- ChimeraX-users - RBVI Mailing Lists

Amber trajectories
by Lewandowski, Jozef 16 Dec '19

16 Dec '19

Hi, Quick question. Are there any plans for ChimeraX to support opening also Amber trajectories (as Chimera does)? Thanks, Józef ------------------------------------------------------------------------------------------------------ Józef R. Lewandowski Professor | Department of Chemistry | University of Warwick<http://www2.warwick.ac.uk/> j.r.lewandowski(a)warwick.ac.uk<mailto:j.r.lewandowski@warwick.ac.uk> | External: +44 (0) 24 76151355 | Internal: 51355 Millburn House: F07 | Coventry CV4 7AL | Find us on the interactive map<http://www2.warwick.ac.uk/about/visiting/maps/interactive/> Lewandowski group website<https://www2.warwick.ac.uk/fac/sci/chemistry/research/lewandowski/lewandows…> | Warwick solid-state NMR group website<http://www2.warwick.ac.uk/fac/sci/physics/research/condensedmatt/nmr/>

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Re: [chimerax-users] [Chimera-users] view MD ChimeraX
by Elaine Meng 16 Dec '19

16 Dec '19

Hi Fabian! The “Molecular Dynamics Viewer" tool is available on ChimeraX Toolshed from outside developers, i.e. it is not written by our group. However, the description on Toolshed pretty much says what it does: it is a simple graphical interface for showing multiframe PDB files as a trajectory. It doesn’t read other trajectory formats. <https://cxtoolshed.rbvi.ucsf.edu/apps/moleculardynamicsviewer> After you install it, it will be under Tools… General in the menu. Starting the tool from that menu will open a window in ChimeraX and then clicking the Open button in that tool will allow you to browse to and open a multiframe PDB file, like 1PLX.pdb downloaded from the RCSB PDB (NMR structure, so it has multiple conformations each as a MODEL in the single PDB file). Then you can use the other buttons, e.g. Start to play as a a trajectory. (I wasn’t sure what you meant by “not able to use it.”) However, *without* this tool: Just using ChimeraX without installing anything extra, you can read in a few trajectory formats and then play them with the “coordset” command or using a slider interface shown with “coordset slider". The trajectory formats known to ChimeraX are listed here: <http://rbvi.ucsf.edu/chimerax/docs/user/commands/open.html#trajectory> <http://rbvi.ucsf.edu/chimerax/docs/user/trajectories.html> See also “coordset” and “coordset slider” <http://rbvi.ucsf.edu/chimerax/docs/user/commands/coordset.html> <http://rbvi.ucsf.edu/chimerax/docs/user/commands/coordset.html#slider> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco P.S. There is also a chimerax-users(a)cgl.ucsf.edu mailing list, CC’d here. > On Dec 15, 2019, at 1:50 AM, Fabian Glaser <fglaser(a)technion.ac.il> wrote: > > Hi, > I installed Molecular Dynamics Viewer in ChimeraX but I am not able to use it, . I use it successfully in Chimera (no X). But in ChimeraX. > Can you please help me? > Best, > Fabian

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SSL expiry
by James Walshe 13 Dec '19

13 Dec '19

Hi Guys, Hope you’re well. I’m trying to download some ChimeraX plugins. It appears the toolshed security certificate has expired. https://cxtoolshed.rbvi.ucsf.edu/ Just letting you know if you were unaware. Kind regards, James ______________________________________________________________________ The Victor Chang Cardiac Research Institute's Email is scanned by the MessageLabs Email Security System.

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multiple conformations in one pdb chain
by Linda Schulte 12 Dec '19

12 Dec '19

Hi everyone, I have two conformation in a single PDB chain, see example below: ATOM 90444 N APHE z 9 253.604 183.844 259.994 0.50 47.28 N ATOM 90455 N BPHE z 9 253.778 183.499 258.715 0.50 47.28 N Chimera can read in this two conformations of the chain, while chimerax shows only the A atoms of the chain. How can I read in also the B atoms? Thanks a lot for your help. Best, Linda -- Linda Schulte Goethe-Universität Frankfurt am Main Institut für Organische Chemie und Chemische Biologie, AK Schwalbe Max-von-Laue-Straße 7 D-60438 Frankfurt am Main N160/300 +49 (0)69 / 798-29956 schulte(a)nmr.uni-frankfurt.de

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Saving ChimeraX session error on macOS
by Yixiao Zhang 11 Dec '19

11 Dec '19

Dear all, I'm preparing a movie in chimeraX on macOS. There are more than 25 maps opened and also another 20 low-pass filtered maps generated within chimeraX by "vol gaussian". There are also ~20 pdb models, several positions saved by "view name" and ~20 2dlabels. I got the following error message when I save the .cxs file, and the session was not saved. RuntimeError: Unable to restore objects of LabelModel class in ChimeraX-Label bundle because the class name is not listed in the name to class table for session restore File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/chimerax/core/session.py", line 142, in from_obj (obj_cls.__name__, bundle_info.name)) See log for complete Python traceback. The session is still alive, and I have no problem when I save other much simpler sessions. Is there a way that I can get this big session saved? Is the error related to 2dlabels? Many thanks, Yixiao

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Starting ChimeraX programmatically with remotecontrol
by Mungo Carstairs (Staff) 11 Dec '19

11 Dec '19

Hi there, Jalview has the ability to launch Chimera with "--start RESTServer", capture the port number from the response, and drive Chimera with REST commands. I'm trying to figure out whether this mechanism is also provided with ChimeraX. I've read http://plato.cgl.ucsf.edu/pipermail/chimerax-users/2017-July/000113.html and looked at http://www.rbvi.ucsf.edu/chimerax/docs/user/startup.html and http://www.rbvi.ucsf.edu/chimerax/docs/user/options.html#start but so far I can't see that "RESTServer" is a startable tool. Is this, or is it planned to be, possible somehow? Thanks, Mungo [University of Dundee shield logo]<http://uod.ac.uk/sig-home> Mungo Carstairs Jalview Computational Scientist The Barton Group Division of Computational Biology School of Life Sciences University of Dundee, Dundee, Scotland, UK www.jalview.org<http://www.jalview.org> www.compbio.dundee.ac.uk<http://www.compbio.dundee.ac.uk> g.m.carstairs(a)dundee.ac.uk<mailto:g.m.carstairs@dundee.ac.uk> [University of Dundee Facebook]<http://uod.ac.uk/sig-fb> [University of Dundee Twitter] <http://uod.ac.uk/sig-tw> [University of Dundee LinkedIn] <http://uod.ac.uk/sig-li> [University of Dundee YouTube] <http://uod.ac.uk/sig-yt> [University of Dundee Instagram] <http://uod.ac.uk/sig-ig> [University of Dundee Snapchat] <http://uod.ac.uk/sig-sc> We're Scottish University of the Year again!<http://uod.ac.uk/sig-strapline> The Times / Sunday Times Good University Guide 2016 and 2017 The University of Dundee is a registered Scottish Charity, No: SC015096

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Rotate bond move large/small option in VR
by Lewandowski, Jozef 09 Dec '19

09 Dec '19

Hi, Is there a way to change the option from the default “move small” to “move large” of the Bond rotation tool in VR? Ideally, it would be great if I could switch between these options on the fly with some combination of buttons on the controllers. If nothing like that is implemented is there a way I could change the “move” default for the Bond rotation tool in VR using the command line? Thanks, Józef ------------------------------------------------------------------------------------------------------ Józef R. Lewandowski Professor | Department of Chemistry | University of Warwick<http://www2.warwick.ac.uk/> j.r.lewandowski(a)warwick.ac.uk<mailto:j.r.lewandowski@warwick.ac.uk> | External: +44 (0) 24 76151355 | Internal: 51355 Millburn House: F07 | Coventry CV4 7AL | Find us on the interactive map<http://www2.warwick.ac.uk/about/visiting/maps/interactive/> Lewandowski group website<https://www2.warwick.ac.uk/fac/sci/chemistry/research/lewandowski/lewandows…> | Warwick solid-state NMR group website<http://www2.warwick.ac.uk/fac/sci/physics/research/condensedmatt/nmr/>

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Relative paths to source files in saved sessions
by Christophe Leterrier 04 Dec '19

04 Dec '19

Hi, I'm working on multiple Chimera sessions on different computers, syncing the content of the folders and cxs files. However when opening a cxs file on a different computer, I have to manually relocate all the source files every time (in my case tif stacks, and even navigate for each of them from the cxs folder to the source files folder because the folder is reset at every source file selection). Would it be possible to somehow store the relative path between the cxs file and the source files in the cxs file, or try relative if absolute paths fail? I have no idea how this is done currently, so sorry if this is an unrealistic/undesirable proposal. Thank you, Christophe

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Main interface does not start
by Thomas G. Laughlin III 04 Dec '19

04 Dec '19

Hi, I've been using ChimeraX 0.9 for a while, but today when I tried to open it, the group photo comes up and "initializing bundles" then disappears without starting the main interface/GUI. I recently installed items from the toolshed for the first time (2 days ago but ChimeraX worked the day of install) and I tried re-installing ChimeraX without success. This is on a Windows 10 OS with intel integrated graphics. Any suggestions on what to do to diagnose and correct the problem? Thanks for the help, -Tom -- Thomas G. Laughlin III PhD MCB (BBSB, Candidate) | *Univ. of California-Berkeley* | Present BS Biochemistry | *Univ. of Missouri-Columbia* | 2014 t.laughlin(a)berkeley.edu <thomas.laughliniii(a)gmail.com>

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Fw: Multi-user sessions: development
by Williams, Joanne 03 Dec '19

03 Dec '19

________________________________ From: Grime, John M. <jgrime(a)ou.edu> Sent: Monday, December 2, 2019 1:12 PM To: chimerax(a)cgl.ucsf.edu <chimerax(a)cgl.ucsf.edu> Subject: Multi-user sessions: development Hello! We have some use cases where multi-user VR sessions in ChimeraX would be very useful. We already have out own in-house networked VR software, and I was wondering if the source code to ChimeraX is available for academic users so we can see if we can add similar functionality? Thanks! John Grime, Ph.D. Emerging Technologies Developer University of Oklahoma Libraries

