- ChimeraX-users - RBVI Mailing Lists

Troubles when saving a map
by Stéphane ROCHE 17 Jun '21

17 Jun '21

Dear Mr/Mrs, I am new to ChimeraX (v 0.7) and I have a trouble when saving a map. I am working with a .ccp4 map from an electron microscopy project. I would like to slightly change the pixel size that was inaccurately estimated during data processing and chimeraX seems to be the program for doing that. - Opening the map is fine. - Then I change the pixel voxelsize which is also fine. - I then save the modified map (I use the .mrc format here given that I do not find a .ccp4 format). - However if I then use the map with my usual softwares (phenix, coot) it looks like pure noise. But the map looks normal with some other softwares (e.g. pymol). I also have no problem usually with my .mrc maps with any software so I would assume the problem is with the .mrc map I created Do you know what I could do to solve this problem ? Thanks, Stephane Roche Institut de Biologie Intégrative de la Cellule 91198 Gif sur Yvette France

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listing all-by-all atom distances
by Elaine Meng 15 Jun '21

15 Jun '21

> On Jun 15, 2021, at 9:33 AM, Juliana Glavina <jglavina(a)gmail.com> wrote: > > Hi Elaine, > I am trying to calculate the distance between one residue and a set of residues (within a name selection). I couldn't do this in Chimera either and I couldn't find the answer online. > Thanks! > Juliana Hi Juliana, (We recommend using the chimerax-users address CC'd here for questions, so that the Q & A will be archived and searchable.) One way to do it in ChimeraX is with the "contacts" command or Contacts tool. In this case you aren't necessarily using it to find contacts, but instead to measure and list atom-atom distances. You say "residues" but really all the distances are measured from atom to atom. You will get all by all distances between two sets of atoms, where the first set is your first residue and the second set is all the residues in your named selection. In ChimeraX, you can name the current selection or some other specification with the "name" command. To name the current selection "blah" it would be command: name frozen blah sel See "name" help: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/name.html> Then if you want to measure all atom-atom distances between (1) atoms in residue 55 of chain A of model 1 and (2) your named selection "blah" and show them in the Log, you could use a command something like contacts #1/A:55 restrict blah overlap -1000 log true The large negative overlap value is used to force measuring all the distances even if the atoms are 1000 Angstroms apart, instead of the usual behavior of finding only the contacts. The Log will have lines like the following, where the last column is the distance between atomic centers: 1728 contacts atom1 atom2 overlap distance /A BGC 310 C6 /A TYR 10 CE2 0.018 3.622 /A BGC 310 O6 /A HIS 152 NE2 -0.134 2.834 /A BGC 310 O4 /A TRP 183 CG -0.202 3.272 /A BGC 310 C3 /A TRP 183 CE3 -0.253 3.893 /A BGC 310 C2 /A PHE 16 CD1 -0.323 3.963 /A BGC 310 C5 /A HIS 152 NE2 -0.360 3.880 /A BGC 310 C6 /A HIS 152 NE2 -0.366 3.886 /A BGC 310 O4 /A TRP 183 CD2 -0.424 3.494 /A BGC 310 C5 /A TRP 183 CE2 -0.429 3.919 /A BGC 310 O6 /A HIS 152 CD2 -0.490 3.710 /A BGC 310 C3 /A TRP 183 CZ3 -0.495 4.135 /A BGC 310 O4 /A TRP 183 CD1 -0.499 3.719 /A BGC 310 O6 /A HIS 152 CE1 -0.556 3.776 /A BGC 310 C5 /A TRP 183 NE1 -0.596 4.116 [...] The lines are in order of largest VDW overlap which is similar to shortest distance but not exactly the same. If you save to text file you can then sort by column, for example, by the second residue number to group those together, or by the distance. The "contacts" command has a lot of options including saving results to text file, as detailed here: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/clashes.html> You can do the same thing in Chimera, name selection and use "findclash" but the exact commands and their syntax are slightly different. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco

