December 2011 - Chimera-users - RBVI Mailing Lists

Error in using Chimera
by Poornima Josyula 14 Dec '11

14 Dec '11

Hi, I installed Chimera 1.5.3 in my system today. I have a Windows 7 64-bit machine with a processor that is, Intel i7-2600, CPU@ 3.40 GHz. After I open the image, I get the following error. I copied this from the debug window of Chimera. * initializing general preferences loading Tix initializing graphics create application loading Pmw creating main window creating menus creating toolbar creating viewer initializing OpenGL initializing preferences initializing dialogs initializing COM initializing extensions Return code: -1073741819 Press return or enter to to exit* I would be glad if anyone can help me fix this issue. Thank you. -- With best regards, Poornima Josyula Ph.D. Scholar Fluid Mechanics Laboratory Dept. of Applied Mechanics IIT, Madras India E-mail: poornima.josyula(a)gmail.com

2 1

Regarding estimation of volume in 2D
by Poornima Josyula 14 Dec '11

14 Dec '11

Respected Sir/Madam, My name is Poornima and I am a Ph.D. student from India. My area of research is Biofluid Mechanics. I am modeling bubble transport in bifurcating microchannels. I am performing 2D simulations for the above problem using a commercial Computational Fluid Dynamics (CFD) software called ANSYS Fluent. ImageJ is currently used for the purpose of post processing. But, I haven't entirely been successful in estimating the volume accurately. Please find attached a snapshot of the simulation. In that snapshot, my region of interest (ROI) is the red colored area whose volume I have to find out. Is there a way Chimera can help me estimate this volume? Please let me know your suggestions. Thank you for your time and patience in reading my mail, despite your busy schedule. Kindly excuse me for any inconvenience caused. Look forward to receive a positive response at the earliest. Have a good day. -- With best regards, Poornima Josyula Ph.D. Scholar Fluid Mechanics Laboratory Dept. of Applied Mechanics IIT, Madras India E-mail: poornima.josyula(a)gmail.com

3 3

how to change the atom type in chimera
by Hina 13 Dec '11

13 Dec '11

Dear All, Can you kindly let me know how to change or edit atom typing in chimera and how to visualize the ligands in the form that double bond single bonds aromatic centers are clearly seen.

2 1

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

2 1

Simple distance to .txt scripting question
by Andrew Hagen 10 Dec '11

10 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

2 1

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

2 1

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

2 1

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 *-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*

2 4

Re: [Chimera-users] MD plots
by Elaine Meng 07 Dec '11

07 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 >

1 0

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

2 1

Chimera-users December 2011