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Segment map feature only available to Mac users ?
by WERNERT Florian 29 Nov '19

29 Nov '19

Hi ChimeraX users developers and maintainers, I've been able to experiment with the segment map<https://www.cgl.ucsf.edu/chimerax/docs/user/tools/segment.html> feature provided by Segger package on the Mac daily-build, on a colleague's Mac. However I downloaded the Linux daily build on my Linux machine and it appears that this function is not present in the menu. Is it a bug or is the "segment map" feature only available to Mac ? If this is the case, would someone be able to give some guidance on how to port the feature to Linux ? I'm quite experienced in C, C++, Java and Python coding, having the coding skills shouldn't be an issue in order to do it. Thanks, Florian W

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ChimeraX stalls when trying to display surfaces from a (strange) group of atoms
by Christophe Leterrier 27 Nov '19

27 Nov '19

Hi, I'm trying to use ChimeraX to visualize Single-Molecule Localization Microscopy (SMLM) data. In short, the output of an SMLM acquisition and processing is a list of fluorophores XYZ coordinates with associated uncertainty, that can be used to reconstruct a 3D image. I have made a script that make a pdb file from these localization so that I can directly display the resulting structure as if it was a protein with a number of random atoms (the only difference is that angstroms in ChimeraX are really nanometers in my data). The rendered pqr file is here (I use a pqr pdb format to specify the radius to the localization uncertainty, hence the variable diameter of each sphere): http://www.neurocytolab.org/up/Example_File.pqr The rendering with the "Spheres" view of atoms works well, see a screenshot here: http://www.neurocytolab.org/up/Render.png However, when I try to get the enveloppe of the resulting object using the "Surfaces" display (click on Surfaces>Show), ChimeraX hangs (I'm on OSX and get the dreaded infinite rainbow beachball). Is there a chance that I can get ChimeraX to render the enveloppe object this way, or is it really too far from what it's supposed to do? I can imagine that I'm trying to use ChimeraX for something completely different than its intended use, but it definitely has a lot of potential for this. Thank you, -- Christophe Leterrier NeuroCyto lab INP CNRS UMR 7051 Aix Marseille University, France

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Color key
by Ricardo Righetto 18 Nov '19

18 Nov '19

Hi, Apologies if this has already been asked or documented somewhere, but I could not find it. Is there a way in ChimeraX to create a bar showing the color scale ("Color Key" in Chimera) e.g. when coloring a map by local resolution? Thank you! -- Ricardo Diogo Righetto

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How to select one of ligands which is named in different numbers
by Meinan Lyu 11 Nov '19

11 Nov '19

Hi, I am having trouble in how to select one of the ligands which named LIG 1, LIG 2, LIG 3, LIG 4, etc. when I hide all of them and want to specifically show LIG 1, using "show LIG 1 target a" command does not work. How to deal with this that the ligand name have a space inside? Thank you very much. Best regards Meinan

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surface cap transparent when surface dust on ?
by bertrand beckert 06 Nov '19

06 Nov '19

Hi All, I have been recently trying to color a volume by a map value... So far it worked really well using the color command.... color sample #1 map #2 offset 0.1 palette " values" But my problem is the following: when I clip the volume the surface cap is now transparent... is there a way to have the surface cap not transparent but instead colored according to the map value like it is in Chimera? Also another thing, I usually do is the following: open volume1.mrc volume surfaceSmoothing true surface dust #1 lighting soft Then, when I clip through the map the surface cap is again transparent unless dust is turn off (suface undust #1)... I also tried surface cap false and then true but nothing changes... Is there a way around it? or does the surface dust function is somehow turn the surface cap always transparent? Thanks for the hard work and the nice software! Best Bertrand

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Catalina woes
by ubaumann 05 Nov '19

05 Nov '19

Dear all I am trying to use ChimeraX after a clean install upgrade to Catalina, OSX 10.15.1 I get the attached error message that the software can’t be scanned for malicious code Is there any way around this, please? Same holds for Chimera ( and other programs….) Thanks a lot! Kind regards, Ulrich

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Trouble initializing ChimeraX on CentOS
by Brown, Alex 18 Oct '19

18 Oct '19

Hello and good morning, I have always had a great experience using Chimera and so I was hoping to try out ChimeraX for some of our larger cryo-em data sets. However, following download and an install that did not seem to produce an error message, I can not seem to initialize the program. I have copied the output from the command prompt below. Beyond that, I should probably also mention that we are running the centos-release-7-6.1810.2.el7.centos.x86_64 operating system with intel chips and nvidia graphics cards. [root@gaolab ~]# chimerax-daily NOTE: available bundle cache has not been initialized yet WARNING: could not retrieve bundle list from toolshed NOTE: Traceback (most recent call last): File "/opt/UCSF/ChimeraX-daily/lib/python3.7/runpy.py", line 193, in _run_module_as_main "__main__", mod_spec) File "/opt/UCSF/ChimeraX-daily/lib/python3.7/runpy.py", line 85, in _run_code exec(code, run_globals) File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site- packages/ChimeraX_main.py", line 871, in <module> exit_code = init(sys.argv) File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site- packages/ChimeraX_main.py", line 580, in init check_available=opts.get_available_bundles) File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site- packages/chimerax/core/toolshed/__init__.py", line 1681, in init _toolshed = Toolshed(*args, **kw) File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site- packages/chimerax/core/toolshed/__init__.py", line 359, in __init__ if not available.has_cache_file(self._cache_dir): File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site- packages/chimerax/core/toolshed/available.py", line 109, in has_cache_file return os.path.exists(os.path.join(cache_dir, _CACHE_FILE)) File "/usr/bin/../../opt/UCSF/ChimeraX-daily/lib/python3.7/posixpath.py", line 80, in join a = os.fspath(a) TypeError: expected str, bytes or os.PathLike object, not NoneType BUG: TypeError: expected str, bytes or os.PathLike object, not NoneType File "/usr/bin/../../opt/UCSF/ChimeraX-daily/lib/python3.7/posixpath.py", line 80, in join a = os.fspath(a) _See log for complete Python traceback._ Thanks in advance for any support you may be able to provide on this! -Alex Alexander Brown IV, PhD Postdoctoral Researcher Horae Gene Therapy Center Li Weibo Institute for Rare Diseases Research University of Massachusetts Medical School 368 Plantation Street, AS6-2011 Worcester, MA 01605 Phone: (508) 856-3316 Email: alex.brown(a)umassmed.edu<mailto:alex.brown@umassmed.edu> Confidentiality Notice: This e-mail message, including any attachments, is for the sole use of the intended recipient(s) and may contain confidential, proprietary and privileged information. Any unauthorized review, use, disclosure or distribution is prohibited. If you are not the intended recipient, please contact the sender immediately and destroy or permanently delete all copies of the original message.

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problem of chimerax
by 陈柳青 18 Oct '19

18 Oct '19

Hello! I tried install either daily builds or release 0.9 of chimeraX on my win10 64 system, but both encounter the same problem showed in the attachment. After startup, i can't see any menu! but when i move mouse on the menu , it will appear sub menu. How can solve this bug? sincerely Liuqing chen

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macOS Catalina gives PermissionError opening files
by Tom Goddard 16 Oct '19

16 Oct '19

If you are thinking of upgrading to the new macOS Catalina (10.15) and want to use ChimeraX on it you might hold off. We have found that opening files using the ChimeraX open command or the recent files thumbnails often causes PermissionError and fails to open the files. This is caused by a new macOS Catalina security feature when any app that tries to open a file under Desktop, Downloads, or Documents must first raise a permission dialog asking if the app is allowed to open files from that directory. When using the ChimeraX File / Open dialog (from the File menu) the permission dialog is shown and works. But if you use the ChimeraX open command of recent files thumbnails on directories that you have not granted permission for with the Open dialog, then those fail with PermissionError -- apparently those methods of opening are not able to show the permission dialog. Other applications (e.g. photo editing program Gimp) have the same problem. We do not yet know how to solve this. Tom

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Re: [chimerax-users] [Chimera-users] surface color
by Elaine Meng 14 Oct '19

14 Oct '19

Hi Mike, So close! You’re only missing the “palette” keyword before “rainbow” … try: color height #1 center 0,0,0 axis z palette rainbow <http://rbvi.ucsf.edu/chimerax/docs/user/commands/color.html#distance> <http://rbvi.ucsf.edu/chimerax/docs/user/commands/color.html#palette-options> (By the way, there is a chimerax-users(a)cgl.ucsf.edu list CC’d here if you have questions specifically about ChimeraX.) I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Oct 14, 2019, at 2:43 PM, Schmid, Michael F. <m-schmid(a)slac.stanford.edu> wrote: > > I’m trying to do the same thing as Chimera’s “Surface Color”, but in ChimeraX, on the command line. After reading the docs, I tried “color height #1 (the map designation) center 0,0,0 axis z rainbow”. It gave “expected a keyword”. What did I miss? > Thanks, > Mike

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show stands' arrows a little werid
by Meinan Lyu 14 Oct '19

14 Oct '19

Dear Dr., The attached is a picture I saved which the stands' arrows are so wide when using chimeraX to draw some figures, could you please tell me how to make it normal? The problem showed after I put into these two command(not quite sure yet):1. zone #3:Lig residueDistance 5 label false 2. cartoon #3/b suppressBackboneDisplay true. Thank you very much！ Best regards, Meinan CWRU

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Soft lighting changes when additional model is displayed
by Gabor PAPAI 14 Oct '19

