- Chimera-users - RBVI Mailing Lists

Rendering into 3d
by Rebecca Swett 17 Apr '14

17 Apr '14

Hey All, I'm looking at rendering some movies output from chimera as a 3d movie for viewing with nvidia 3d vision pro glasses. From everything I've read as long as the left/right eye frames are sequential, making the movie with ffmpeg should work fine. The problem I'm having is that ffmpeg has no way to alternate between 0-left.ppm 0-right.ppm 1-left.ppm 1-right.ppm, which is how chimera saves images when recording movies in stereo mode. If those same images were named 1.ppm 2.ppm 3.ppm 4.ppm, there would be no problem. Is there a quick fix that can be inserted to change the naming of the recorded frames? Any other suggestions? Rebecca Swett

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morphs
by Moses Adenaike 17 Apr '14

17 Apr '14

Hello Chimera users, Is there a way to make a morph between two PDBs that don't have the same amount of atoms or chains. For example, I want to morph between an enzyme bound to DNA and one without DNA. Moses

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call file-> open gui popup from script ?
by Katrina Lexa 17 Apr '14

17 Apr '14

Hello All, I’m wondering if there is a way to call the file->open popup within chimera when running a python script? I know that it’s possible to run the script on the command line and read the desired arguments in that way, and obviously the files I want could be coded in and then changed every time I want to look at something new, but I’m not seeing an obvious option from the mailing list or in the runCommand list for writing in a mid-script call for the user to select a file. Is such a thing possible? Thanks for your help, -- Katrina

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Doubts regarding building a structure using Build Structure option
by Garg, Ayush A. 16 Apr '14

16 Apr '14

Dear Developer I was working with with UCSF Chimera. I was trying to reproduce structure 1V4S - Glucokinase structure using the Build Structure option under the tab Structure Editing in Tools. I have the sequence of the 455 amino acids and also know the sequence which is alpha helix, beta helix but the sequence of connectors between these structures is not a secondary structure. I was wondering how to reproduce those using your structure builder option. I have attached a word file with the sequence and the image of 1V4S in UCSF Chimera. I hope that will help you understand my doubt better. Thank and Regards Ayush Arpit Garg Graduate Student Ohio State University

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Working with several proteins
by Navya Shilpa Josyula 16 Apr '14

16 Apr '14

Hi, I am working on a set of 400 proteins and for all these proteins I have specific list of amino acid residues. I wanted to know if there is any available script or a command to get the following 1. atomic areaSAS 2. atomic B-factor values 3. CASTp identified pocket residues and 4. CASTp identified pocket volumes for all the residues of these 400 proteins to be written in a single file. Kindly help me at your earliest. Thank you in advance for your help. Regards, Navya

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Relevant interacting amino acids between molecules
by Ogunniyan, Abisola 15 Apr '14

15 Apr '14

Hi, My name is Abisola Abisoye-Ogunniyan, a first year Biology Graduate student in Tuskegee University. I got to learn about the use of Chimera in my Biochemistry Class. I have been having difficulty in trying to determine the relevant interacting amino acids between molecules. Please, I will really appreciate it if this is made clearer to me. Thank You. Best Regards, Abisola Abisoye-Ogunniyan.

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Structure editing: addH
by George Tzotzos 10 Apr '14

10 Apr '14

Hi everybody, I’ve been trying to add hydrogens to a ligand (7-octenoic acid) obtained from docking. Hydrogens are added but not on the carboxyl group. I’m attaching the ligand.pdb for easy reference. I’d appreciate any suggestions regarding this behavior Best regards George

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Request for guidance
by MUHAMMAD RAMZAN MANWAR 08 Apr '14

08 Apr '14

Dear Dr. Ferrin, Hope this email finds you the best of your health. First of all, I did appreciate the effort that You and Your team did in the form of UCSF Chimera. Being the part of academic/government university, I have used Chimera tool for protein modeling and cited in my two articles: one published in JCB-Wiley and other in Hundawi in 2014. Current email I am sending to request for guidance about how can I substitute an amino acid (wild type to mutant residue) within protein 3D model by using Chimera. I will be thankful for your guidance, if possible. With regards Hussain MR PACER-HD, KAU, KSA

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Surprising "measure symmetry" result
by ingvar 08 Apr '14

