- Chimera-users - RBVI Mailing Lists

closing the surface of a monomer from a dimer PDB
by Jakob Suckale 04 Mar '16

04 Mar '16

Hi all, I'm trying to generate a surface structure of tubulin A from a dimer coordinates file like 1TUB. Surfaces generated from the Action menu are cut open at the contact site between the monomers (see attachment). How can I generate a continuous surface for only one protein monomer? All the best, Jakob

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Difference mapping
by Saumya Verma 02 Mar '16

02 Mar '16

Hello everyone! I am relatively new to cryoEM and am solving my first structure. I have a question about difference mapping using Chimera, and Id like to apologize in advance if its too naïve a question for this forum. I have a cryoEM structure of a mutant virus; the x-ray structure of the wild-type virus is known. To see the differences between the two structures, I am following the following steps: - Deleting the mutated chains from the pdb (so that Ill be able to detect these in the cryoEM map) and converting the crystal structure .pdb file to .mrc, low pass filtering it to the resolution of the cryo-em refined structure and matching box size and A/pix - Fitting the two maps in Chimera and subtracting the volumes (using the command vop subtract) My question is - how do we decide the resolution to which to lowpass filter the original structure? The reason Im asking is because while my cryoEM structure is 13.3A (FSC gold standard) (Ive also checked with ResMap majority of the voxels are ~14A), it looks very less detailed when compared to the lowpass-filtered map of the original pdb. And when Im fitting the two, there are major differences in the contours, which I think is giving me false differences. Can someone please let me know what would be the best way to compare the cryoEM structure of mutant virus with the published structure of the wild-type virus. Thank you very much. Regards, Saumya PhD Student Indian Institute of Technology Delhi, India

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Re: [Chimera-users] Screen shots from coot
by Oliver Clarke 02 Mar '16

02 Mar '16

Hi John, don't know how to do exactly what you want re raster3d, but in order to avoid fiddling with the volume viewer I use a couple of aliases which make things faster, perhaps they will be useful to you too: #Usage cootmode_wire alias ^cootmode_wire ~rib; disp; color gold; color byhet; repr wire; setattr m lineWidth 2; volume # capfaces false style mesh meshlighting false squaremesh false color "#3333851effff" step 1; sop cap off; set depthCue; set dcStart 0.5; set dcEnd 0.7; background solid black; cofron; symclip 5 #Usage cootmode_wire_white alias ^cootmode_wire_white ~rib; disp; color gold; color byhet; repr wire; setattr m lineWidth 2; volume # capfaces false style mesh meshlighting false squaremesh false color "#00000000cccc" step 1; sop cap off; set depthCue; set dcStart 0.2; set dcEnd 1; background solid white; cofron; symclip 5 Also, to set maps or diffmaps to given rms level: # Sets map to x*RMS # Usage: sig #map_id rms alias ^map_sig volume $1 sdlevel $2 alias ^diffmap_sig volume $1 rmsLevel -$2 color #da1200000000 rmsLevel $2 color #0000bda00000 Or to just load map and diffmap with model from pdb, and set display settings of maps: #Load pdb and associated maps from EDS # Usage: load_pdb_and_maps pdb_id alias ^load_pdb_and_maps open 1000 $1; open 1001 edsID:$1; open 1002 edsdiffID:$1; cootmode_wire; map_sig #1001 1; diffmap_sig #1002 3 (Requires that the other aliases mentioned already exist, of course) Cheers, Oli.

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MatchMaker
by sdimicco 01 Mar '16

01 Mar '16

Dear Developer, I am using MatchMaker to compare some peptides. I would like to know if the RMSD value is referenced to the backbone atoms or to whole atom structure. Thank you in advamce. All the best.

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Screen shots from coot
by John Rose 01 Mar '16

01 Mar '16

Hi, I colleague of mine just showed me that pyMOL can display great looking ED images from COOT which were saved in RASMOL format. Is there a way for CHIMERA to do this. John Rose John Rose Ph.D. Associate Professor B204B, The Fred C. Davison Life Sciences Complex 120 Green Street Department of Biochemistry and Molecular Biology University of Georgia Athens, GA 30602-7229 ========================================= Phone: 706-542-1750 Fax: 706-542-3077

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multiple mutations
by Andrew N 29 Feb '16

29 Feb '16

Hello: How can mark (change color) for ~ 100 mutations at once? Is it possible to write a "code" for that? I would like to have random (different) colors for every mutation. It the case, if mutation lay down very close and same color would make it difficult to tell them apart. Another question: How to add a label like "V75" (Amino acid and position, not "V75.A") with all with black color (not the same color that marks mutation on 3D structure)? Thank you. Sincerely, Andrew

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Mutagenesis
by Andrew N 29 Feb '16

29 Feb '16

Is it possible to change a single amino acid to see 3D structure changes? Thank you. Sincerely, Andrew

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Temperature during chimera minimization (pdb)
by Vasantha Kumar 29 Feb '16