14 Oct '19

Dear ChimeraX team, If I open a second model in ChimeraX (0.91) the ambient occlusion in soft lighting mode on the first model disappears or becomes diminished. How can I revert this effect? I attach an image to illustrate this phenomenon. The only change between the two displays that I opened a model of DNA and placed close to the first model. Best regards, Gabor [cid:6AAD58A0-1B6C-4362-8C29-57D033327EBF@igbmc.u-strasbg.fr] --- Gabor Papai IGBMC Integrated Structural Biology 1, rue Laurent Fries, Bp 10142 67404 Illkirch, France Tel: +33-3-69485288

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issues with rotamers tool
by Llorente, Alejandro 09 Oct '19

09 Oct '19

Hi, I am new PhD student using ChimeraX and I am very interested in learning how to work with this program. I am trying to introduce some mutations in my protein in some specific amino acids that I have selected. When I introduce an Alanine in my position of interest (using dunbrack) I have no issues, but when I try any other amino acids (as Phe or Thy) the program has no problem giving me the prediction for the rotamers, but I have some issues. After select some of the most probable rotamers, all the amino acids of my protein change to that kind of amino acid (not just the specific one that I have selected). Another problem is that I have is that when I select a specific atom of an amino acid, the program also select similar atoms but in all the others amino acids of my protein. I really hope that someone can help me with these issues. Thank You very much Alejandro Llorente. Lab of Dr. Nancy Carrasco. Department of Molecular Physiology & Biophysics, Vanderbilt University. 2215 Garland Ave Nashville, TN 37232-0615, room 711. Mobile phone: +34 626586236

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Unable to use Viewdockx
by Abhijeet Kumar 07 Oct '19

07 Oct '19

hi, I am a college student and I am working on a project on protein docking visualization and came across ChimeraX. I am not able to use Viewdockx and the user guide for viewdockx gives a 404 page not found error. So, can you help me with this? Thank you.

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Cuved helix tubes
by Ernesto Arias Palomo 02 Oct '19

02 Oct '19

Good morning, We are using the modeHelix tube to represent the secondary structure. However, our structure contains some long and curved helices, and the representation does not follow their shape with enough precision. Is there any option to increase the fit of the tube to the overall shape of long helices? Thank you very much for your help. Kind regards, Ernesto. -- Ernesto Arias Palomo, PhD Group Leader Biological Research Center (CIB-CSIC) Ramiro de Maeztu, 9. 28040. Madrid. Spain earias(a)cib.csic.es +34 91 837 31 12 ext 4446

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Calculation of polar and apolar surface area
by Gorman, Scott Daniel 02 Oct '19

02 Oct '19

Hi All, I was wondering if anyone has a preferred way of calculating the polar and apolar surface areas for a macromolecule with ChimeraX? I've tried deleting all of the solvent and then using the command "measure sasa @N @O @S" for the polar surface area and then "measure sasa @C" for the apolar surface area, but the calculation for either comes up with a number too close to the total surface area, i.e. apolarSASA + polarSASA > totalSASA. So clearly I'm not approaching this problem correctly. Scott Gorman PhD Candidate Boehr Lab PSU Chemistry

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GUI not properly visualized
by Pascal Albanese UU 25 Sep '19

25 Sep '19

Hi Chimera staff, i just changed PC ad now i have huge visualization problems of the GUI, when opening is fine but when i open any pdb file or session all buttons and commands in the window disappear. Command line actually works but all i see is this: [image: image.png] do you have any explanation? i tried different releases (0.9 official, daily builds) I'm using W10 enterprise, 64bit, intel i9 9900, UHD graphics 630. Thanks for the support, best regards, -- Pascal Albanese Ph.D PostDoc Biomolecular Mass Spectrometry and Proteomics Utrecht Institute for Pharmaceutical Sciences Utrecht University Padualaan 8 3584 CH, Utrecht The Netherlands Telephone: +31 30 253 6805 https://www.hecklab.com/

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ray tracing
by Ahel,Juraj 24 Sep '19

24 Sep '19

Dear all, pardon me if this has already been answered elsewhere, but I failed to find any information about this in the publication, webpage, or the mailing list archive. Is there a way to generate images of ray-traced maps in ChimeraX? I was often using it in Chimera but I can't find the option to do it in ChimeraX. Was it not included as a feature? Many thanks! Juraj

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Manually imposed symmetry
by Shahid Khan 16 Sep '19

16 Sep '19

Hello I am having difficulty in manually imposing symmetry on a map (*.mrc file) and then extracting the unit cell for the subsequent fitting of PDB structures with fitmap. (1) When I use the command "Volume symmetry #1, C33 axis z centerIndex 107.5" I get the error message "No placements for #1" that I do not understand. (2) I cannot figure out from the help documentation on how to save and display one of the created segments. Any ideas? Thanks Shahid -- Dr Shahid Khan Senior Scientist Molecular Biology Consortium Lawrence Berkeley National Laboratory

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render buriedArea surface?
by Alexis Rohou 10 Sep '19

10 Sep '19

Hi all, I would like to depict the buried surface area between two chains. I have used "measure buriedarea" to measure it, and I can use "surface" to display the surfaces of either set of atoms, but I'd like to depict the surface of one of the chains, highlighting the region buried by the other chain. Is there a way to do this in ChimeraX? If not, does anyone have a recommendation as to how to achieve this? Perhaps by pre-computing the surfaces in another program? Thanks in advance! Cheers, Alexis

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vdw representation in chimeraX
by Elena Zehr 09 Sep '19

09 Sep '19

Hello, In chimera one can display dot van der Waals surfaces for atoms. *vdw* *atom-spec* <https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/frameatom_spec.html> What would be the equivalent command in ChimeraX? Thank you, Elena

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Open days EPFL - ChimeraX VR
by Krapp Lucien Fabrice 05 Sep '19

05 Sep '19

Hello, We are creating some small VR demos in ChimeraX for the EPFL open days in a few weeks (https://www.epfl.ch/campus/events/celebration-en/portes-ouvertes/) It is an event to show to a broader audience what the university is doing. The demos consists of small proteins up to density maps of bacteriophage with a few simple animations and menus to interact with the structures. Everything is almost done, I'm currently trying to fix the last issue but I didn't find a solution in the documentation. For two of the demos we would like the user to move a selection in VR with one of the VR controller right out of the box without having to go in the VR menu and click on the "move selected" button. I was able to make it work on Linux by loading the session though the remote API with the right part selected but it doesn't seem to work on Windows. The log shows a status change when clicking on the button "move selected" in VR but not the actual command to change the mode. Do you know if there is a way to change the mode of the VR controller without having to manually go through the menu in VR ? In the mean time, I will try different saved sessions and (remote) commands to try and solve the issue. If the demos are a success we will most likely make them available online so that anybody can try and improve them. Thank you in advance for your help. best, Lucien

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semitransparent volumes with ambient occlusion
by Sindelar, Charles 03 Sep '19

03 Sep '19

Dear Elaine, Eric, Tom, and team, I am happy to see ChimeraX is continuing to move forward! Here is a little request. For the figures that I am now making for publications, I have a special interest in showing semitransparent molecular maps together with the corresponding models, with ambient occlusion lighting on. I think ambient occlusion makes this kind of figure much easier to interpret and more beautiful. What I have noticed is ambient occlusion seems to get automatically turned off as soon as a map becomes less than 100% opaque. I always assumed this was due to some kind of rendering difficulty. But then, I noticed that sometimes I can “trick” an old version of ChimeraX to do exactly what I want! Below is an example. Basically, in ChimeraX 0.6 I can set up everything just the way I want with an opaque map, then turn down the map opacity and get a nice, pretty figure just the way I like it. But then, as soon as I show/hide anything in the Model Panel, the ambient feature gets turned off! I noticed that in the most recent daily build, this “trick” no longer works and I can’t seem to ever get the pretty combination of transparent maps and ambient occlusion lighting that I like. I sure would like to have this option! I guess there must be some reason it is disabled? Best, Chuck Sindelar Opaque map + PDB (ChimX v0.6) (pretty but the PDB is obscured) [cid:image001.png@01D55FF9.D8266CF0] After adjust to 80% map opacity (ChimX v0.6) (pretty!) [cid:image002.png@01D55FF9.D8266CF0] After unshow/show PDB model (ChimX v0.6) (argh!) [cid:image003.png@01D55FF9.D8266CF0]

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silhouette of transparent density
by YAO HE 31 Aug '19

31 Aug '19

Hi, I am using ChimeraX now to show the overlay between atomic model and transparent EM densities. However, when I enable the silhouette feature, only the transparent EM densities are affected. I am wondering if it is possible to also silhouette the atomic model inside. Just like "setattr M silhouette true #3" in Chimera. Best, Yao

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silhouette of transparent density
by heyao 30 Aug '19

30 Aug '19

Hi, I am using ChimeraX now to show the overlay between atomic model and transparent EM densities. However, when I enable the silhouette feature, only the transparent EM densities are affected. I am wondering if it is possible to also silhouette the atomic model inside. Just like "setattr M silhouette true #3" in Chimera. Best, Yao

1 0

Chimera X and the Oculus Quest
by Thomas Gluick 28 Aug '19

28 Aug '19

HI First please excuse my computer language ignorance. My question is: Is the Oculus Quest compatible with Chimera X; if it is, is software available to link the program to the Quest. I am aware already that the Rift can be connected and also certain phones. Thank you for you time. Best Tom Dr. Thomas Gluick Assistant Professor of Chemistry School of Science and Technology 770-842-5532

2 1

Question about Calphas and line between them
by Yazan Abbas 21 Aug '19

21 Aug '19

Hi, While looking through the user guide, I came across an option to draw a line between consecutive Calphas that are displayed. I made a mental note to use that option in my figure, but I failed to bookmark it or write down what the command was. I've been through the user guide several times again, but can't seem to find it. Would appreciate it if someone could jog my memory. Thanks, Yazan