08 Apr '14

Hello, I fetched entry EMD-2463 from EMDB and issued: measure symmetry #0 nMax 24 and got the result "Symmetry emd_2463.map: C13, center 64 64 37" Increasing the number of sampling points does not change the result, but if I increase the correlation criteria a little, to say 0.992, I get the expected C12 symmetry. Also if I change the contour level to 0.05, the author recommended level, I get C12 again. Looking at the volume at several different contour levels, it is difficult to see how it could be considered C13, and also how it would go from C13 to C12. Kind Regards, Ingvar Lagerstedt -- Ingvar Lagerstedt European Bioinformatics Institute (EMBL-EBI) European Molecular Biology Laboratory Wellcome Trust Genome Campus Hinxton Cambridge CB10 1SD Tel: +44 (0)1223 492533

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Docking ligands and protein using Chimera
by Sook Wong 08 Apr '14

08 Apr '14

Good morning, I am currently doing research with a professor for protein-ligand structure and would like to dock the receptor molecule (pdb file of the protein) and ligands (pdb file of the sugars). Since I have both the structure files from Chimera, how would I predict and assume which orientation bound to each other forming a stable complex? Looking forward to hear from you. Thank you so much! Sincerely, Sook Y Wong Chemical and Biomolecular Engineering '14 A. James Clark School of Engineering University of Maryland, College Park, MD 20742 swong18(a)terpmail.umd.edu

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Calculating SAS and SES with Chimera-MSMS wrap
by Jaime Rodríguez-Guerra 07 Apr '14

07 Apr '14

Dear Chimera dev team, I am trying to use your MSMS wrapper to compute some SAS/SES values for a given set of atoms. As suggested in a previous post in this list, I've taken a look into Measure.measure.buried_area() and I think I've got it, but just wanted to make sure. Here is my current procedure: ``` import chimera, Measure, MoleculeSurface atoms = chimera.selection.currentAtoms() xyzr_data = Measure.measure.atom_xyzr(atoms) surfaces = MoleculeSurface.xyzr_surface_geometry(xyzr_data) for i, a in enumerate(atoms): print "Atom: {0}, SAS: {1}, SES: {2}".format(a.name, surfaces[3][i,0], surfaces[3][i,1]) ``` Is this OK? I don't know how to handle all that output that MSMS is giving back! Thanks in advance, Jaime.

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Re: [Chimera-users] Reaction Mechanism Movie
by Eric Pettersen 07 Apr '14

07 Apr '14

On Apr 5, 2014, at 1:06 PM, Moses Adenaike wrote: > Dear Dr. Pettersen, > I am wondering how I would go about making a moive detailing a biochemical reaction. For example, I want to show a DNA polymerase reaction, essentially a ligation between the backbone of two nucleotides. How would I go about doing so? I know chimera has a make new bond function but I haven't been too successful at getting that to work. Hi Moses, It is typically better to send questions like this to the chimera-users mailing list than to me directly so that others can benefit from the answer and in case others on the list have more expertise on the topic than I do. The simplest method is to decide which frame# you want the bond to start existing and use the "Define script…" entry in MD Movie's Per-Frame menu to define a one-command script to execute at that frame. For example, if you wanted a bond between :337.A@P and :338.A@O3' to exist starting with frame 53, in the Per-Frame dialog you would set "Interpret script as" to "Chimera commands" and enter as your script: #53 bond :337.A@P :338.A@O3' There is also a hidden capability in Chimera to compute all bonds on a per-frame basis. I can tell you how to access that if it turns out you really need it. However, for the purpose of making a movie it might be nice to have a more "continuous" representation of the bond forming than just the binary on/off that the above approaches give you. I have attached a Python script that you can use the Per-Frame dialog (with "Interpret script as" set to Python, and reading in the script with the "Insert text file…" button) to have a bond form (by starting out very thin and becoming thicker) as two designated atoms approach each other. There are some values at the top of the script that you can edit to make it work best in your situation. There is a distance value for when the bond begins to exist (noBond, default 3.5) and when it reaches full size (fullBond, default 2.0). There is a two-member list of residue IDs (resIDs) for the atoms involved in the bond, and a list of atom names (atomNames). Let me know if you need more help than this. Hmmm, this all assumes you have a trajectory of the reaction. You may have to use the Morph Conformations tool to create such a trajectory if you don't have one already. --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu

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presets-interactive 3-hydrophobicity surface- those water molecules stay!
by Ying-Chieh Sun 06 Apr '14

