- Chimera-users - RBVI Mailing Lists

comparing angles in 28 structures
by Elaine Meng 08 Mar '13

08 Mar '13

Hi Paola, Other than measuring the angle in each one, the only other idea I have is to open the 28 structures as a single trajectory in the MD Movie tool. You can only do that if each file has the same atoms with the same names. Then you can plot the angle across the 28 "frames" in the trajectory. However, if the structures do not have the exactly the same atoms, I don't know any other method than opening and measuring each one individually. There are several trajectory input options including multiple PDB files, although in that case you would need to give the files names including numbers and ending in ".pdb". The MD Movie tool including input options is described here: <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/movie/framemovie.h…> After you open the trajectory, you can use the MD Movie controller to "play" through the 28 frames. You can plot values such as the angle of interest, see the MD Movie menu: Analysis.... Plot <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/movie/movie.html#p…> 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 P.S. this is a "user" question, so chimera-users(a)cgl.ucsf.edu (CC'd here) is a better place to send it than chimera-dev, which is for programming questions On Feb 21, 2013, at 12:30 PM, Paola Peshkepija wrote: > Good afternoon, > I am a new chimera user. I am using Chimera to look at the backbone dihedral angle variations for 28 GFP structures. I was wondering if there is a way I can look at the changes in dihedral angles using the 28 structures altogether rather than looking at each structure individually. Please, let me know. > Thank you in advance for your help! > Paola

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Chimera Tutorial in Boston area
by Scooter Morris 06 Mar '13

06 Mar '13

Hi all, I'll be teaching a Chimera tutorial scheduled as part of the VizBI conference <http://vizbi.org/2013/> in Cambridge, MA. See the Program <http://vizbi.org/2013/Program/> for information about what we'll be covering, or just bring your favorite structure and we'll explore some of Chimera's new features. -- scooter

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Re: [Chimera-users] How to fork/specify a web browser
by Greg Couch 06 Mar '13

06 Mar '13

Forgot to include list in reply. -------- Original Message -------- Subject: Re: [Chimera-users] How to fork/specify a web browser Date: Wed, 6 Mar 2013 09:23:11 -0800 From: gregc(a)cgl.ucsf.edu To: Yasha Karant <ykarant(a)csusb.edu> > For certain of the tutorials, help files, etc., Chimera linux displays a > comment to use a web browser in order to use a URL file://foobar . > How does one configure Chimera to automatically use a specified browser > to diplay the URL generated by Chimera? I have not been able to find a > preferences setting for this, nor an answer on the web or in the Chimera > manuals/help. I have not perused the source code for Chimera to find a > solution. > > Yasha Karant > Chimera uses Python 2.7's webbrowser module to open files in a web browser. For Linux, if you are using a GNOME or KDE desktop environment, then it will use the default browser that is configured for that environment. Otherwise, it looks for firefox (and derivatives), kfm, konqueror, galeon, epiphany, skipstone, opera, mosaic, and grail(!). You can override the the search order with the BROWSER environment variable. You may have noticed that Google's chrome is not on that list. Chrome support is included in Python 3's webbrowser module. But, that support would only be needed if you are not using a GNOME or KDE desktop environment. I will look into how much work it would be to backport Python 3's webbrowser module to Chimera. HTH, Greg

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How to fork/specify a web browser
by Yasha Karant 06 Mar '13

06 Mar '13

For certain of the tutorials, help files, etc., Chimera linux displays a comment to use a web browser in order to use a URL file://foobar . How does one configure Chimera to automatically use a specified browser to diplay the URL generated by Chimera? I have not been able to find a preferences setting for this, nor an answer on the web or in the Chimera manuals/help. I have not perused the source code for Chimera to find a solution. Yasha Karant

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Guessing net charge
by Miro Moman 05 Mar '13

05 Mar '13

Hello, When computing partial charges in Chimera, the user is prompted to indicate the net charge of the "non-standard" residues. However, more often than not, the suggested value is correct. I would like to know how this guess is made and whether or not the net charge of small organic molecules can be guessed in batch mode using Chimera (or other tools). Best regards, Miro Moman -- http://www.e-moman.eu