2 1

discontinuous helices in tube mode
by Yazan Abbas 19 Aug '19

19 Aug '19

Hi, Is there a parameter that can be changed to control how "cartoon style modeH tube" draws a continuous helix? In my model, most of my helices are broken up into 2-4 discontinuous helices (especially the long, curved ones). In pymol (cylinders mode) and chimera (pipes and planks depiction), the same helices are drawn as a single, continuous helix, suggesting that my model is ok. I tried adding a HELIX definition in the pdb file, and also tried forcing chimeraX to draw a helix using the setattr command, but neither strategy has helped. I also tried playing with the dssp energyCutoff with no success. Thanks, Yazan

2 3

Question about "color sample" command
by Sean Connell 19 Aug '19

19 Aug '19

Hello I have a question about the "color sample" command (Chimerax-daily version 0.91 2019-08-14) and its use in coloring a volume based on the values of a second volume (i.e. local resolution maps from relion) The command works great when I load the volumes in to chimerx but after I load them I want to transform them using matchmaker and the bring option so that all the volumes I want to view are in a common frame of reference. After I transform the volumes though if i re-issue the "color sample" command it seems to color the first volume according to the values in the un-transformed second volume I am guessing? Is this correct and expected or am I just doing something wrong? if this is what is happening is there a way to force color sample to read the transformed values or to re-sample the transformed maps so they are correctly read? Also the output of the color sample command reports the min,max and mean values, just to confirm this corresponds to the values of all the voxels displayed at the current threshold level right? Finally is there a way to show a key for the coloring in chimerax? Many thanks for any advice you can provide. Sean

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Fly function in ChimeraX - 2
by Gabor PAPAI 16 Aug '19

16 Aug '19

Dear developers, I’ve seen that two years ago the fly command from Chimera was not implemented in ChimeraX. Is it implemented now? Or does ChimeraX have a similar function? I tried the view command inside the perframe function, unfortunately this didn’t result in a smooth transition between two named views. The only option I have now is to translate, zoom and rotate the scene with the individual commands, however this is quite tedious to set. Best regards, Gabor --- Gabor Papai IGBMC Integrated Structural Biology 1, rue Laurent Fries, Bp 10142 67404 Illkirch, France Tel: +33-3-69485288

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RESMAP output superposition.
by chimerax-announce-owner＠cgl.ucsf.edu 15 Aug '19

15 Aug '19

From: Shahid Khan <outlook_CD0472DE47DC92D6(a)outlook.com <mailto:outlook_CD0472DE47DC92D6@outlook.com>> Subject: RESMAP output superposition. Date: August 14, 2019 at 7:33:59 PM PDT Hello The python script for mapping the RESMAP local resolution output does not work in ChimeraX. Has anybody modified it so that it does? Or written a new script with the same purpose for ChimeraX. Sent from Mail <https://go.microsoft.com/fwlink/?LinkId=550986> for Windows 10

2 1

Understanding the output of the align command
by Yazan Abbas 14 Aug '19

14 Aug '19

Hi, I am trying to make a movie to rotate density in a manner that follows rotation between two atomic coordinates. To do that, I am aligning the two models and using the reportMatrix output to inform turn and move commands in order to transform the density. However, I am encountering some difficulty, and I'm not sure if this is related to bugs or my lack of understanding. For example, if I want to move from the position of model #1 to model #2, "align #1/b toAtoms #2/b move nothing reportMatrix true" produces the following: *Axis 0.11 -0.018 0.99Axis point 166 190 0Rotation angle (degrees) 108Shift along axis -0.24* I would think my turn command should be *turn 0.11,-0.018,0.99 108 models #1 center 166,190,0* But that doesn't work. I can get it to work if I assume that the reported axis is x,z,y instead of the expected x,y,z. Also, I have to use a rotation angle of -108 instead of 108. I'm not sure if I am using the axis point value correctly though, is it correct to use that as my center of rotation? It's location (166, 190, 0) places at the top of the box, which seems unusual to me. And finally, would I use this same information in a move command (i.e. move axis distance(shift), as reported by the align command? Many thanks in advance, I hope explained this clearly. Best, Yazan

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Morphing atomic models and volumes in a single movie
by Yazan Abbas 05 Aug '19

05 Aug '19

Hi, I am trying to create a movie that is morphing between 3 atomic models while simultaneously morphing between the 3 corresponding volumes. The following is my script for recording this movie: *set max 25windowsize 1080 1080view frame1movie record supersample 3wait 1volume morph #12,13,14,15 frames 181 playStep 0.005524861878453038 constantVolume true modelId #16perframe "surface dust #16 size 40" frames 181coordset #10 1,181wait 181movie stopmovie encode test_full.mp4 quality high* There are 4 maps in my morph, but the fourth map is simply a copy of the first in order to mimic the *wrap true* option of the atomic model morph. I am encountering the following issue during the volume morph step: somewhere in between the morph between volume #14 and #15, the map disappears for a fraction of a second in the movie. I suspect its because of a calculation/waiting issue, because if I record the movie using filtered versions of the volumes (*volume guassian sDev 2*), I don't have the same issue. Am I correct in my interpretation of the issue? Is there a way to modify my recording script to avoid this? Thanks, Yazan

2 1

pixel size
by Yazan Abbas 01 Aug '19

01 Aug '19

Hi, I am trying to create a scale bar using the following method: 1. camera is set to ortho 2. save image image.png width 4000 height 4000 transparentBackground true 3. check pixel size in chimeraX using the zoom command (which shows Pixel size at center of rotation is 0.178) 4. in imageJ, set the scale to be 0.178Å/pixel which turns into 5.618 pixels/Å 5. Show scale bar of desired in length in ImageJ However, the resulting scale bar looks unusually small given the dimensions of my particle. Have I misunderstood something about the pixelSize settings? The user guide doesn't say anything about pixelSize when one of or both of width and height are specified in the same image command, so I assumed the pixel size of the saved image would be the same as in the graphics window. Thanks, Yazan

2 3

Runing multiple command lines in ChimeraX
by Marie Locard-Paulet 26 Jul '19

26 Jul '19

Hello, I am running ChimeraX version 0.9 (2019-02-16) on a Mac (macOS Mojave version 10.14.6). It works fine, and I can work by adding commandes in the command “box” in the bottom. But I would like to open a text file with multiple ChimeraX command lines (for reproducibility and gain of time). I saw the command “open” that should open a document with the suffix “.com” or “.cmd”. It doesn’t work in my hands. It says it does not recognise the suffix. Is there something I am missing? Could you please help? Kind regards, Marie. --------------------------- Marie Locard-Paulet NNF Center for Protein Research Faculty of Health Sciences University of Copenhagen, Denmark

2 1

ChimeraX Side View
by Elaine Meng 19 Jul '19

19 Jul '19

In response to a question about Side View... From: Elaine Meng <meng(a)cgl.ucsf.edu> Subject: Side View Date: July 19, 2019 at 10:34:44 AM PDT Hi Zhijie, Thanks for your registration comments! You will be happy to know that ChimeraX does have Side View. You can choose it from the menu: Tools… General. <http://rbvi.ucsf.edu/chimerax/docs/user/tools/sideview.html> To make a tool (Side View, etc.) start automatically every time you start ChimeraX, right-click in that tool (or Ctrl-click on some systems) to show the context menu, and from that menu choose “Start at ChimeraX Startup” <http://rbvi.ucsf.edu/chimerax/docs/user/window.html#context-menu> <http://rbvi.ucsf.edu/chimerax/docs/user/window.html#tool-context>

1 0

Zalman 3D monitor support
by Tom Goddard 19 Jul '19

19 Jul '19

Hi Zhijie, We are not likely to support Zalman 3D monitors (row interleaved stereo mode) in ChimeraX. Those monitors were made 2009-2011 and then discontinued. We don't have the funding to support technology from long ago. Tom

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Fw: Genentech ChimeraX source code inquiry
by Williams, Joanne 18 Jul '19

18 Jul '19

________________________________ From: Slaton Lipscomb <lipscomb.slaton(a)gene.com> Sent: Thursday, July 18, 2019 10:00 AM To: chimerax(a)cgl.ucsf.edu <chimerax(a)cgl.ucsf.edu> Subject: Genentech ChimeraX source code inquiry Hi, Genentech has a commercial license for ChimeraX. However we have run into challenges installing it for our high performance computing cluster because of the binary-only distribution model. We automate the build and deployment of applications for our HPC cluster using the tool EasyBuild. It's far easier to do this when working from source code. Is the source code for ChimeraX available to license holders? thanks slaton -- Slaton Lipscomb gRED IT Scientific Computing Support for gRED IT Scientific Computing services<https://urldefense.proofpoint.com/v2/url?u=https-3A__rochewiki.roche.com_co…> FAQs for gRED Scientific Computing services<https://urldefense.proofpoint.com/v2/url?u=https-3A__rochewiki.roche.com_co…>

1 0

Molecular Dynamics Viewer
by James Starlight 16 Jul '19

16 Jul '19

Dear ChimeraX users! I would like to make a movie of molecular dynamics trajectory that has been pre-converted to pdb format (totally 250 frames). 1) Firstly, I have a problem with the recognition of the SS elements of that ensemble in ChimeraX, where each snapshot looks just like a mixture of points ( i tried to use dssp but it did not solve the issue). At the same time the snapshots looks fine in another viewers including UCSF Chimera (not X) 2) If I have a pdb of the same protein with mapped B-factors and then I colored it using color byattribute bfactor palette rainbow range 2,100 2) would it be possible to map the trajectory to that pdb in order to see the motions (observed in MD) mapped onto the structure that has been coloured by b-factors? Thanks for help!