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Adjusting coil width
by Edgar A Hodge 15 Jun '21

15 Jun '21

Hello, I'm struggling to adjust the coil width. This seems easy to do using the "cartoon style" command, but I can't seem to figure it out with coils. Thanks! Eddie

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align peptide to model sequence
by Lagerwaard, I.M. (Ilse) 15 Jun '21

15 Jun '21

Hi everyone, I want to write a script that can align the sequences of peptides to a model sequence and return the identical residues. Because I am new to programming, I could really use some help to get started. Could I use the search() method of the Sequence class for this? And if so, how could I go about this? Kind regards Ilse Lagerwaard

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Mesh resolution/smoothness
by Saren Tasciyan 15 Jun '21

15 Jun '21

Hi, I am trying to generate STL files out of protein models. Often the problem is that the mesh doesn't as smooth as the models (see pics below). I wonder if this is an artifact of rendering in ChimeraX or the mesh is actually hard coded to have certain resolution, which makes it look like this? I tried to find out why and ended up in custom_x3d function but didn't notice anything. Post-export smoothing is an option but I wonder, if that's the optimal approach? Perhaps, smoothing can create collisions between 2 STL models, where a higher resolution export may avoid this. Best, Saren -- Saren Tasciyan /PhD Student / Sixt Group/ Institute of Science and Technology Austria Am Campus 1 3400 Klosterneuburg, Austria

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dual conformation
by Wen-Jin Winston Wu 14 Jun '21

14 Jun '21

Hi, I am trying to use Chimera X to display an amino acid with dual side chain conformations (PDB code: 7a5v) together with its cryoEM density map (EMDataResource: <https://www.emdataresource.org/EMD-11657> EMD-11657). For example, Tyr 66 have two side chain conformations, however using the command below, it only showed one conformation. resfit /a:66 map #1 (a very nice command, by the way) I then used Chimera 1.15 to view the PDB coordinate, and it showed two side chain conformations for Tyr66 (as I saw in PyMol); on the other hand, Chimera X only shows a single conformation. Is there any way to display the two alternative conformations using Chimera X? Thanks a lot for your time, and possible help! Best wishes, Winston ************************* ATOM 495 N ATYR A 66 124.799 162.717 112.222 0.50 11.67 N ATOM 496 N BTYR A 66 125.017 162.760 112.080 0.50 12.99 N ATOM 497 CA ATYR A 66 124.008 162.914 110.998 0.50 12.05 C ATOM 498 CA BTYR A 66 124.035 162.916 111.002 0.50 14.20 C ATOM 499 C ATYR A 66 124.638 164.062 110.190 0.50 11.84 C ATOM 500 C BTYR A 66 124.433 164.115 110.140 0.50 13.40 C ATOM 501 O ATYR A 66 125.008 165.077 110.788 0.50 11.86 O ATOM 502 O BTYR A 66 124.411 165.246 110.660 0.50 14.99 O ATOM 503 CB ATYR A 66 122.562 163.249 111.355 0.50 13.02 C ATOM 504 CB BTYR A 66 122.666 163.125 111.624 0.50 17.22 C ATOM 505 CG ATYR A 66 121.759 162.139 111.997 0.50 14.56 C ATOM 506 CG BTYR A 66 121.542 163.315 110.654 0.50 21.09 C ATOM 507 CD1ATYR A 66 121.860 161.839 113.348 0.50 16.21 C ATOM 508 CD1BTYR A 66 120.718 162.258 110.325 0.50 25.90 C ATOM 509 CD2ATYR A 66 120.832 161.436 111.248 0.50 17.74 C ATOM 510 CD2BTYR A 66 121.189 164.579 110.209 0.50 29.25 C ATOM 511 CE1ATYR A 66 120.974 160.942 113.960 0.50 18.53 C ATOM 512 CE1BTYR A 66 119.590 162.443 109.543 0.50 32.51 C ATOM 513 CE2ATYR A 66 119.990 160.494 111.824 0.50 18.57 C ATOM 514 CE2BTYR A 66 120.067 164.784 109.421 0.50 27.89 C ATOM 515 CZ ATYR A 66 120.076 160.228 113.177 0.50 20.29 C ATOM 516 CZ BTYR A 66 119.252 163.714 109.107 0.50 30.80 C ATOM 517 OH ATYR A 66 119.241 159.287 113.722 0.50 24.21 O ATOM 518 OH BTYR A 66 118.168 163.886 108.291 0.50 39.05