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Re: [Chimera-users] [chimera-dev] 2-D projection of volume in Chimera
by Tom Goddard 04 Mar '13

04 Mar '13

Hi Jesus, There is a tricky way to do a projection of a map in Chimera. You can use the map binning capability. For example, if map #0 has 144 planes along the z axis I can add all those planes with vop bin #0 binsize 1,1,144 This can be done with a dialog instead of a command using Tools / Volume Data / Volume Filter, filter type bin and type in the bin size as 1 1 144. You also want a view along an axis other than x, y or z it sounds like. To do that you would resample the map on a new rotated grid so that the z axis is along the desired projection axis. The following video shows how to use the Chimera volume dialog subregion selection capability to do that http://www.cgl.ucsf.edu/chimera/videodoc/rotatedbox/ Tom -------- Original Message -------- Subject: Re: [chimera-dev] 2-D projection of volume in Chimera From: Elaine Meng To: Jesus Montoya Date: 3/4/13 11:59 AM > Hi Jesus, > Sorry, I don't think there is a way, currently. Here is the most recent information I could find on that topic: > > <http://plato.cgl.ucsf.edu/pipermail/chimera-users/2010-April/005124.html> > > Regards, > Elaine > ---------- > Elaine C. Meng, Ph.D. > UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab > Department of Pharmaceutical Chemistry > University of California, San Francisco > > p.s. For future questions, you may want to send to chimera-users(a)cgl.ucsf.edu (chimera-dev is mainly for programming questions). > > On Feb 26, 2013, at 5:28 PM, Jesus Montoya wrote: > >> Hi, >> >> Is there a way to project a 3-D volume into a single 2-D image plane in Chimera? >> >> For example, I want to load a volume twice into Chimera and view the two copies side by side in an identical orientation (manually set by rotating the volumes with the mouse). >> Then, I want to view one of them as a 2-D projection along the axis that comes out of the screen. >> >> While a "solid" representation of the volume is similar, it is not exactly what I need... >> >> Thanks! >> >>

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Thank You
by Noel Pace 04 Mar '13

04 Mar '13

thank you to all of you who helped me in compiling a DEMO which I will be using for my dissertation project. I will be making this DEMO public once it has been tested and modified accordingly. Noel Pace Malta

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Question about using the volume command
by Henning Stahlberg 04 Mar '13

04 Mar '13

Hi, The command volume #5 level 2.30 color 0.6,0.6,0.6 transparency 0.4 style solid doesn't work on my computer (OSX), Chimera (Version 1.7, build 38197) requests that "Solid level must be <data-value,brightness-level>". What am I doing wrong? Thanks for any suggestions, Henning.

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Work with Volumetric Data
by esserlo＠helix.nih.gov 01 Mar '13

01 Mar '13

Hi, I am using Chimera to render electron density in gaussian cube files and it works well. I am wondering though whether it is possible to integrate the e-density inside the current volume as defined by the closed surface. If there are people with expertise in this field of volumetric data (processing), I would be interested in obtaining C or C++ libraries that provide functions to calculate volume, surface areas etc. Thanks, Lothar

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vop morph map color
by Steve Reichow 01 Mar '13

01 Mar '13

Hi, I am writing a movie script that uses the vop morph command to morph between two EM maps #0 and #1: vop morph #0,1 The output map #2 from this command is displayed in a random default color that I would like to change. I have tried the following: vop morph #0,1 volume #2 color khaki This works, but the very first frame in the movie following the vop morph still contains the default color, while the following frames contain the set color 'khaki'. This results in a flicker in the movie with the wrong color. Any help/suggestions on how to get this set correctly? Let me know if there needs clarification - thanks! I am using Chimera Version 1.6 Mac OSX -- ~~~~~~~~~~~~~~~~~~~~~~ *Steve Reichow *Email: slreichow(a)gmail.com ~~~~~~~~~~~~~~~~~~~~~~

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