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session files do not save "color zone" command actions
by Rasmus Kock Flygaard 15 Jul '19

15 Jul '19

Hi all, I'm using chimerax-daily-build (downloaded two weeks ago, Chimerax-0.91). I am using a model to color EM density maps per subunit using the "color zone ..." command, but when I save Chimerax session files these colored zones are not saved and I have to redo all of them to fully restore a session. Is there any way to include these colored zones in the saved sessions files? Kind regards, Rasmus ------------------------------------ Rasmus Kock Flygaard, Ph.D Postdoc, Amunts' Lab SciLifeLab, Stockholms University Sweden

2 1

MLP value of the ASP and GLU carboxylate
by Zhijie Li 13 Jul '19

13 Jul '19

Hello, I noticed that the lipophilic atomic potentials of OD2 and OE2 are set to very positive values in mlp.py: 'ASP': {'C': -0.54, 'CA': 0.02, 'CB': 0.45, 'CG': 0.54, 'N': -0.44, 'O': -0.68, 'OD1': -0.68, 'OD2': 0.53} 'GLU': {'C': -0.54, 'CA': 0.02, 'CB': 0.45, 'CD': -0.54, 'CG': 0.45, 'N': -0.44, 'O': -0.68, 'OE1': -0.68, 'OE2': 0.53}, As as result the hydrophobic surface representation always show hydrophobic patchs on the carboxylates, which look quite odd to me. Is there a justification for this setting? In addition, aren't the two oxygens in the carboxylate equal considerting that they are in resonance? Zhijie

3 5

mesh lineThickness
by Yazan Abbas 12 Jul '19

12 Jul '19

Hi, In chimera the volume mesh lineThickness option could be changed. I can't seem to find the equivalent option in chimeraX. Is it possible to change the thickness of mesh lines? Thanks, Yazan PS apologies if you received this message twice, there was an error in my browser when first sent...

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WebGL apps still in the pipeline?
by Oliver Clarke 11 Jul '19

11 Jul '19

Hi, Loving the regular improvements to ChimeraX! Just wondering regarding a web viewer - the original roadmap for chimeraX mentioned “WebGL apps” (http://www.rbvi.ucsf.edu/chimera/data/adcom15/chimera2.html <http://www.rbvi.ucsf.edu/chimera/data/adcom15/chimera2.html>), and original Chimera had a limited capacity to export scenes as interactive html files. Is this still something that is in the pipeline for ChimeraX? I would really love to be able to export ChimeraX scenes in a format that I can share on the web, without the need for users to download and know how to use ChimeraX. Ideally the user would be able to rotate, zoom and slab, but perhaps not translate - that is, the center of rotation would be fixed. The idea would be to enable sharing of “interactive figure” kind of views of the molecule/map (perhaps allowing switching between multiple scenes/views within one session). Cheers Oli

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Appearance of thick edges
by Yazan Abbas 11 Jul '19

11 Jul '19

Hi all, While playing around with lighting settings, thick black lines appear on the edges of my model (picture attached) that do not go away when I reset lighting conditions. Is it a "feature" or a bug? I tried playing around with all or most of the lighting options to find one that would get rid of them, but that didn't work. Thanks, Yazan

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feature request / suggestion
by Alexis Rohou 10 Jul '19

10 Jul '19

Hello, Apologies if this already exists, but I'd like to suggest a new option to the show/hide command: show /spec/ toggle which would behave like the toggle option of volume (one of my favorite chimeraX features by far), but would work on atomic models. Within the spec, anything currently shown would become hidden, and vice versa. Cheers, Alexis

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Re: [chimerax-users] [Chimera-users] Using ChimeraX in no-gui mode
by James Starlight 08 Jul '19

08 Jul '19

Hi Greg, sorry for some delay :-) Actually I just checked and indeed, there is still problem with rendering of the images with chimera-X using here is the detailed output if it would help chimerax-daily --offscreen --nogui "${output}/!temp/chimeraX.${pdb_name}.cxc" INFO: Offscreen rendering is not available. INFO: module 'OpenGL.osmesa' has no attribute 'OSMESA_DEPTH_BITS' INFO: UCSF ChimeraX version: 0.9 (2019-04-03) INFO: © 2016-2019 Regents of the University of California. All rights reserved. INFO: Executing: open /home_pers/novikov/Bureau/test/test/!temp/chimeraX.0476.cxc INFO: Executing: open /home_pers/novikov/Bureau/test/test/!temp/B-factors_0476.pdb INFO: Summary of feedback from opening /home_pers/novikov/Bureau/test/test/!temp/B-factors_0476.pdb --- _warning_ | Ignored bad PDB record found on line 2 REMARK THIS IS A SIMULATION BOX INFO: _B-factors_0476.pdb_ title: **Gallium Rubidium Oxygen Manganese Argon Carbon Silicon** [[more info...]](cxcmd:log metadata #1) INFO: Chain information for B-factors_0476.pdb #1 --- Chain | Description [ ](cxcmd:select :1-219 "Select chain") | [No description available](cxcmd:sequence chain #1/ "Show sequence") INFO: Executing: open /home_pers/novikov/Bureau/test/test/florence.pdb INFO: Chain information for florence.pdb #2 --- Chain | Description [ ](cxcmd:select #2:1-219 "Select chain") | [No description available](cxcmd:sequence chain #2/ "Show sequence") INFO: Executing: mmaker #1 to #2 INFO: Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 INFO: Matchmaker florence.pdb, chain (blank) (#2) with B-factors_0476.pdb, chain (blank) (#1), sequence alignment score = 1131.8 STATUS: Matchmaker florence.pdb, chain (blank) (#2) with B-factors_0476.pdb, chain (blank) (#1), sequence alignment score = 1131.8 STATUS: RMSD between 194 pruned atom pairs is 0.859 angstroms; (across all 219 pairs: 2.266) INFO: RMSD between 194 pruned atom pairs is 0.859 angstroms; (across all 219 pairs: 2.266) INFO: INFO: Executing: hide #2 models INFO: Executing: wait ERROR: wait requires a frame count argument unless motion is in progress ERROR: wait requires a frame count argument unless motion is in progress INFO: Executing: dssp #1 INFO: Executing: zoom 1.3 ERROR: turn x 15 y 15 z -40 ERROR: ..........^ ERROR: Expected an integer >= 1 or a keyword ERROR: Expected an integer >= 1 or a keyword INFO: Executing: wait ERROR: wait requires a frame count argument unless motion is in progress ERROR: wait requires a frame count argument unless motion is in progress INFO: Executing: preset "'overall look'" publication INFO: Preset expands to these ChimeraX commands: _set bg white; set silhouettes t_ INFO: Executing: set silhouettes true INFO: Executing: set silhouetteColor indigo INFO: Executing: set silhouetteDepthJump 0.02 INFO: Executing: color byattribute bfactor palette rainbow range 2,100 INFO: 16875 atoms, 4661 residues, atom bfactor range 0 to 367 STATUS: 16875 atoms, 4661 residues, atom bfactor range 0 to 367 INFO: Executing: cartoon style width 2.4 thickness 0.50 xsection barbell INFO: Executing: 2dlabels create title text '"Cluster 0476"' color red font gothic xpos .01 ypos .90 size 36 INFO: Executing: lighting depthCueStart .4 depthCueEnd .8 INFO: Executing: lighting full intensity 1.4 shadows true qualityOfShadows finer INFO: Executing: save image /home_pers/novikov/Bureau/test/test/!plots/visu_0476.png format png width 600 height 600 supersample 4 transparentBackground false and this is my script open /home_pers/novikov/Bureau/test/test/!temp/B-factors_0472.pdb open /home_pers/novikov/Bureau/test/test/florence.pdb mm #1 to #2 hide #2 models wait dssp #1 #view zoom 1.3 turn x 15 y 15 z -40 wait # options for appearance preset 'overall look' publication # set bg powder blue set silhouettes t; set silhouetteColor indigo; set silhouetteDepthJump 0.02 color byattribute bfactor palette rainbow range 2,100 cartoon style width 2.4 thickness 0.50 xsection barbell # make info of the screen 2dlab create title text "Cluster 0472" color red font gothic xpos .01 ypos .90 size 36 # options for light light depthcuestart .4 depthcueend .8; lighting full intensity 1.4 shadows true qualityOfShadows finer save image /home_pers/novikov/Bureau/test/test/!plots/visu_0472.png format png width 600 height 600 supersample 4 transparentBackground false exit пн, 22 апр. 2019 г. в 23:38, Greg Couch <gregc(a)cgl.ucsf.edu>: > > Salut, > > Does ChimeraX work in offscreen mode for you now? I believe it is fixed. > > -- Greg >

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Re: [chimerax-users] [Chimera-users] Cylinder coloring extension
by Elaine Meng 03 Jul '19

03 Jul '19

Hi Thomas, Chimera “pipes” are always a single color each. <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/pipesandplanks/pi…> However, our new program ChimeraX has a cylinder-helix representation in which each residue’s segment can be a different color. Like Chimera, ChimeraX is a free download for noncommercial use. Commands are similar but not identical between the two programs. <http://www.rbvi.ucsf.edu/chimerax/index.html> In ChimeraX, if I open 2gbp and from the menu apply preset “cylinders/stubs” and then preset “publication” I get this: ... and then command “color by bfactor palette rainbow” gives this: Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Jul 3, 2019, at 3:48 AM, Thomas Marcellino <marcellino.tom(a)gmail.com> wrote: > > Dear Chimera Team, > > I am aiming to color a stucture according to the B factor and represent it as a cylinder (pipes and planks) is there any possibility to apply different colors within the same cylinder or assign the coloring scheme to the cylinder representation in the same way as doing it with surface ? > > Looking forward to an answer, > Thank you for your time reading my suggestion. > > Thomas M

1 0

mclip - surface clipping per-model
by bertrand beckert 03 Jul '19

03 Jul '19

Hi Elaine, I just wonder if the option clipping per-model has also been introduced in ChimeraX like it is in chimera ( https://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/per-model/per-mod…) ? Apparently the command mclip doesn't seem to exist... Has it been replaced? Best Bertrand

2 1

MacOS two-finger swipe on help window
by Alexis Rohou 03 Jul '19

03 Jul '19

Hi all, Not sure this is a bug, but on my MacOS laptop when I use two finger swipe motion while hovering over the help window (to browse up and down the page), the help page is scrolled as expected, but simultaneously the view in the main window is rotated. Is this expected behavior? It seems a bit counter productive to me. Cheers, Alexis