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using pandas
by Lagerwaard, I.M. (Ilse) 11 Jun '21

11 Jun '21

Hello everyone, Is it possible to use the pandas package in ChimeraX? I tried opening a Python script containing the line 'import pandas', but I get the error: 'ModuleNotFoundError: No module named 'pandas''. Kind regards, Ilse

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Independent centres of rotation
by Shahid, Taha (Dr.) 10 Jun '21

10 Jun '21

Hi, Is there a method, even if an indirect one via a long command or a series of commands, to set independent rotation centres for a series of (cryo-EM) maps that would then turn together. This could be easily achieved by 'set independent' in the original Chimera, and is much missed by our group of structural biologists. Kudos otherwise on a wonderful upgrade to the program. Many thanks, Taha

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Re: [chimerax-users] saving multiple .obj files from a morph
by Elaine Meng 09 Jun '21

09 Jun '21

On Jun 9, 2021, at 3:38 AM, Brett Murrah <murrahx5(a)att.net> wrote: > I’m trying my best to use the perframe command to save each frame / model out from a morph and slider animation after morphing some pdbs. It is exporting something.. but only 1k files. I’m not sure what I’m doing wrong. Any help? My command is this: > > perframe "save D:/Projects/OBJs/model$1.obj model #3.$1" frames 10 > > PS, I put model #3 because the ID’s for 1 and 2 are the models I used for the morphs. The final morph is #3. If I export each slider frame by hand.. that seems to work. Trying to automate it best I can. > > Thanks you for any help! > Brett Hi Brett, I'm guessing you meant to send this to chimerax-users(a)cgl.ucsf.edu (CC'd here, the recommended address for questions). The morph #3 is a trajectory model. It does not have the frames as submodels #3.1, 3.2, ... so your save command doesn't make sense. I don't know what you mean by "1k files" either... do you mean it makes 10 files but they are too small? You would use "perframe" in combination with "coordset" to replay the existing morph trajectory. E.g. put something like this into a command file (plain text named something.cxc) and then open it in ChimeraX: perframe "save D:/Projects/OBJs/model$1.obj models #3" coordset #3 1,10; wait 10 ~perframe <https://rbvi.ucsf.edu/chimerax/docs/user/commands/coordset.html> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/perframe.html> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/save.html> The reason I say to put it in a command file is to make the commands execute instantly one afer the other. I expected it to work when I entered them all as one long line in the command line (with semicolon separators) but then I got a parsing error, possibly due to a bug. E.g. I tried entering this as one long line (the mail tool may choose to break it up): perframe "save D:/Projects/OBJs/model$1.obj models #3"; coordset #3 1,10; wait 10; ~perframe ... but that gave an "incomplete quoted text" error which I will report as a bug. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco

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Change default volume display settings?
by Oliver Clarke 08 Jun '21

08 Jun '21

Hi, Is there any way in ChimeraX to change default volume display settings? For example, I would like to set all volumes to "step 1" by default - in Chimera I can set these defaults in the Volume Viewer menu but I can't see an equivalent in ChimeraX. Sort of related - I wonder if it would be possible to have the option to set default display preferences for molecules or maps? Or more generally, have a script that executes when a file of a particular type is loaded - similar to how the startup commands are executed when ChimeraX is started, but triggered by the opening of a particular filetype and applied to that particular model? Cheers Oli

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Surface Coloring
by Juliana Glavina 07 Jun '21

