedral angles<br>Message-ID: <<a href="mailto:7B28F8D4-11F4-4AFE-ABC9-8F93A5770C7D@cgl.ucsf.edu">7B28F8D4-11F4-4AFE-ABC9-8F93A5770C7D@cgl.ucsf.edu</a>><br>
Content-Type: text/plain; charset="us-ascii"; Format="flowed";<br> DelSp="yes"<br><br>On Apr 12, 2010, at 9:12 AM, <a href="mailto:eduardo.troche@uvigo.es">eduardo.troche@uvigo.es</a> wrote:<br>
<br>> Hi all,<br>><br>> I'm a new Chimera user. I'm performing some molecular dynamics with<br>> a more or less simple system with Amber,and now that I have them<br>> done, I would like to analyze some specific data,like changes in a<br>
> dihedral angle during the dynamic process, or distances between<br>> pairs of atoms. If I select several dihedral angles in Chimera and I<br>> play the dynamic movie, I can see these changes, but is it possible<br>
> to get a table of results that shows the value of this angle for<br>> each step of the dynamic process?<br><br>Hi Eduardo,<br> You can get this information by defining some actions to perform at<br>each frame. To do this use MD Movie's Per Frame->Define Script...<br>
menu item. This will bring up a dialog that allows you to define<br>Chimera commands or Python code to execute at each frame (controlled<br>with the "Interpret script as..." menu at the top of the per-frame<br>
dialog). The Chimera command "angle" can be used to report dihedrals<br>to the reply log, so something like:<br><br> angle #0:5@o4',c1',n9,c4<br><br>would report the specified dihedral angle to the reply log. Something<br>
similar can be done with the "distance" command but it's a little<br>trickier since the distance command sets up a distance monitor and it<br>won't let you set up a duplicate monitor, so you need to clear<br>
existing distance monitors first (with "~dist"). So something like<br>this:<br><br> ~dist all<br> dist #0:6@o4',h8<br><br>would report the given distance to the reply log. If you are<br>reporting many distances/angles you might consider using the "echo"<br>
command to insert additional text into the reply log to help you keep<br>track of things. Also, you can use the "help" command (e.g. "help<br>echo") to get more info on any command.<br> I hope this helps.<br>
<br>--Eric<br><br> Eric Pettersen<br> UCSF Computer Graphics Lab<br> <a href="http://www.cgl.ucsf.edu/" target="_blank">http://www.cgl.ucsf.edu</a><br><br>
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<br>------------------------------<br><br>Message: 3<br>Date: Tue, 13 Apr 2010 11:24:14 +0200<br>From: <a href="mailto:sette@uniroma2.it">sette@uniroma2.it</a><br>To: <a href="mailto:chimera-users@cgl.ucsf.edu">chimera-users@cgl.ucsf.edu</a><br>
Subject: Re: [Chimera-users] Analysis of dihedral angles<br>Message-ID: <<a href="mailto:20100413112414.5835742ht7fe8f26@webmail.uniroma2.it">20100413112414.5835742ht7fe8f26@webmail.uniroma2.it</a>><br>Content-Type: text/plain; charset=ISO-8859-1; DelSp="Yes";<br>
format="flowed"<br><br><br>Hi all,<br><br>my reply is not really related but similar.<br>I work with NMR data and often we need list of distances or dihedral<br>angles for the whole molecule, like distances between a NH protons and<br>
the rest of the molecule, or list of the chi1 dihedral angles. It<br>seems that at present there is no way to get this. Scripts are possible?<br><br>Thanks,<br>Marco<br><br><br><br>Def. Quota "Eric Pettersen" <<a href="mailto:pett@cgl.ucsf.edu">pett@cgl.ucsf.edu</a>>:<br>
<br>> On Apr 12, 2010, at 9:12 AM, <a href="mailto:eduardo.troche@uvigo.es">eduardo.troche@uvigo.es</a> wrote:<br>><br>>> Hi all,<br>>><br>>> I'm a new Chimera user. I'm performing some molecular dynamics with<br>
>> a more or less simple system with Amber,and now that I have them<br>>> done, I would like to analyze some specific data,like changes in a<br>>> dihedral angle during the dynamic process, or distances between<br>
>> pairs of atoms. If I select several dihedral angles in Chimera and<br>>> I play the dynamic movie, I can see these changes, but is it<br>>> possible to get a table of results that shows the value of this<br>