06 Apr '14

Hi, I did a simulation using Amber package and saved a snapshot into its pdb file, and use Chimera to open it. The pdb file contains a protein-ligand complex plus a box of about 20000 TIP3P water molecules. When I pressed presets-interactive 3-hydrophobicity surface, there are 8 water molecules stayed close to the ligand binding site. I am wondering how these 8 water molecules were determined? The reason I ask is because we are trying to find a way to determine 'crystal (or say, ordered) water molecules'. This presets-interactive 3-hydrophobicity surface seems to perform this function in some way. Thank you for your help. Ying-chieh Ying-Chieh Sun, Professor of Computational Chemistry Chemistry Department National Taiwan Normal University Taipei, Taiwan 11617 Tel: +886-2-7734-6215 Fax: +886-2-2932-4249

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Resolution of .stl file of ribbon representatiom
by Gavin Whittaker 04 Apr '14

04 Apr '14

Dear all, I'm in the process of 3d printing a large protein in ribbon format; I've generated the .stl file, but the resolution of the mesh that Chimera creates means that the resulting file is too large to use easily. I've managed to use other software to reduce the resolution of the mesh, so I /can/ now get around the problem, but can anyone tell me if it's possible to reduce the resolution of the mesh in Chimera to save me a step for future models? I know how to reduce the resolution of a surface mesh, but files of ribbon representations remain obstinately large. One method I've used that gives limited results is to simplify the cross-sectional form of the ribbon, but I wonder, am I missing something obvious and more effective? thanks! Gavin

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query
by Bhaskar Bagchi 04 Apr '14

04 Apr '14

Respected Sir I want to calculate surface area of different atoms in a molecule. Is it possible in chimera? Please help me. Thanking you Yours faithfully, Bhaskar Bagchi Research Scholar Raiganj University College Email: bhaskarbagchi(a)gmail.com

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ellipsoid main axis alignment ?
by Hugo J Bohorquez 03 Apr '14

03 Apr '14

Hi, I am writing a script in python for generating a series of ellipses linking the nuclei a molecule. Every ellipsoid should be positioned at a specific location *P* = (X,Y,Z) and should be aligned with the orthonormal vectors describing its main directions-*A*, *B*, *C*. However, when I create an ellipsoid with shape_command it gets located correctly at *P* but it is aligned with the global axis. I can't find a general way to reorient an object so its original axes point along the vectors *A*, *B*, and *C*. I will appreciate any suggestion how to do it. -- Hugo J Bohórquez <https://sites.google.com/site/hugojbohorquez/home>, PhD *Investigador* Grupo de Biofísica Fundación Instituto de Inmunología de Colombia TEL. +57 +1 -3158920 Ext. 122 CEL. +57 315-6169069 *The Pauli energy grows exponentially with the electronic localisation <http://dx.doi.org/10.1080/00268976.2013.836605>*

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resampling maps
by Jason Kaelber 03 Apr '14

03 Apr '14

Hi all, I decided to do a rough alignment of density maps manually and resample onto a common coordinate system to feed the output mrc files into my fine aligner. But, when I vop resample #1 onGrid #0, I get, TypeError: Cannot cast ufunc add output from dtype('float32') to dtype('uint8') with casting rule 'same_kind' What might I be doing wrong to get this error? As far as I know, all the maps should be uint8 since they were most recently operated on by David Mastronarde's newstack command which outputs them as unsigned bytes. Thanks, Jason <type 'exceptions.TypeError'> Exception in Tk callback Function: <bound method MidasUI.processCommand of <Midas.midas_ui.MidasUI instance at 0x276b2d88>> (type: <type 'instancemethod'>) Args: (<Tkinter.Event instance at 0x276a2ea8>,) Event type: KeyPress (type num: 2) Traceback (innermost last): File "/opt/UCSF/Chimera64-1.8.1/lib/python2.7/site-packages/Pmw/Pmw_1_3/lib/PmwBase.py", line 1747, in __call__ return apply(self.func, args) File "/opt/UCSF/Chimera64-1.8.1/share/Midas/midas_ui.py", line 283, in processCommand midas_text.makeCommand(cmdText) File "/opt/UCSF/Chimera64-1.8.1/share/Midas/midas_text.py", line 69, in makeCommand f(c, args) File "/opt/UCSF/Chimera64-1.8.1/share/VolumeFilter/ChimeraExtension.py", line 24, in vop_cmd vop_command(cmdname, args) File "/opt/UCSF/Chimera64-1.8.1/share/VolumeFilter/vopcommand.py", line 91, in vop_command doExtensionFunc(func, fargs, specInfo = spec) File "/opt/UCSF/Chimera64-1.8.1/share/Midas/midas_text.py", line 435, in doExtensionFunc extFunc(*tuple(processedArgs), **kw) File "/opt/UCSF/Chimera64-1.8.1/share/VolumeFilter/vopcommand.py", line 553, in resample_op boundingGrid, False, None, modelId) File "/opt/UCSF/Chimera64-1.8.1/share/VolumeFilter/vopcommand.py", line 168, in add_operation scale = scale[i]) File "/opt/UCSF/Chimera64-1.8.1/share/VolumeViewer/volume.py", line 1535, in add_interpolated_values m[:,:,:] += values <type 'exceptions.TypeError'>: Cannot cast ufunc add output from dtype('float32') to dtype('uint8') with casting rule 'same_kind' ================================================ Event contents: char: delta: 36 height: ?? keycode: 36 keysym: Return keysym_num: 65293 num: ?? send_event: False serial: 39103 state: 16 time: 139539396 type: 2 widget: .59791048.661335648.802317088.802317376.802317448 width: ?? x: 159 x_root: 524 y: 9 y_root: 988 TypeError: Cannot cast ufunc add output from dtype('float32') to dtype('uint8') with casting rule 'same_kind' File "/opt/UCSF/Chimera64-1.8.1/share/VolumeViewer/volume.py", line 1535, in add_interpolated_values m[:,:,:] += values See reply log for Python traceback. -- National Center for Macromolecular Imaging, N420 Baylor College of Medicine, MS BCM125 1 Baylor Plaza Houston, TX, USA