07 Jun '21

Dear All, I am moving from Chimera to ChimeraX and I am trying to reproduce some of things that I used to do in Chimera. I managed to colour the surface by the kdHydrophobicity scale. However, the coloring is discrete with sharp edges between the residues. I was wondering if it was possible to smooth the edge between two different colors on the surface - similar to mlp but with customized attributes. Thank you very much in advance UCSF ChimeraX version: 1.2.3 (2021-05-13) Ubuntu 20.04 Juliana

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Re: [chimerax-users] Unit cell orientations
by Elaine Meng 04 Jun '21

04 Jun '21

> On Jun 4, 2021, at 10:39 AM, Silva, Chinthaka Mahesh <silva228(a)llnl.gov> wrote: > > Hi Elaine, > Is it possible to orient a unit cell along different axes in ChimeraX? I tried using ‘Unit cell’ option, but not sure if this is the correct place to do it. > Thanks! > -chinthaka Hi Chinthaka, (CC to chimerax-users(a)cgl.ucsf.edu ... please use that address for ChimeraX questions) Sorry, I don't understand the question. You can build the unit cell or a block of multiple unit cells with the Unit Cell tool: <https://rbvi.ucsf.edu/chimerax/docs/user/tools/unitcell.html> The axes of the unit cell are defined in the data... it is not something that you control. Of course, you can rotate it after you build it. Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco

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Consultation about developing plug-ins in ChimeraX
by Chen, Xiang 28 May '21

28 May '21

Dear Sir or Madam, I am a graduate student in the Department of Computer Science at the Memorial University of Newfoundland. I am currently engaged in developing and researching VR applications to visualize biological microstructures. I learned that Chimerax is a relatively mature piece of software, containing many excellent functions and features. So I'd like to know: 1. Is ChimeraX completely open-source and free? I will only use it for research and non-profit purposes. 2. If ChimeraX is open source, is there a description or summary of the structure/principles of the source code? (In order to learn what features are implemented by each code file.) 3. May I develop new plug-ins/bundles/modules based on ChimeraX's VR mode to implement one or more new features/functions? Could you please briefly describe the feasibility of developing it? Best regards, Xiang Chen --- Xiang Chen, M.Sc. # 201992538 Department of Computer Science Memorial University of Newfoundland St. John's, NL, Canada T (709) 219-2960 / E xiangc(a)mun.ca

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Structure move
by Silva, Chinthaka Mahesh 28 May '21

28 May '21

Hello, If I have more than one structure opened in ChimeraX and want to move them apart, can I do that? I see that I can move a structure model using 'right mouse' option, but not the structures. Chimera had the option to do this by deactivating a structure. Thanks! -chinthaka

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Pair-fitting in ChimeraX
by Rachael Coleman 28 May '21

28 May '21

Hello again, You guys were so helpful last time I figured I'd just ask for help again! I'm trying to do something that I know is a feature in PyMol but I'm not sure if it is a feature in ChimeraX (yet). In PyMol, there is a function to pair fit over specific atoms between two different structures. I have tried using the Matchmaker tool in ChimeraX to do this, but I think the dilemma is I'm trying to align the protein relative to the position of specific atoms in a heme cofactor across two different structures and that isn't something in the primary sequence of the protein. I also could just be doing something wrong in the matchmaker process. Do you know if there is an easy way to accomplish this in ChimeraX? Best regards, Rachael Coleman -- *Rachael E. Coleman* PhD Candidate, Lancaster Group Department of Chemistry and Chemical Biology Cornell University Ithaca, NY 14853 Pronouns: She, her, hers

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ChimeraX version 1.2 released!
by Elaine Meng 28 May '21

28 May '21

UCSF ChimeraX version 1.2 has been released! Major changes since v1.1 (Aug 2020) include: - Surface Color tool - Unit Cell tool - Color Key tool and command - Crystal Contacts tool and command - volume tools: Hide Dust, Color Zone, Surface Zone - Meeting panel for multiperson VR - "fly" command for smooth motion along multiple saved views - "rmsd" command for calculating RMSD in current positions (w/o fitting) - nucleic-acid building - bond deletion/addition - UniProt fetch includes sequence feature annotations (domains, mutations, modification sites, etc.) - support for Amber netCDF trajectories - smaller session files - faster saving of sessions with maps - mouse mode for moving a clicked model without having to select it For more details, see the ChimeraX change log: https://www.rbvi.ucsf.edu/trac/ChimeraX/wiki/ChangeLog Downloads: https://www.rbvi.ucsf.edu/chimerax/download.html