2 3

color a surface by volume data
by bertrand beckert 02 Jul '19

02 Jul '19

Dear all, I have been searching in the documentation for quite a while and I haven t yet found the solution of how we can in chimeraX color a surface/volume by a volume data like in chimera ... i.e: local resolution map in cryo-em... in chimera: volume viewer/Tools/Surface color/color suface by is it possible to do so in ChimeraX? Any Help would be really appreciated! Thanks also for the amazing software ! Best Bertrand

2 1

An error opening chimerax seesion
by Yehuda Halfon 02 Jul '19

02 Jul '19

Hi all, I'm using chimeraX 0.8 (2018-12-17) on centos 7 (can't remember the build). Sometimes when I load a session that was saved using this version of chimeraX it gives me this error: Unable to restore session, resetting. Traceback (most recent call last): File "/software/graphics/chimerax/lib/python3.6/site-packages/chimerax/core/ session.py", line 593, in restore obj = sm.restore_snapshot(self, data) File "/software/graphics/chimerax/lib/python3.6/site-packages/chimerax/ std_commands/view.py", line 214, in restore_snapshot for k,v in data ['view attrs'].items(): TypeError: 'NoneType' object is not subscriptable After that I can't open the session again, so I need to remake it. Help, Yehuda Halfon

2 4

Placing markers using the VR wands
by Schmid, Michael F. 01 Jul '19

01 Jul '19

Hi- I don’t seem to be able to activate the Marker Placement functions in the menu that it called up by pushing the menu button (above the trackpad of the wand) to display a floating menu. It doesn’t seem to work with “vr off” either, using the mouse. I’d like to place markers in a tomogram, either in a density, or (preferably) at a specific 3D position with the wand. Thanks, Mike Schmid

3 4

suggestion for ChimeraX on MacOS
by Alexis Rohou 01 Jul '19

01 Jul '19

Hi there, I noticed that when I do "open browse", the native MacOS file browser is started, but when I click on File > Save..., a file browser from some other toolkit is used. I find this inconvenient because that file browser does not know about my recent history, bookmarks, etc. Any chance the File > Save... dialog could use the native OS file browser? Cheers, Alexis

2 1

Restoring views and how to use clip
by Yazan Abbas 01 Jul '19

01 Jul '19

Hi, Instead of using chimera sessions (which can get very big) to save my work when preparing figures for publications, I save all my commands in a .cxc file to be read by chimeraX later. Is there a single command that outputs all the necessary information in an appropriate format needed to restore a view? Currently what I have done is *alias myview view matrix; zoom *to output the information into the log, but the output needs to be re-formatted whenever I want to use that information with the view matrix and zoom commands. Is there a command that outputs that information in a format ready for copying and pasting? I know name view can partially fulfil what I am looking for, but it is only session specific. On a related note, I want to also restore the clipping for each figure/panel I create, but I don't seem to be using the clip command appropriately. For example, if I enter the command clip list, and the output is Using 2 clip planes: far -34.697, near -45.723, executing the command clip far -34.697 near -45.723 does not restore the same view. Am I missing something? Thanks, Yazan

3 2

Orientation and pre-superimposition of the PDB
by James Starlight 28 Jun '19

28 Jun '19

Dear Chimera Users! I am dealing with some script that use Chimera X to make a very nice images of the RMSF mapped to the PDB in B-factor column (produced by gromacs as the result of MD simulation). The problem that when I map RMSF onto structure for several different systems (e.g. the different conformations of the same protein) the pdb produced by gmx rmsf in different orientation so Chimera use it for image and the positions of the structure are not the same (thus not being aligned, see the image for example!) Would it be possible by means of some Chimera-X comands to orient pdbs in order to align them in the same way? E.g. I open (in bash loop) many pdbs (the same protein but in different states, which are not aligned before, but I need that on the final images the positions for each PDB would be the same (thus to avoid pre-align the PDBs before opening them in ChimeraX! Thanks in advance!

2 4

Mouse modes
by Yazan Abbas 27 Jun '19

27 Jun '19

Hi, Apologies if this has been posted before, still new to chimerax and the mailing list. Was wondering if there are plans to add support for modifying mouse keys with ctrl (similar to what is in chimera). I am also wondering if there are plans to create a recenter + change pivot button/function that is also part of chimera. Thanks, Yazan

3 4

Map issue after using color zone
by Yazan Abbas 27 Jun '19

27 Jun '19

Hi, I already submitted a bug report for this issue, but was wondering if there was a quick fix. After applying color zone to my map, parts of it appear broken where density is forming protrusion. An image example is attached. Using the latest daily build (jun 25). Thanks, Yazan

2 2

volume splitbyzone and color zone issues
by Yazan Abbas 26 Jun '19

26 Jun '19

Hi, I executed 'color zone #2 near #1 distance 5 sharpEdges true' to colour a map I loaded, followed by "volume splitbyzone #2', but repeatedly would get an error that the volume specified is not coloured by zone. Eventually after trying multiple times, it worked, however the log outputted the following: Traceback (most recent call last): > File > "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-packages/chimerax/core/triggerset.py", > line 130, in invoke > return self._func(self._name, data) > File > "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-packages/chimerax/map/volume.py", > line 3557, in _update_drawings > v.update_drawings() > File > "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-packages/chimerax/map/volume.py", > line 701, in update_drawings > self._update_surfaces() > File > "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-packages/chimerax/map/volume.py", > line 724, in _update_surfaces > s.update_surface(ro) > File > "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-packages/chimerax/map/volume.py", > line 1953, in update_surface > va, na, ta, hidden_edges = self._calculate_contour_surface(matrix, > level, rendering_options) > File > "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-packages/chimerax/map/volume.py", > line 2048, in _calculate_contour_surface > rendering_options, level) > File > "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-packages/chimerax/map/volume.py", > line 2071, in _adjust_surface_geometry > varray, tarray, narray = subdivide_triangles(varray, tarray, narray) > ValueError: not enough values to unpack (expected 3, got 2) > Error processing trigger "graphics update": not enough values to unpack > (expected 3, got 2): > ValueError: not enough values to unpack (expected 3, got 2) > File > "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-packages/chimerax/map/volume.py", > line 2071, in _adjust_surface_geometry > varray, tarray, narray = subdivide_triangles(varray, tarray, narray) I also get the following when using the color zone command, even though color zone works (most of the times, sometimes it fails) Traceback (most recent call last): > File > "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-packages/chimerax/cmd_line/tool.py", > line 254, in execute > cmd.run(cmd_text) > File > "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-packages/chimerax/core/commands/cli.py", > line 2641, in run > result = ci.function(session, **kw_args) > File > "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-packages/chimerax/std_commands/color.py", > line 1248, in color_zone > color_zone(s, spoints, colors, distance, sharp_edges = sharp_edges, > auto_update = update) > File > "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-packages/chimerax/surface/colorzone.py", > line 14, in color_zone > zc.set_vertex_colors() > File > "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-packages/chimerax/surface/colorzone.py", > line 84, in set_vertex_colors > replace = True) > File > "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-packages/chimerax/surface/colorzone.py", > line 123, in color_zone_sharp_edges > ec = _edge_cuts(varray, tarray, i1, n1, points, colors, distance) > File > "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-packages/chimerax/surface/colorzone.py", > line 147, in _edge_cuts > f = _edge_cut_position(varray, v1, v2, p1, p2, points, colors, > distance) > File > "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-packages/chimerax/surface/colorzone.py", > line 181, in _edge_cut_position > raise ValueError('Cut fraction %.5g is out of range (0,1)' % f) > ValueError: Cut fraction 1.8061 is out of range (0,1) > ValueError: Cut fraction 1.8061 is out of range (0,1) > File > "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-packages/chimerax/surface/colorzone.py", > line 181, in _edge_cut_position > raise ValueError('Cut fraction %.5g is out of range (0,1)' % f)

3 2

Distinguishing between upper and lower case chain IDs before and after splitting chains
by Yazan Abbas 25 Jun '19

25 Jun '19

Hi, My model (cif format) contains 34 chains, and so I've been using upper case and lower case letters for chain IDs. When I read in my model, the select command distinguishes between upper case and lower case, but after applying the split command on my model ('split #1 chains'), the select command no longer distinguishes between upper and lower case. I.e. 'select #1/D' will select both chains D and d. The split command works correctly, producing models 1.1-1.34. Also, is it possible to create a model from a selection? I can't find such a command anywhere, and the only thing I can figure out is to do the following: 'save *name* format mmcif models *selecion_name*; open test.cif' Thanks, Yazan

2 1

measure blob - persistent color?
by Alexis Rohou 25 Jun '19

25 Jun '19

Hi there, I absolutely love the new measure blob UI in the daily builds. Very useful. Thank you so much for putting it together. Is there a way to get the blob surface color to persist beyond hiding/showing the volume object? Obviously, in a script I could just re-measure the blob and re-color it, but is there another way to make the color "stick"? (Note, I don't plan to change the isocontour level) Cheers, Alexis

2 4

#2013: Trouble pip-installing Pyyaml prereq for bundle
by Andrés Giner Antón 20 Jun '19

20 Jun '19

Hello, two weeks ago we reported a problem regarding the installation of Pyyaml as a prereq of a bundle that we created, do you have any forecast of when we will get an answer? Here is the URL of the ticket: https://plato.cgl.ucsf.edu/trac/ChimeraX/ticket/2013 Thanks for your attention. Greetings, Andrés Giner Antón