>> angle for each step of the dynamic process?<br>><br>> Hi Eduardo,<br>> You can get this information by defining some actions to perform at<br>> each frame. To do this use MD Movie's Per Frame->Define Script...<br>
> menu item. This will bring up a dialog that allows you to define<br>> Chimera commands or Python code to execute at each frame (controlled<br>> with the "Interpret script as..." menu at the top of the per-frame<br>
> dialog). The Chimera command "angle" can be used to report<br>> dihedrals to the reply log, so something like:<br>><br>> angle #0:5@o4',c1',n9,c4<br>><br>> would report the specified dihedral angle to the reply log.<br>
> Something similar can be done with the "distance" command but it's<br>> a little trickier since the distance command sets up a distance<br>> monitor and it won't let you set up a duplicate monitor, so you<br>
> need to clear existing distance monitors first (with "~dist"). So<br>> something like this:<br>><br>> ~dist all<br>> dist #0:6@o4',h8<br>><br>> would report the given distance to the reply log. If you are<br>
> reporting many distances/angles you might consider using the "echo"<br>> command to insert additional text into the reply log to help you<br>> keep track of things. Also, you can use the "help" command (e.g.<br>
> "help echo") to get more info on any command.<br>> I hope this helps.<br>><br>> --Eric<br>><br>> Eric Pettersen<br>> UCSF Computer Graphics Lab<br>
> <a href="http://www.cgl.ucsf.edu/" target="_blank">http://www.cgl.ucsf.edu</a><br>><br>><br>><br><br><br><br>Dr.Marco Sette, Ph.D.<br><br>Department of Chemical Sciences and Technology<br>
University of Rome, "Tor Vergata"<br>via della Ricerca Scientifica, 00133, Rome, Italy<br>e-mail: <a href="mailto:sette@uniroma2.it">sette@uniroma2.it</a><br>e-mail: <a href="mailto:m77it@yahoo.it">m77it@yahoo.it</a><br>
Tel.: +39-0672594424<br>Fax: +39-0672594328<br><br><br>----------------------------------------------------------------<br>This message was sent using IMP, the Internet Messaging Program.<br><br><br><br>
------------------------------<br><br>Message: 4<br>Date: Tue, 13 Apr 2010 08:58:55 -0700<br>From: Elaine Meng <<a href="mailto:meng@cgl.ucsf.edu">meng@cgl.ucsf.edu</a>><br>To: <a href="mailto:sette@uniroma2.it">sette@uniroma2.it</a><br>
Cc: <a href="mailto:chimera-users@cgl.ucsf.edu">chimera-users@cgl.ucsf.edu</a><br>Subject: Re: [Chimera-users] Analysis of dihedral angles<br>Message-ID: <<a href="mailto:FAB12AC4-ECDF-402C-9C0C-3C964404E94A@cgl.ucsf.edu">FAB12AC4-ECDF-402C-9C0C-3C964404E94A@cgl.ucsf.edu</a>><br>
Content-Type: text/plain; charset=US-ASCII; format=flowed; delsp=yes<br><br>Hi Marco,<br><br>(a) distances. If you have Chimera 1.5 (daily build) you can use the<br>findclash command to find all distances between two sets of atoms.<br>
The two sets can contain the same or different atoms. For example,<br>you could find all distances among NH protons or between NH protons<br>and other protons. See these previous replies:<br><<a href="http://www.cgl.ucsf.edu/pipermail/chimera-users/2010-February/004826.html" target="_blank">http://www.cgl.ucsf.edu/pipermail/chimera-users/2010-February/004826.html</a><br>
><br><<a href="http://www.cgl.ucsf.edu/pipermail/chimera-users/2010-March/004887.html" target="_blank">http://www.cgl.ucsf.edu/pipermail/chimera-users/2010-March/004887.html</a>><br>(except note that the mail program has expanded "@" to " at "!)<br>
<br>(b) peptide dihedrals. The phi,psi,chiN values for amino acid<br>residues are automatically assigned as attributes. You can save an<br>attribute (list of values) to a file from the Render by Attribute tool.<br><<a href="http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/render/render.html#saving" target="_blank">http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/render/render.html#saving</a><br>
><br><br>Currently there is no Chimera command to save attributes, however.<br><br>I hope this helps,<br>Elaine<br>-----<br>Elaine C. Meng, Ph.D.<br>UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab<br>Department of Pharmaceutical Chemistry<br>