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Is there a way to save animation editing process?
by Li, Leon 03 Apr '14

03 Apr '14

Dear all, I'm try to save all my editing of animation, it seems that 'save session' can't save 'scenes', 'timelines', etc. I wonder is there a way to save all the process, so that I can re-open it to edit. Thanks, Leon

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combining different chains
by faeze mohajer 01 Apr '14

01 Apr '14

good day I have modeled heavy and light chains of myosin now I want to combine them through chimera, would you plz help me on that your faithfully *FAEZE SADAT MOHAJERPhD Student * *Faculty of Bioscience and Medical Engineering (FBME)* *Universiti Teknologi Malaysia (UTM)* Buzzdock ads <http://www.buzzdock.com/setting/V2hpbG9raWk=> Search ResultsFaculty of Biosciences & Medical Engineering<http://fbme.utm.my/>

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Re: [Chimera-users] Chimera Shutting Down
by Tom Goddard 31 Mar '14

31 Mar '14

Hi Joshua, Glad to hear that the new graphics driver fixed the Chimera side view crash on your Ubuntu 12.04 system. Maybe this will help some other Chimera users. Tom On Mar 31, 2014, at 12:33 PM, Joshua Broyde wrote: > Dear Tom, > I installed a new graphics driver, so now it works. In case anybody else has this same problem, I installed the Gallium Radeon driver and it worked fine. I followed step 2 from this link: > http://arstechnica.com/civis/viewtopic.php?f=16&t=1137372 > > Thanks for the tip. > Sincerely, > Joshua Broyde > ----- Original Message ----- > From: "Tom Goddard" <goddard(a)sonic.net> > To: "Joshua Broyde" <jb3401(a)c2b2.columbia.edu> > Cc: chimera-users(a)cgl.ucsf.edu > Sent: Thursday, March 27, 2014 12:58:50 AM > Subject: Re: [Chimera-users] Chimera Shutting Down > > The crash is due to a buggy graphics driver and the only fix is likely to be installing a working graphics driver. Sometimes some trick like starting the side view before opening models as described in the post you referenced avoids the problem, but usually there is no way to avoid a graphics driver crash other than replace the driver with one that doesn’t have the bug. > > Tom > > > On Mar 26, 2014, at 6:05 AM, Joshua Broyde wrote: > >> Hi, >> I am using the Chimera Linux 64-bit (chimera-alpha-linux_x86_64.bin), and Chimera shuts down when I try to open the Side View option. I tried the workaround mentioned here: http://plato.cgl.ucsf.edu/pipermail/chimera-users/2013-April/008765.html but it is not working for me. >> >> OS: Ubuntu 12.04 >> Version of Chimera: Linux 64-bit Daily Build (Mar 24, 2014) >> >> >> For what it's worth, on another computer where I am running Ubuntu 12.10, with Chimera Linux 64-bit Daily Build (July 10, 2013), I did not have this problem. >> Is there another workaround that I could do to open the side view? >> >> Thanks! >> >> Sincerely, >> Joshua Broyde >> _______________________________________________ >> Chimera-users mailing list >> Chimera-users(a)cgl.ucsf.edu >> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users >> >