29 Feb '16

Dear Chimera user I have calculated the structures of a peptide at 273K (0 °C), then I have extracted low energy structures and minimization them in chimera. I am not sure chimera performed minimization at 273K or 298K. Could any one suggest me at what temperature chimera performs minimization (with explicit solvent), is there is a way to set different temperature. thank you so much in advance... Vince

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Could chimera draw shapes faster?
by Ferdinando Randisi 26 Feb '16

26 Feb '16

Hi! I'm one of the developers of oxDNA ( https://dna.physics.ox.ac.uk/index.php/Main_Page) a code aimed at simulation of large DNA structures for biology and nanotechnology. We often use chimera because, frankly, it makes gorgeous pictures. Since we simulate DNA as made by rigid nucleotides instead of atoms, we hijack it to make it plot various shapes instead of using atoms directly, but it takes forever to get it to load a configuration like the one attached. Could you guys do something to make it faster/give as some advice on how to make it plot these things faster? We currently use the input files attached. (chimera.txt should be renamed chimera.com so that it can be understood by chimera). Best, Ferdinando -- Ferdinando Randisi

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VR support
by Gökhan Tolun 25 Feb '16

25 Feb '16

Hi, Now that the pre-orders are being placed for VR headsets, are you planning to support the headsets like Oculus Rift and HTC-Vive for 3D stereo Opening rendering? Looks like nVidia is making this easier for developers: https://devblogs.nvidia.com/parallelforall/vr-sli-accelerating-opengl-virtu… Thanks. Gökhan

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minimal graphic card
by Fabian Technion 25 Feb '16

25 Feb '16

Hi, I would like to know your reccomendation for a minimal graphic card standard that will work nicely with chimera. It is for 20 PC for a teaching room. Thanks a lot in advance, Fabian Dr. Fabian Glaser Head of the Structural Bioinformatics section Bioinformatics Knowledge Unit - BKU The Lorry I. Lokey Interdisciplinary Center for Life Sciences and Engineering Technion - Israel Institute of Technology, Haifa 32000, ISRAEL fglaser at technion dot ac dot il Tel: +972 4 8293701 http://bku.technion.ac.il

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Segment according to fitted model
by David Haselbach 25 Feb '16

25 Feb '16

Hi, I do have a cryo EM map of a large complex and I fitted/modeled the individual protein components. Now I would like to segment my map according to those fitted models. Is there a possibility of doing that automatically? Cheers David

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Obtain list of residues in CASTp pocket
by Felipe Vasquez 25 Feb '16

25 Feb '16

Hi, I recently could detect those residues composing certain pocket of my protein, which appeared colored in green at the complete 'sequence' window. However, I wonder if it is possible to obtain these residues as a list (thr59, Val115, etc) useful as a txt or other similar format. Is there some way to achieve this goal? It could be possible for Surfnet also? Thanks in advance for your help. Best regards, *Andrés Felipe Vásquez J., BSc, MSc.* Profesional - Grupo de Fisiología Molecular Subdirección de Investigación Científica y Tecnológica Dirección de Investigación en Salud Pública Instituto Nacional de Salud Avenida calle 26 No. 51-20 - Zona 6 CAN +57 (1) 2207700 ext. 1419 Bogotá, D.C., Colombia

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Assign distance between every atom and an axis or plane to an attribute
by Oliver Clarke 24 Feb '16

24 Feb '16

Hi, I would like to iterate over all atoms in a model, measure the distance between each atom and a predefined axis or plane in the session, and assign the distance to an attribute associated with the atom. For bonus points I would like to do the same for two models (the same protein in different conformations), and then calculate the difference in this distance for matched pairs of atoms. The first part of this - iterating over every atom - I know how to do, more or less, in the scripting interface (I am assuming there is no way to do this kind of "iterate/run command/ assign command output to attribute" operation in the attribute calculator). But how do I measure the distance between an atom and a selected plane/axis, and then assign it to an attribute that I can use for example in Render by Attribute? I can see how to measure the distance between pairs of atoms, but not between atoms and a plane or axis. Cheers, Oli

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Chimera and stereo viewing
by Elaine Meng 18 Feb '16

18 Feb '16

Hello Chimera users, Recently (December 2015), there have been some questions and comments about Chimera and stereo viewing. To summarize: - Except as noted below, “stereo in a window” (quad-buffer stereo) requires a workstation-class graphics card and a good stereo-capable display. - We have not found a consumer-class graphics card that does quad-buffer stereo reliably with Windows 10. For using Chimera with stereo glasses and a consumer-grade card, the only configuration we’ve seen work is the following: - a Windows 8/8.1 PC - an ATI graphics card supporting HD3D - a 3D TV For more details, please see: http://plato.cgl.ucsf.edu/trac/chimera/wiki/hardware On behalf of the Chimera team, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco

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Installing colorbrewer for Chimera Python
by Paul Kibet Korir 18 Feb '16

