- Chimera-users - RBVI Mailing Lists

making movie with animation utility
by Bala subramanian 13 Dec '11

13 Dec '11

Friends, I am using chimera build 34374 (downloaded on 9/1/2011). I opened * tools-utilities-Animation* and added a number of scenes. I want to make a movie out of these scenes that were added into the Animation panel. When click *setting-save*. It says the category animation is saved, however i dnt find any animation saved on my system. In brief, i want to make a movie out of the scenes saved in Animation panel, Kindly write me how to do it. Cheers, Bala

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Simple distance to .txt scripting question
by Andrew Hagen 09 Dec '11

09 Dec '11

Hi everyone, I'm trying to write a script that opens a set of .pdbs, measures the distances between certain atoms, and then writes the distance to a text file for later analysis. It's easy enough to do something like... >>> runCommand("distance #0:519.A@NZ #:1.Y@O4") ...which executes the command and appends the info to the reply log ("Distance between #0 LYS 519.A NZ and #5 X01 1.Y O4: 2.33"). What I'd like to do is have that actual measured distance (2.33) be stored in a variable that I could then write to a text file (I know how to do this bit). Thanks for any thoughts! --Andrew -- Andrew Hagen PhD candidate - Plant and Microbial Biology UC Berkeley - Keasling group

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helix anomaly
by larif sofiene 09 Dec '11

09 Dec '11

Greeting sir I'm studying a protein mutation effect using M.Dynamics, and when got results a used chimera to view my protein. in this snapshot http://imageshack.us/photo/my-images/839/errya.jpg/ you can see the first arrow (helix distortion, which predicted as a mutation effect ) and a second arrow showing the discontinuity the helix,where its final turn is replaced by a coil. My question is this coil a secondary structure detection bug in chimera,because when using other tools (pymol, vmd ) they detect this final coil as a helix. thanks

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problem
by Sidra Saleem 09 Dec '11

09 Dec '11

i have downloaded ucsf chimera many times but its not working and giving a window named chimera error the error is unable to contact UCSF computer graphics lab to check for new version(network disconnected) kindly help me urgently

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Axis vs map rotation
by Nicolas Coudray 09 Dec '11

09 Dec '11

Hi, I'm using the "Feature >> Plane" options of the "Volume viewer tool" to show contour lines in planes of density maps. For the plane, there are 3 options: "X-axis", "Y-axis", and "Z-axis". The plane I'm interested in is none of those. I try to rotate the maps, but the X, Y and Z axis are also rotating... Do you know if there's a way to rotate the "axis" and the "map" independently, please? Thanks in advance, Nicolas *-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*

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Re: [Chimera-users] MD plots
by Elaine Meng 06 Dec '11

06 Dec '11

Hi Luis, This is a new feature added after the 1.5.3 release --- you would need to use a Chimera daily build to try this feature. Daily build download: <http://www.cgl.ucsf.edu/chimera/download.html#daily> List of new features since the 1.5 release series: <http://www.cgl.ucsf.edu/chimera/docs/relnotes/snapshot.html> Enjoy! 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 Dec 6, 2011, at 4:33 PM, lecan wrote: > Hi Elaine. > I was following this item that George asked about the plotting of distances in a MD and I got interest in plotting distances as well. But I can not find the plot button in Chimera 1.5.3. Could you please tell where is the plot button in this version? In the MD movie window at the analysis pull down only appear "Calculate occupancy", "Cluster" and "RMSD map". > > Thank you in advance, > > Luis L. > > > On Mon, 5 Dec 2011 13:18:09 -0800, Elaine Meng <meng(a)cgl.ucsf.edu> wrote: >> Hi George, >> The distance command is for showing the distance monitor (dashed line >> and angstrom label). For MD movie plotting, you need only select the >> two atoms and then click the Plot button on the dialog. In the image >> you sent, the dialog is showing an error message that suggests you do >> not have exactly two atoms selected (i.e. either fewer or more atoms >> than two seem to be selected). Try clearing the selection before you >> select the two atoms. Also make sure your selection is really getting >> only two atoms. >> >> For example, realize ":124@H" could select more than one atom. There >> might be residue 124 in both chain A and chain B, and/or in model 0 >> and model 1, etc. >> >> You can see how many atoms are selected, for example by clicking the >> green magnifying glass on the lower right corner of the Chimera window >> to open the Selection Inspector. >> 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 >> >> >> >> >> _______________________________________________ >> Chimera-users mailing list >> Chimera-users(a)cgl.ucsf.edu >> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users >

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Flip maps
by Mario Dejung 06 Dec '11

06 Dec '11

Hi everybody, since the newest version of chimera, it is not longer possible to flip a map via the Voxel Size. In older versions, I could just write 2 2 -2 and my map was flipped. Is there still a way to flip my map within Chimera, or do I have to flip it in a different program and load this new map into chimera. Thanks Mario

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mmView - a tool for mmCIF exploration
by Daniel Svozil 06 Dec '11

06 Dec '11

Dear colleagues, We would like to announce the availability of mmView - the web-based application which allows to comfortably explore the structural data of biomacromolecules stored in the mmCIF (macromolecular Crystallographic Information File) format. The mmView software system is primarily intended for educational purposes but it can also serve as an auxiliary tool for working with biomolecular structures. The mmView application is offered in two flavors: as a publicly available web server http://ich.vscht.cz/projects/mmview/, and as an open-source stand-alone application (available from http://sourceforge.net/projects/mmview) that can be installed on the user’s computer. Petr Cech and Daniel Svozil -- Daniel Svozil, PhD Head of Laboratory of Informatics and Chemistry Institute of Chemical Technology Czech Republic phone: +420 220 444 391 http://ich.vscht.cz/~svozil

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Re: [Chimera-users] MD plots
by George Tzotzos 05 Dec '11

05 Dec '11

Apologies for repeating this. Here are the snapshots On Dec 5, 2011, at 9:58 PM, turk(a)lmb.uni-muenchen.de wrote: > have you tried: > >> distance model_number:residue_A@atom model_number:residue_B@atom > > > George Tzotzos <gtzotzos(a)me.com> wrote : > >> I'm trying to plot the distance between two atoms is a MD trajectory. >> >> I use the command line to select, for example :124@H :121@O >> >> The window in MD Plots fails to show my selection. >> >> Is there something I get wrong? Your help will be much appreciated >> >> Regards >> >> George >> >> _______________________________________________ >> Chimera-users mailing list >> Chimera-users(a)cgl.ucsf.edu >> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users > >

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Re: [Chimera-users] MD plots
by George Tzotzos 05 Dec '11

05 Dec '11

Thanks for this. I tried, still the result is the same. I'm attaching two snapshots in case it helps with the diagnostics. All the best George On Dec 5, 2011, at 9:58 PM, turk(a)lmb.uni-muenchen.de wrote: > have you tried: > >> distance model_number:residue_A@atom model_number:residue_B@atom > > > George Tzotzos <gtzotzos(a)me.com> wrote : > >> I'm trying to plot the distance between two atoms is a MD trajectory. >> >> I use the command line to select, for example :124@H :121@O >> >> The window in MD Plots fails to show my selection. >> >> Is there something I get wrong? Your help will be much appreciated >> >> Regards >> >> George >> >> _______________________________________________ >> Chimera-users mailing list >> Chimera-users(a)cgl.ucsf.edu >> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users > >

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