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Binding pocket surface command script not working
by Markus Heller 28 Mar '14

28 Mar '14

Hello, I'm trying to reproduce the Binding Pocket Surface image from the Gallery with a different pdb file. I can successfully reproduce with the pdb used in the example (2zcp), but not with 2v5z. Running latest Chimera. Steps to reproduce: open 2v5z delete :.b split atoms :sag surface measure contactArea #0.2 #0.1 3 slab -.1,0 color tan gives an error: error: Array must be 2-dimensional, got 1-dimensional File "C:\Program Files\Chimera 1.8.1\share\MeasureVolume\__init__.py", line 60, in surface_area area = surface_area(varray, tarray) See reply log for Python traceback. Why, and would it be helpful to file a bug report? Thanks and Cheers Markus -- Markus Heller, Ph.D. NMR Scientist CDRD - The Centre for Drug Research and Development 2405 Wesbrook Mall, Fourth Floor | Vancouver, BC V6T 1Z3 | Main: (604) 827-1147 Direct: (604) 827-1122 | F: (604) 827-1299 | E: mheller(a)cdrd.ca<mailto:mheller@cdrd.ca> | www.cdrd.ca [cid:image007.png@01CF49BD.0097D1F0] Follow us: [Description: cid:image003.jpg@01CD86A6.39B41A10] <https://twitter.com/C_D_R_D> [Description: cid:image005.jpg@01CD86AE.B197F5D0] <http://www.linkedin.com/groups/CDRD-3186016/about?report%2Esuccess=3NcE4iZo…> [Description: cid:image009.png@01CD86AE.B197F5D0] <https://www.facebook.com/pages/The-Centre-for-Drug-Research-and-Development…> [Description: cid:image010.png@01CD86AE.B197F5D0] <http://www.youtube.com/user/CDRDCVI?view_as=public> This email and any files transmitted with it are confidential and intended solely for the addressee. If you are not the named addressee you should not disseminate, distribute, copy, or alter this email.

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Chimera surface error
by Elaine Meng 28 Mar '14

28 Mar '14

On Mar 28, 2014, at 4:27 AM, Uzma Saqib wrote: > Hi Elaine, > Chimera is not showing me the surface of my protein file and gives the attached eror. > i tried what it suggested, but no improvement. > plz help. > attashed , is the pdb. This is a common problem in Chimera. Some explanation and all of our ideas for possible solutions are in this page (no use for me just to repeat that information here): <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/surfprobs.html> #3 and #4 in that page will always work because they use different methods instead of the standard molecular surface calculation. Sorry for the inconvenience, 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. better to send chimera questions to chimera-users(a)cgl.ucsf.edu, unless including private data

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Measuring surface area of region
by Anindito Sen 27 Mar '14

27 Mar '14

Dear all, I was wondering if there is any way one can measure the surface area with a threshold higher than its neighbouring region in a TEM micrograph ? Thanks Andy Dr. Anindito Sen (Ph.D) >

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Chimera Shutting Down
by Joshua Broyde 26 Mar '14

26 Mar '14

Hi, I am using the Chimera Linux 64-bit (chimera-alpha-linux_x86_64.bin), and Chimera shuts down when I try to open the Side View option. I tried the workaround mentioned here: http://plato.cgl.ucsf.edu/pipermail/chimera-users/2013-April/008765.html but it is not working for me. OS: Ubuntu 12.04 Version of Chimera: Linux 64-bit Daily Build (Mar 24, 2014) For what it's worth, on another computer where I am running Ubuntu 12.10, with Chimera Linux 64-bit Daily Build (July 10, 2013), I did not have this problem. Is there another workaround that I could do to open the side view? Thanks! Sincerely, Joshua Broyde

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Viewing Gromacs 4.6.5 trajectories
by William McDonald 26 Mar '14

26 Mar '14

Hello Chimera users, I recently upgraded my gromacs simulation software from 4.5.5 to 4.6.5; however, when I attempt to load a new simulation trajectory (either a .xtc or .trr file), Chimera allocates ~13GB RAM causing my machine to swap, and Chimera never loads the trajectory. The old trajectories from gromacs 4.5.5 load with out any problems. Has anyone else experienced this? I am using 64 bit Chimera 1.8.1 on a dual quad-core Mac Pro running OS 10.6.8. The simulation has ~50000 atoms of protein, lipid, and water and is 1ns long. -- William J. McDonald Postdoctoral Scholar Department of Chemistry and Biochemistry University of California, Santa Cruz

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