18 Feb '16

Hi, I want to use the chimera API and I've managed to configure a successful import of chimera except that I get that colorbrewer is not installed. >>> import chimera Traceback (most recent call last): File "<stdin>", line 1, in <module> File "/Applications/Chimera.app/Contents/Resources/share/chimera/__init__.py", line 73, in <module> import palettes File "/Applications/Chimera.app/Contents/Resources/share/chimera/palettes.py", line 103, in <module> _initPresets() File "/Applications/Chimera.app/Contents/Resources/share/chimera/palettes.py", line 95, in _initPresets from colorbrewer import ColorBrewer ImportError: cannot import name ColorBrewer What is the right way to go about this? (I could create a symbolic link to my system colorbrewer, but that doesn't seem clean). -- With kind regards, *Paul K Korir, PhD* /Scientific Programmer/ EMBL-EBI Main Building, A2-35, WTGC, Hinxton, Cambridge CB10 1SD P: +44 1223 49 44 22 F: +44 1223 49 44 68

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Query
by manan 17 Feb '16

17 Feb '16

Chimera allows users to add ions to a given structure using Amber tools. This option has a predecided set of ions. Is it possible to add ions other than those mentioned in the add ions option. For example,Ca2+ is not included in the list, so is it possible to add Ca2+ ions? -- Manan Desai Research Student Department of Biochemistry The Institute of Science 15 Madame Cama Road, Mumbai-400 032 India

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Error when starting Chimera
by Jérémie KNOOPS [531802] 16 Feb '16

16 Feb '16

Dear Chimera Users, When I launch chimera, I get directly the "Chimera Launcher Error" box with this message : "chimera exited abnormally; the exit code was: 1" I got this screen when I used the debugging command:

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StructureViz and Chimera Path in Cytoscape
by Pat Daley 12 Feb '16

12 Feb '16

Hi, It doesn't remember the path to Chimera after closing/opening Cytoscape. Any ideas? Can I manually write the path into a config file somewhere? Thanks!

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mapping between MRC and PDB
by rongjian li 12 Feb '16

12 Feb '16

Hi, I am a beginner in using Chimera. I have a simple question for you experts and I really appreciate any guide for me. I am working on a project needs to create a one-to-one mapping between MRC grid and PDB atoms. For example, from the PDB file, I know the physical coordinates of each atom. I want to know whether each atom is out of the 3D volume of MRC or not. If it is inside the volume, I hope to know which voxel grid this atom is in. I have figured out the mapping between the physical origin of PDB system and its grid index in MRC using Chimera Volume Viewer -- > Features ---> Coordinates ----> Origin Index. But I am not sure whether the information of 'Rotation axis' is also very important, which is usually [0,0,1] in Chimera Volume Viewer -- > Features ---> Coordinates ----> Rotation axis. Thank you very much. Best, Rongjian

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Will ChimeraX be built with a universal undo?
by Oliver Clarke 10 Feb '16

10 Feb '16

I realise this is probably impossible to alter in the current version of chimera, but will the next-gen Chimera be built with a universal (or at least much expanded) undo function (or set of functions)? Or if not what are the devs thoughts on this - I know it is a complicated issue, but the capacity to backtrack after making a color change, deleting a selection, etc, would be very very welcome. Cheers, Oli

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Thoughts re enhancements for ChimeraX
by Oliver Clarke 10 Feb '16

10 Feb '16

Hi, just thinking about a couple of possible enhancements relating to things that are probably difficult to fix in the current framework, feel free to take or leave them. * Hover to label residue is useful, but slow. Maybe hold down alt/option and have the residue currently under the cursor instantly bring up a residue label (or put the residue label in the lower status bar, and have it change when the cursor moves over another residue)? * Selecting molecules inside (e.g. mesh) density maps is a little cumbersome in that it requires un-showing the mesh map first, even though model is clearly visible - ctrl-clicking on an atom usually selects the map instead (which is only rarely the desired outcome). perhaps a modifier key to specifically allow selecting atoms, ignoring maps, would be useful in this instance? Cheers, Oli.

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Do attribute names have to be case sensitive?
by Oliver Clarke 10 Feb '16

10 Feb '16

Apologies for spamming the message board... in Chimera at present, attribute names (e.g. stickScale) are case sensitive. I understand that this is the way it was built and there is probably no changing it in the current version of Chimera, but assuming ChimeraX has a similar concept of attributes built in, would it be possible to make these case-insensitive? I can't imagine there are many situations where case would make a difference to the intended attribute (and if there are there probably should not be). I have many cases where I type e.g. "setattr m stickscale 2.0", nothing happens and there is no error message, and I am confused until I realise I should have typed "setattr m stickScale 2.0". Alternatively, raising an error message in the status bar when a user attempts to alter a nonexistent attribute would also be helpful. Cheers, Oli.

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measure distance
by Jingchuan Sun 09 Feb '16

09 Feb '16

Hello, I use "measure center #11 mark true radius 20" to make a ball to represent a model, then use "measure distance #13 #14 show true". I get a number of distance between the two balls. Is it pixel value or angstrom? Is it between the center or surface of the two balls? Best, Jingchuan

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uninscribe
by Barry Lever 08 Feb '16

08 Feb '16

-- A. B. P. Lever, FRSC Distinguished Research Professor Emeritus Chemistry, CB124, York University 4700 Keele St., Toronto, Ont., Canada M3J 1P3 Tel:416-736-2100 x22309 http://www.chem.yorku.ca/profs/lever

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