2 1

ISOLDE 1.0b3 now released for ChimeraX 0.9
by Tristan Croll 17 Jun '19

17 Jun '19

Dear ChimeraX users, Just letting you know that I've released ISOLDE 1.0b3 on the ChimeraX Tool Shed for use with ChimeraX 0.9. If you're not familiar with ISOLDE, you can get an overview at https://isolde.cimr.cam.ac.uk/. In brief, ISOLDE is designed to allow the high-fidelity, interactive remodelling/refinement of atomic models into low-medium resolution cryo-EM or crystallographic electron density maps. In designing ISOLDE, I've always had two groups in mind. The first is, of course, the experimental structural biologists whose job it is to solve the structures of new macromolecules and their complexes. The second (and, to my mind, equally important) group is the downstream *users* of such models. Like every other human endeavour, macromolecular model building is an imperfect field, and (particularly in the worse-than-2-Angstrom resolution range targeted by ISOLDE) many deposited models contain serious errors that are eminently fixable with modern tools. My hope is that ISOLDE will become a useful tool allowing you to directly inspect your model of interest in the context of its original data, providing you with a feasible pathway towards fixing any issues you find (or, failing that, moving to a new target) prior to committing serious resources to its study. Please enjoy. Constructive feedback is always welcome. Best regards, Tristan

1 0

Transparent background movie
by Norberto Escudero 14 Jun '19

14 Jun '19

Hi, I have succesfully created images with transparent background, but it seems is an impossible task for a movie. Is there any way around this? Thanks and regards, -- Dr Norberto Escudero Urquijo Prof. A. Warren's group Cambridge Institute for Medical Research (CIMR) Hills Road, Cambridge, CB2 0XY

3 2

Saving stereo pairs
by Gyunghoon Kang 14 Jun '19

14 Jun '19

?Hi, apologies if this information is available somewhere but all my searches returned information for the original Chimera. Is there a way to generate stereo pairs either in the command line or GUI? Best, Gyunghoon Kang

2 1

set silhouettes false for volume mesh only?
by Alexis Rohou 14 Jun '19

14 Jun '19

Hi there, Is there a way to set silhouettes false for volume meshes, but keep it true for other object types (ribbons, surfaces,...)? Cheers, Alexis

2 1

SMILES Input With ChimeraX
by Victor Blaga 05 Jun '19

05 Jun '19

Hello, I am just wondering if there is a way to input a SMILES string with ChimeraX, as with Chimera? I can't seem to find it in the documentation so I just want to confirm this functionality has indeed been dropped? Thank you, Victor Blaga Research Assistant McMaster University Department of Biochemistry and Biomedical Sciences

2 2

equivalent command for coloring elements specific colors?
by Liz Kellogg 30 May '19

30 May '19

Hi, There used to be this handy command in Chimera to color oxygen atoms and nitrogen atoms specific colors: color @O red,a color @N blue,a but I can't find the corresponding command in ChimeraX. Is there a way to color all nitrogen atoms blue and all oxygen atoms red? When I try what I think the equivalent command should be (I'm displaying cartoon backbone with stick side chains): color @O red target a color @N blue target a it says 'Colored 1120 atoms' but none of the sidechains are colored differently. Thanks for the help Liz

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crossfade warps image when transitioning
by Liz Kellogg 24 May '19

24 May '19

Hi all OK I have a real problem this time (not a silly problem on my end). I'm trying to make movies in chimerax, and I used to be able to use the crossfade function in Chimera to smoothly interpolate two images to change the scene. However, in ChimeraX, when I use the crossfade function it either warps the first image or it somehow interpolates a zoomed in view of the lower left corner of the first image into the second, which makes for a jarring transition. Closing and re-opening ChimeraX seems to change the behavior, but I still can't get a smooth transition between image 1 and image 2. Any idea how to fix this? I thought perhaps setting the view size before starting to record the movie would help, but that doesn't seem to work. Thanks a bunch. Best Liz

2 2

nucleotides command not found in chimerax
by Liz Kellogg 22 May '19

22 May '19

Hi ChimeraX users, I am dabbling around in ChimeraX, and it seems that the documentation doesn't quite match up with the commands that are available. For example, this command: nucleotides https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/nucleotides.html would be useful, but when I enter this into the command line it says "unknown command" I downloaded the nightly chimerax build for mac, so it can't be a problem with an out of date version. Is this command not currently implemented? and if not, how many commands are listed in the documentation that aren't implemented? Best Liz

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Re: [chimerax-users] tile command in chimeraX
by françois SERRA 22 May '19

22 May '19

Hi Elaine, thanks for the quick reply. my usual routine with 3D models involves loading tens of them, match them (now align :P) and then "tile", so yes its a bit tedious. I'll keep doing this in "old" chimera, and look forward for the advances in chimeraX. thanks again for the tool!! francois On Mon, 20 May 2019 at 19:25, Elaine Meng <meng(a)cgl.ucsf.edu> wrote: > Hi Francois, > Not a dumb question, but sorry, there is no “tile” equivalent in ChimeraX > currently. If you don’t have too many structures, you could first > superimpose them all in the middle, zoom out somewhat (“zoom” command) and > then translate them individually up/down (y axis) and left/right (x axis) > with the “move” command, but it would be a little tedious and require some > trial and error as to spacing. It may be useful to save/restore positions > with the “view” command. > > <http://rbvi.ucsf.edu/chimerax/docs/user/commands/zoom.html> > <http://rbvi.ucsf.edu/chimerax/docs/user/commands/move.html> > <http://rbvi.ucsf.edu/chimerax/docs/user/commands/view.html#name> > > 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 20, 2019, at 3:17 AM, françois SERRA <serra.francois(a)gmail.com> > wrote: > > > > Hi, > > sorry for the stupid question, but I spent quite some time searching for > it. > > Is there some alternative to the "tile" command in chimera X? > > thanks! > > great tool :) > > francois > > -- *François Serra* **senior researcher - comparative epigenomics** *Computational Biology Group - *Barcelona Supercomputing Center (BSC) C/ Jordi Girona, 29 08034 Barcelona *Tel: +34 934 137 97*

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Fwd: tile command in chimeraX
by Elaine Meng 20 May '19

20 May '19

> > From: Elaine Meng <meng(a)cgl.ucsf.edu> > Subject: Re: [chimerax-users] tile command in chimeraX > Date: May 20, 2019 at 10:25:27 AM PDT > To: françois SERRA <serra.francois(a)gmail.com> > Reply-To: ChimeraX Users Help <chimerax-users(a)cgl.ucsf.edu> > > Hi Francois, > Not a dumb question, but sorry, there is no “tile” equivalent in ChimeraX currently. If you don’t have too many structures, you could first superimpose them all in the middle, zoom out somewhat (“zoom” command) and then translate them individually up/down (y axis) and left/right (x axis) with the “move” command, but it would be a little tedious and require some trial and error as to spacing. It may be useful to save/restore positions with the “view” command. > > <http://rbvi.ucsf.edu/chimerax/docs/user/commands/zoom.html> > <http://rbvi.ucsf.edu/chimerax/docs/user/commands/move.html> > <http://rbvi.ucsf.edu/chimerax/docs/user/commands/view.html#name> > > 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 20, 2019, at 3:17 AM, françois SERRA <serra.francois(a)gmail.com> wrote: >> >> Hi, >> sorry for the stupid question, but I spent quite some time searching for it. >> Is there some alternative to the "tile" command in chimera X? >> thanks! >> great tool :) >> francois >

1 0

tile command in chimeraX
by françois SERRA 20 May '19

20 May '19

Hi, sorry for the stupid question, but I spent quite some time searching for it. Is there some alternative to the "tile" command in chimera X? thanks! great tool :) francois -- François Serra *senior researcher - comparative epigenomics* Computational Biology Group - Barcelona Supercomputing Center (BSC) C/ Jordi Girona, 29 08034 Barcelona Tel: +34 934 137 97

1 0

smoothen coils
by Gabor PAPAI 13 May '19

13 May '19

Dear developers, I would like to show helices as tubes (this I know how to do) and coils between them with smooth trajectories, more schematic, as it is drawn in Chimera using Pipes and Planks (or even more). I would appreciate your help! Best regards, Gabor --- Gabor Papai IGBMC Integrated Structural Biology 1, rue Laurent Fries, Bp 10142 67404 Illkirch, France Tel: +33-3-69485288

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Feature Request: Dust ranges and new object as output
by Scott, Brandon L. 30 Apr '19

30 Apr '19

We can currently remove objects of a given size; it seems like it would be fairly straightforward to allow a range of object sizes to be kept from the middle, i.e. remove objects less than 20 and greater than 1000. Additionally, it would be really helpful if we could output the 'dusted' components as a new model so they could be individually colored and displayed, or be able to access the measured sizes of the objects for further analysis. Cheers, -Brandon ____________________ Brandon Scott, PhD SDSMT, Nanoscience

2 1

morph with molecular surface for part of molecule
by Susan Lea 30 Apr '19

30 Apr '19

How can I generate a morph with a molecular surface representation? many thanks Susan Prof. Susan M. Lea, FMedSci tel: +44 1865 275181 ------------------------------------------------------------------------------------------ Director of the Central Oxford Structural Microscopy and Imaging Centre & Professor of Microbiology Sir William Dunn School of Pathology, Oxford OX1 3RE Professorial Fellow @ WadhamCollege

2 3

Some preferences will reset
by Eric Pettersen 25 Apr '19

25 Apr '19

Hi all, In order to improve the modularity and maintainability of the ChimeraX code, the way some settings/preferences were handled was changed so that the code for that setting/preference could be kept in the appropriate tool bundle rather than in the ChimeraX core. A consequence of this change is that for settings/preferences that moved, they will revert to their initial default values rather than any values you may have saved for them. This will only happen for builds later than today, and furthermore if you go back to an older build it will still have your old values. For most settings/preferences this is not a big deal — you can easily just change them and save them again. The one setting that may be a little tricky is the “Startup commands” setting since there might be a lot of text saved in that one. Nonetheless, as long as you don’t delete your old build you can just start that and copy the commands from that into the new build. The preference categories that got moved are: Clipping Distances Labels Log Startup Trackpad Window —Eric Eric Pettersen UCSF Computer Graphics Lab

