- Chimera-users - RBVI Mailing Lists

problem with match function (superposition)
by Ken Shimo 14 Dec '11

14 Dec '11

Hello, I'm working with evolutionary algorithms applied to protein-protein docking. I'd like to calculate de RMSD between the native complex and the complex achieved with my docking model. For that I was trying to make the superposition of the complexes using the match function through the Chimera command line. I called the function as: match #0 #1 and got the following message: Atoms in each selection must be in the same model I'd like to know what am I doing wrong, or if there is anyway other way to obtain the RMSD and the superposed complexes. I'm using the complex code PDB 1CHO. Thanks for any help, -- Helder Ken Shimo BSc in Biomedical Informatics (University of São Paulo - Brazil) MSc candidate in Bioinformatics (University of São Paulo - Brazil) -- "When I get sad, I stop being sad and be awesome instead." (Neil Patrick Harris as Barney Stinson)

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Error in using Chimera
by Poornima Josyula 13 Dec '11

13 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

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Regarding estimation of volume in 2D
by Poornima Josyula 13 Dec '11

13 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

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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.

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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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MD plots
by George Tzotzos 05 Dec '11

05 Dec '11

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

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add custom residues to rotamer library or for swapaa command
by Sabuj Pattanayek 05 Dec '11

05 Dec '11

Hi, How do I add custom residues so that they're usable with swapaa or the rotamer tool? Thanks, Sabuj

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CASTp unable to recognise pdb format
by George Tzotzos 03 Dec '11

03 Dec '11

Hi everybody, I used Modeller to generate a structure which I then saved using Chimera. The CASTp server complains that the structure is not in pdb format. I'm attaching the pdb file to help with the diagnostics. Good weekend to all George

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Cando
by poorvi garg 02 Dec '11

02 Dec '11

Hii.., I have generated the json files by sending it to cando . The files we have generated is opened in UCSF Chimera but I am not able to perform any options or operations of the tool . Could you tell me how to perform operations on bld files of the json file obtained. thanks Regards, Poorvi Garg

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volume calculation
by sdimicco 02 Dec '11

02 Dec '11

Dear Chimera developers, is it possible to calculate the volume of the binding site by the softwere? How can I do it? Thank you in advance. Simone

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Multi-align: retract
by George Tzotzos 01 Dec '11

01 Dec '11

I'd like to retract the previous message. I found a way to edit the protein names. It's a bit roundabout but it works. I saved the alignment in Clustal, opened with an text editor, edited the names and saved. Then I opened the file in Chimera. Regards George

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Multi-align
by George Tzotzos 01 Dec '11

01 Dec '11

Hi everybody, I'm wondering if there's a way to edit the protein names in Multi-align. It seems that protein names are generated automatically. An example is attached. The problem is that in scalable eps, sometimes the names overlap with the line numbers. Reducing the ellipsis in Multi-align preferences truncates the names. Thanks for any suggestions George

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PDB splitting
by Milen Raytchev 30 Nov '11

30 Nov '11

Hi everyone, First, thank you Tom for redirecting me. I am trying to split a long single chain which is contained in a PDB file into several shorter chains, each to be contained in individual PDB files. I have tried Chimera (save as) and PDBEditor.jar software to do that but each approach messes the format somehow and I cannot use it in Chimera later (visualization suffers). Could you recommend me a way to do this splitting properly such that the PDB format is not messed up in the resultant 6 AAA domains and I can use the files further in Chimera. The file is attached if of any use. Thank you in advance and I do appreciate your help. Sincerely, Milen Raytchev

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Ice Crystal Surface
by Nancy 30 Nov '11

30 Nov '11

Hi All, I would like to perform molecular simulations with an ice crystal surface; does anyone know if such a structure file can be obtained online? Thanks, Nancy

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shortest distance
by Bishwajit Das 30 Nov '11

30 Nov '11

How to find out the shortest distance between two atom? help me -- * BISHWAJIT DAS* *+91-9433237920* KOLKATA

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help with error message
by Susan Tsutakawa 28 Nov '11

28 Nov '11

I am opening up a pdb that has been generated after MD simulations. Waters have been removed. I am getting an unusual error. I have two pdb files that were generated similarly, but only one gives me the error. Traceback (most recent call last): File "/Applications/Chimera.app/Contents/Resources/share/chimera/tkgui.py", line 343, in openPath mols = chimera.openModels.open(path, type=ftype) File "/Applications/Chimera.app/Contents/Resources/share/chimera/__init__.py", line 1541, in open models = func(filename, *args, **kw) File "/Applications/Chimera.app/Contents/Resources/share/chimera/__init__.py", line 770, in _openPDBModel errOut=errLog) error: radius must be positive Error reading bfactor-911_changed.pdb: error: radius must be positive File "/Applications/Chimera.app/Contents/Resources/share/chimera/__init__.py", line 770, in _openPDBModel errOut=errLog) If someone can help, I would appreciate it.

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