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Downloading Daily builds
by Moradkhan, Tiglath A 27 May '21

27 May '21

Hi, I don't know why the Fetch Additional Scores button is not returning these scores. I get the message that scores have been initiated but then nothing happens. It's annoying that I keep have to download newly released daily builds on my computer, so I can use it. Thank you Tiglath

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Web services down
by Eric Pettersen 25 May '21

25 May '21

Hi all, Due to computing cluster maintenance starting this evening (5/25) through tomorrow evening (5/26), the web services in Chimera and ChimeraX that use our cluster will be down. The frequently used web services are BLAST and Modeller for both programs, and for Chimera only: sequence realignment via Clustal Omega or MUSCLE; SAXS2; and 2D ligand depiction. --Eric Eric Pettersen UCSF Computer Graphics Lab

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Fwd: Wireframe option
by Eric Pettersen 24 May '21

24 May '21

> Begin forwarded message: > > From: "Silva, Chinthaka Mahesh" <silva228(a)llnl.gov> > Subject: Wireframe option > Date: May 24, 2021 at 12:38:13 PM PDT > To: "chimerax-bugs(a)cgl.ucsf.edu" <chimerax-bugs(a)cgl.ucsf.edu> > > Hello, > > Can you tell me how to draw pdb models using the ‘wireframe’ mode? > > Thanks! > -chinthaka

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moving map with model in chimerax
by Fabian Glaser 20 May '21

20 May '21

Dear experts, I am preparing figures for a paper, and I would like to color several structures using apbs dx maps. I manage todo that, but I need to move or align the coordinates of the pdb in order to map several different maps, and when I save the chimerax session and reopen, the map is not aligned with the new coordinates of the pdb, so the colouring fails. So is there a way to move or associate the map with a certain model, and move it together with it? Tahnks a lot, Fabian ---------------------------------------------------------------------------- Fabian Glaser PhD Bioinformatics Knowledge Unit - BKU The Lorry I. Lokey Center for Life Sciences and Engineering Technion - Israel Institute of Technology, Haifa, Israel Web https://lokey.technion.ac.il/bioinformatic-knowledge-unit/ <https://lokey.technion.ac.il/bioinformatic-knowledge-unit/> Tel +972 (0) 4 8293701

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Questions:how to clean the dashed lines in chimeraX?
by 段泽林 20 May '21

20 May '21

Dear ChimeraX developers, When I opened my structure in chimeraX, I see dashed lines inside my model,those dashed lines represent the gap inside the model because I cannot model these gaps due to bad density. Now I want to clean these dashed lines, I can use the inspect selection panel to clean these dashed lines in chimera, but I cannot do that in chimeraX, would you please tell me how to do that? either in command line or GUI many thanks Zelin

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Colour residues by local resolution estimation map
by Ioannis Skalidis 20 May '21

20 May '21

Dear all, I am trying to color a protein model based on the local resolution of the corresponding map. I can color the overall surface of the model, but not the residues themselves. Is there a way to do this, e.g, color the model backbone somehow? Thanks a lot for your help! Cheers, Yiannis -- Skalidis Ioannis, MSc Biochemistry & Cryo-EM Scientist PhD Candidate Kastritis Laboratory for Biomolecular Research Cryo-Electron Microscopy & Computational Structural Biology ________________________________________________ Martin-Luther-Universität Halle-Wittenberg Biozentrum, Room A.2.21 IWE ZIK HALOmem NWG III "Kryo-Elektronenmikroskopie an Membranproteinkomplexen" Weinbergweg 22, 06120 Halle tel: +49 345 5524986 web (Lab): https://blogs.urz.uni-halle.de/kastritislab/ web (HALOmem): https://www.halomem.de/en/