University of California, San Francisco<br><br>On Apr 13, 2010, at 2:24 AM, <a href="mailto:sette@uniroma2.it">sette@uniroma2.it</a> wrote:<br><br>> Hi all,<br>> my reply is not really related but similar.<br>> I work with NMR data and often we need list of distances or dihedral<br>
> angles for the whole molecule, like distances between a NH protons<br>> and the rest of the molecule, or list of the chi1 dihedral angles.<br>> It seems that at present there is no way to get this. Scripts are<br>
> possible?<br>> Thanks,<br>> Marco<br><br><br>------------------------------<br><br>Message: 5<br>Date: Tue, 13 Apr 2010 10:03:35 -0700<br>From: Eric Pettersen <<a href="mailto:pett@cgl.ucsf.edu">pett@cgl.ucsf.edu</a>><br>
To: "<a href="mailto:chimera-users@cgl.ucsf.edu">chimera-users@cgl.ucsf.edu</a> BB" <<a href="mailto:chimera-users@cgl.ucsf.edu">chimera-users@cgl.ucsf.edu</a>><br>Subject: Re: [Chimera-users] Analysis of dihedral angles<br>
Message-ID: <<a href="mailto:37EE9CFA-AA27-45C2-843B-EF516634707F@cgl.ucsf.edu">37EE9CFA-AA27-45C2-843B-EF516634707F@cgl.ucsf.edu</a>><br>Content-Type: text/plain; charset="us-ascii"; Format="flowed";<br>
DelSp="yes"<br><br>On Apr 13, 2010, at 8:58 AM, Elaine Meng wrote:<br><br>> (b) peptide dihedrals. The phi,psi,chiN values for amino acid<br>> residues are automatically assigned as attributes. You can save an<br>
> attribute (list of values) to a file from the Render by Attribute<br>> tool.<br>> <<a href="http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/render/render.html#saving" target="_blank">http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/render/render.html#saving</a><br>
> ><br><br>Also, a short Python script could be used for this:<br><br>from chimera import openModels, Molecule<br>for m in openModels.list(modelTypes=[Molecule]):<br> for r in m.residues:<br> print r, r.chi1<br>
<br>If you save the above in a file ending in .py and open it in Chimera<br>(e.g. File...Open, or the "open" command) then the chi1 angles of all<br>residues will be printed to the reply log.<br><br>--Eric<br><br>
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<br>------------------------------<br><br>Message: 6<br>Date: Tue, 13 Apr 2010 11:08:01 -0700<br>From: Tom Goddard <<a href="mailto:goddard@cgl.ucsf.edu">goddard@cgl.ucsf.edu</a>><br>To: "Li, Zongli" <<a href="mailto:Zongli_Li@hms.harvard.edu">Zongli_Li@hms.harvard.edu</a>><br>
Cc: Chimera BB <<a href="mailto:chimera-users@cgl.ucsf.edu">chimera-users@cgl.ucsf.edu</a>><br>Subject: Re: [Chimera-users] Display a spider volume data in a<br> specific orientation<br>Message-ID: <<a href="mailto:4BC4B301.7020709@cgl.ucsf.edu">4BC4B301.7020709@cgl.ucsf.edu</a>><br>
Content-Type: text/plain; charset="iso-8859-1"; Format="flowed"<br><br>Hi Zongli,<br><br> I've improved the Chimera Transform Molecule Coordinates dialog to<br>allow using Euler angles to reorient volume data and other non-molecule<br>
models. The dialog has been renamed to "Transform Coordinates" and is<br>under the Tools / Movement menu. You can get this improved version in<br>tomorrow's Chimera daily build.<br><br> There are alternate Euler angle conventions. Chimera only uses the<br>
chi-convention as described in the Chimera manual:<br><br><a href="http://www.cgl.ucsf.edu/chimera/current/docs/ContributedSoftware/transform/transform.html" target="_blank">http://www.cgl.ucsf.edu/chimera/current/docs/ContributedSoftware/transform/transform.html</a><br>
<br>"Euler angles [? ? ?] - rotations defined by the ?-convention, where the<br>first rotation is by an angle ? about the Z-axis, the second is by an<br>angle ? (potentially ranging from 0 to ?) about the new X-axis, and the<br>
third is by an angle ? about the new Z-axis."<br><br> Hope this is the Euler angle convention you are using.<br><br> Tom<br><br><br><br><br>> Thanks a lot, Elaine. I'll try it your way before I got other suggestions.<br>
><br>> Best,<br>><br>> Zongli<br>><br>> ________________________________________<br>> From: Elaine Meng<br>> Sent: Wednesday, April 07, 2010 3:30 PM<br>> To: Li, Zongli<br>> Cc: Chimera BB<br>