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Measuring surface area of a colored portion of the map
by Y. Mutum 19 May '21

19 May '21

Hi This problem relates to surface area of a low-resolution EM map using ChimeraX I have opened the following map and the corresponding model using the following commands in ChimeraX. >>> open 4uq8; open 2676 from emdb >>> color #1 green; color zone #2 near #1 dist 4 As many parts of the map are unmodelled, I am interested 'how much of the map is unmodelled' in terms of surface area. This is mainly because the model is not accurate and I am trying to only use the raw-data (map) to estimate the surface area and avoid using the model. Is there a way to figure out how much of the map is unmodelled in terms of surface area? In this case, count the number of 'outer pixels of a map' that are colored green or gray, at a given map contour? Could you please help with a way to measure this without using the 'volume splitbyzone' command? Thanks Yaikhomba [cid:71184965-9ba5-4374-82b3-bd2b264b4b0c]

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Re: [chimerax-users] How to change the palette of hydrophobicity in ChimeraX
by Le Han 19 May '21

19 May '21

Hi Elaine, Thank you so much for your help. I managed to change it. Have a nice day! Han From: Elaine Meng<mailto:meng@cgl.ucsf.edu> Sent: Tuesday, 18 May 2021 18.12 To: Le Han<mailto:han.le@aalto.fi> Cc: chimerax-users(a)cgl.ucsf.edu<mailto:chimerax-users@cgl.ucsf.edu> Subject: Re: [chimerax-users] How to change the palette of hydrophobicity in ChimeraX Hi Han, Although the icon just uses the "mlp" command with the default palette, you can use the "mlp" command with any palette that you want. The "palette" option specifies palette and "range" specifies value range. Instructions on "mlp" command and how to specify palettes: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/mlp.html> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/color.html#palette-options> The hydrophobic coloring icon in the Toolbar "Molecule Display" tab uses command: mlp ...which is same as: mlp palette lipophilicity range -20,20 To use the same value range but get blue for hydrophilic and red for hydrophobic, you could use, for example, command: mlp palette blue-white-red range -20,20 Since red-white-blue is traditionally used for electrostatic coloring, however, you will have to be sure to explain the image so that people understand it is showing hydrophobicity instead. In the "mlp" instructions linked above, you can see there are several other options of the command that may interest you. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On May 18, 2021, at 6:55 AM, Le Han <han.le(a)aalto.fi> wrote: > > Hi, > I’d like to change the colour palette of hydrophobicity to red (most hydrophobic) – white – blue (most hydrophilic). Is it possible to do so in ChimeraX and how can I change? > Thank you in advance, > Han

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Proxy setting with user authentication
by fukamitka＠chugai-pharm.co.jp 18 May '21

18 May '21

Dear ChimeraX developers, I’m a new user of ChimeraX. How can I set username/password for HTTP/HTTPS proxy settings? Our firewall is strict and requires username/password authentication. I’d like to install ISOLDE (we purchased the license), but I can’t install it via Tools > More Tools... I downloaded the .whl file for ISOLDE from the ChimeraX Toolshed page (https://cxtoolshed.rbvi.ucsf.edu/apps/chimeraxisolde) and tried the command below in ChimeraX windows, toolshed install /path/to/the/ChimeraX_ISOLDE-1.2.0-cp38-cp38-manylinux_2_17_x86_64.whl but failed during pip install (by SSLError, which means proxy was not set correctly). Enviroment variables http_proxy and https_proxy were set when ChimeraX executed, but not worked. Best regards, Takaaki ----- Dr. Takaaki Fukami (mailto:fukamitka@chugai-pharm.co.jp) Protein Science Dept. (Protein Science 2 Gr.) Chugai Pharmaceutical Co.,Ltd. 200 Kajiwara, Kamakura, 247-8530 Japan Tel: +81-467-47-6178

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