> Subject: Re: Display a spider volume data in a specific orientation<br>><br>> Hi Zongli,<br>> This is not my area of expertise (our expert is currently out of town)<br>> -- at first I thought you could use "Transform Molecule<br>
> Coordinates" (under Tools... Movement), but now I see that it works<br>> only on atomic structures rather than maps:<br>> <<a href="http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/transform/transform.html" target="_blank">http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/transform/transform.html</a><br>
> ><br>><br>> It only works on molecular structures because it actually changes the<br>> atomic coordinates, without changing the model transformation.<br>><br>> I've figured out one workaround, but it is both crazy and slightly<br>
> tedious:<br>> (1) open your map (say as model 0).<br>> (2) open any atomic-resolution structure, it doesn't matter what, and<br>> open it twice -- now you have three models. Don't move them<br>> separately from the map (yet). Let's say the atomic structures are<br>
> models 1 and 2.<br>> (3) use "Transform Molecule Coordinates" with desired Euler angles and<br>> shift on one copy of the atomic structure (say model 1).<br>> (4) use the match command to superimpose the other copy of the atomic<br>
> structure on the one that was transformed:<br>> match #2 #1<br>> (the command can use the whole models since they should have exactly<br>> the same atoms)<br>> (5) use the matrixcopy command to apply the transformation matrix of<br>
> the second copy of the atomic structure to the map:<br>> matrixcopy 2 0<br>><br>> You might think "why do I need two copies of the atomic structure?<br>> can't I just transform one copy and then use matrixcopy?" ... in fact<br>
> that's what I tried first, but after it didn't work, I realized it was<br>> because the Transform tool works by changing the coordinate values and<br>> not the stored matrix of the model. It is necessary to match the<br>
> second copy to generate a corresponding matrix, and then matrixcopy<br>> can be used.<br>><br>> I'm CC-ing the <a href="mailto:chimera-users@cgl.ucsf.edu">chimera-users@cgl.ucsf.edu</a> list in case other Chimera<br>
> users have suggestions. Our expert Tom G should be back next week and<br>> he might also have ideas. In general, it's better to send Chimera<br>> questions to that mailing list instead of just me, because I could be<br>
> away from work or (like now) lacking a good answer!<br>><br>> I hope this helps,<br>> Elaine<br>> -----<br>> Elaine C. Meng, Ph.D.<br>> UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab<br>> Department of Pharmaceutical Chemistry<br>
> University of California, San Francisco<br>><br>> On Apr 7, 2010, at 11:51 AM, Li, Zongli wrote:<br>><br>><br>>> Hi Elaine,<br>>> I have a spider volume data (or mrc density map) from which I got a<br>
>> serious 2D projections. I have the Euler angles for each projection.<br>>> Is there a way in Chimera that I can use those Euler angles to<br>>> display the 3D spider volume data (or mrc density map) in a specific<br>
>> orientation that corresponding to that 2D projection?<br>>> Thank you very much in advance.<br>>> Best,<br>>> Zongli<br>>><br>>> ****************************************<br>>> Zongli Li, Ph.D.<br>
>><br>>> Howard Hughes Medical Institute<br>>> Department of Cell Biology<br>>> Harvard Medical School<br>>> C Building, Room 420B<br>>> 240 Longwood Avenue<br>>> Boston, MA 02115<br>
>><br>>> ***************************************<br>>><br>>><br><br>-------------- next part --------------<br>An HTML attachment was scrubbed...<br>URL: <<a href="http://www.cgl.ucsf.edu/pipermail/chimera-users/attachments/20100413/e1532ed5/attachment.html" target="_blank">http://www.cgl.ucsf.edu/pipermail/chimera-users/attachments/20100413/e1532ed5/attachment.html</a>><br>
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<br><br>End of Chimera-users Digest, Vol 84, Issue 12<br>*********************************************<br></blockquote></div><br>