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ChimeraX python crush in no-gui mode
by James Starlight 16 Apr '19

16 Apr '19

Dear ChimeraX users! I am using a cxc script together with the following options to run ChimeraX in no-gui mode. chimerax-daily --offscreen --nogui test.cxc here is my scrript # chimeraX script windowsize 800 600 open ./test.pdb view; zoom 1.0; turn x 90; turn z -80; preset 'overall look' publication color byattribute bfactor palette rainbow range 2,100 # make info 2dlab create title text "B-factors for" color red font gothic xpos .04 ypos .90 size 30 # options for light light depthcuestart .4 depthcueend .8; lighting full save image ./test.png format png width 800 height 600 supersample 4 transparentBackground false This script works fine with GUI producing very good picture but with the --nogui it gave me error: Traceback (most recent call last): File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-packages/ChimeraX_main.py", line 699, in init commands.run(sess, 'open %s' % arg) File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-packages/chimerax/core/commands/run.py", line 31, in run results = command.run(text, log=log) File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-packages/chimerax/core/commands/cli.py", line 2616, in run result = ci.function(session, **kw_args) File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-packages/chimerax/core/commands/open.py", line 41, in open from_database=from_database, ignore_cache=ignore_cache, **kw)) File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-packages/chimerax/core/commands/open.py", line 117, in open models = handle_unknown_kw(session.models.open, paths, format=format, name=name, **kw) File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-packages/chimerax/core/commands/open.py", line 62, in handle_unknown_kw return f(*args, **kw) File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-packages/chimerax/core/models.py", line 601, in open session, filenames, format=format, name=name, **kw) File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-packages/chimerax/core/io.py", line 467, in open_multiple_data models, status = open_data(session, fspec, format=format, name=name, **kw) File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-packages/chimerax/core/io.py", line 421, in open_data models, status = open_func(*args, **kw) File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-packages/chimerax/core/scripting.py", line 115, in open_command_script run(session, text) File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-packages/chimerax/core/commands/run.py", line 31, in run results = command.run(text, log=log) File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-packages/chimerax/core/commands/cli.py", line 2616, in run result = ci.function(session, **kw_args) File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-packages/chimerax/core/commands/save.py", line 61, in save fmt.export(session, filename, fmt.nicknames[0], **kw) File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-packages/chimerax/core/io.py", line 203, in export result = self.export_func(session, path, **kw) File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-packages/chimerax/core/image.py", line 43, in save_image raise LimitationError("Unable to render images to save them") chimerax.core.errors.LimitationError: Unable to render images to save them could you help me how it may be fixed? Thank you in advance! Gleb

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Re: [chimerax-users] [Chimera-users] Using ChimeraX in no-gui mode
by Elaine Meng 15 Apr '19

15 Apr '19

Hi James, There is a different email address for asking ChimeraX questions (CC’d here). Yes, you can script imaging in ChimeraX with nogui if you are using Linux and start with the “nogui” and “offscreen” options on the system command line (they have dash-dash in front but my Mail keeps editing it to a long hyphen instead). <http://rbvi.ucsf.edu/chimerax/docs/user/options.html> In ChimeraX the command script filenames end in .cxc <http://rbvi.ucsf.edu/chimerax/docs/user/commands/usageconventions.html#cxc-…> The commands may be different than in Chimera. Open is with “open” save is with “save” and there is no publication preset but you can change to white background and show silhouettes with the “set” command. See the individual command help pages <http://rbvi.ucsf.edu/chimerax/docs/user/index.html#commands> making images <http://rbvi.ucsf.edu/chimerax/docs/user/images.html> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Apr 15, 2019, at 2:14 AM, James Starlight <jmsstarlight(a)gmail.com> wrote: > > Dear Chimera users! > > Would be possible to use new ChimeraX for execution of some simple > scripts for structure visualisation and imaging via no-gui mode? > > I am using bash script to loop over pdbs and would like to > > 1) open each pdb which contains b-factors info in chimeraX > 2) apply preset publication > 3) colour the pdb using "color byattribute bfactor palette rainbow ave residue" > 4) save high quality image at the selected directory using chimera render > > Would it be possible to do these things directly from linux terminal > providing each time pdb and some script file with the list of the > applied commands? > > chimerax-daily ${pdb} ${script} > > Thank you in advance!

1 0

Dome projection camera mode
by Tibor Füzik 11 Apr '19

11 Apr '19

Dear ChimeraX developers, I have not found the "dome" projection camera mode in ChimeraX (as it is in Chimera). Is there any equivalent projection (camera mode) or a workaround to get it? Would it be hard to implement it ChimeraX? Thanks. All the best, Tibor

3 2

PDBe-KB ligand centric pages survey
by Lukas Pravda 04 Apr '19

04 Apr '19

Dear ChimeraX users, We are in the process of redesigning the ligand pages of PDBe and we would be grateful if you could fill out a short survey to help us understand what information about small molecules / ligands you would find useful. The survey is available at https://bit.ly/2FFmHFG. Recently, we have introduced protein-specific aggregated views on the structural data (pdbe-kb.org/proteins) as a part of Protein Data Bank in Europe Knowledge Base (PDBe-KB). We highlight the available information related to structures of specific proteins, including structural and functional annotations, domains, ligand-binding sites and interfaces. In the next step we would like to present a similar aggregated view from a small molecule / ligand perspective. Thank you for your time, Lukas -- Lukas Pravda, Ph.D. Bioinformatician/Scientific Programmer Protein Data Bank in Europe (PDBe) European Bioinformatics Institute (EMBL-EBI) Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD United Kingdom

1 0

Feature request: save cxc
by Zack Gainsforth 02 Apr '19

02 Apr '19

Hi, I am finding that saving my visualization as a cxc (scripting command) file leads to good reproducibility. Often, when I save a session (cxs) file, it doesn’t open again later (I think because directory path names change), but if I produce the visualization by coding a cxc file instead, then it hasn’t failed (yet!). In addition, I want to keep track of actions such as median filters, and filter parameters, pixel scaling, all that jazz. When I code this into a cxc file, all that info is in the code record. When I save a session file I often cannot find that information again later (was it a gaussian filter? median? What do I write in the paper!?) I would suggest a feature to save a cxc file or output a journal of all changes for a cxs file so I can see what I did at least for documentation/reproducability later. Cheers, Zack

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Re: [chimerax-users] Output motion prickle magnitude
by Scott, Brandon L. 02 Apr '19

02 Apr '19

Based on previous correspondence I added an output option in motion.py. Is there anyway to do a pull request or something similar, so that I don't have to make the changes everytime I stay up to date with the nightly builds? Thanks, -Brandon

2 1

Transparency bugs with ribbons and density maps
by Pascal Albanese 27 Mar '19

27 Mar '19

Dear all, I'm haviong troubles with visualization of trasnparencies when using EM maps and PDBs. See in the example here: [image: image.png] The ribbon in the front is completely transparent (with silhouettes), the surface is set with a 50% transparency, and the pseudobonds inside or behind can be only visible when transparency of pbonds is set to 0 (at 5 already they disappear). Does anyone already experience these issues? Bests, Pascal -- Pascal Albanese, PhD *Post-doc*, Politecnico di Torino Dipartimento DISAT, BioSolar Lab@Environment Park Via Livorno 60 10144 Torino e-mail: pascal.albanese(a)polito.it Phone number: +39 011 2257655 <+39%20011%20225%207655>

2 1

Coulombic surface coloring
by Gabor PAPAI 27 Mar '19

27 Mar '19

Dear ChimeraX team, I would like to color a protein surface by electrostatic potential. Is there a way in ChimeraX to do that? My protein is too large (more than 20 000 atoms) to create a surface in Chimera, but ChimeraX has no problem to create it. Thank you in advance for your help! Best regards, Gabor --- Gabor Papai IGBMC Integrated Structural Biology 1, rue Laurent Fries, Bp 10142 67404 Illkirch, France Tel: +33-3-69485288

2 1

Implement Crosslinks/pseudobond/distances subselections and/or export
by Pascal Albanese 22 Mar '19

22 Mar '19

Dear ChimearX Users and developers, I'm using ChimeraX for visualization and analysis of pseudobonds datasets from Crosslinking-MS and i found new features very useful (min max selection etc). I think it would be useful (but i don't know how much effort will be required) to be able to select subsets of distances (e.g. form 15 to 24 Angstroms, or involving chain A and B) and being able to create and export these subsets. for instance i have a Complex of A, B and C and i want to select all pseudo-bonds involving A and B and export them as pb file (to be able to load them as a separate model lateron). Or to sel min 15 max 24, and then export them as pb file (with "save" function). I think it would be really useful for both crosslinks visualization and analysis (i work with datasets of thousands of crosslinks on big complexes which make difficult to subselect them, i have to do it with pymol, then generate subsets and reformat them as .pb files). i had a look to previous threads, but i didn't found similar topics. If i'm wrong my apologize. Thank you! Pascal -- Pascal Albanese, PhD *Post-doc*, Politecnico di Torino Dipartimento DISAT, BioSolar Lab@Environment Park Via Livorno 60 10144 Torino e-mail: pascal.albanese(a)polito.it Phone number: +39 011 2257655 <+39%20011%20225%207655>

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Re: [chimerax-users] [Chimera-users] color key in chimera X
by Elaine Meng 18 Mar '19

18 Mar '19

Hi Pranav, ChimeraX does not yet have color-key drawing, sorry. One possibility for now is that even if you want to make the main image in ChimeraX, you could still make the color key separately in Chimera and then combine them in some image-editing program like Photoshop. In Chimera, you could use the “colorkey” command as Ibrahim suggests, or the GUI (Tools… Utilities… Color Key). Either way you would have to define the colors and set values “manually” to match the coloring in ChimeraX, so we understand it is not as convenient as when the image and key are in the same program. <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/2dlabels/2dlabels…> There is also a ChimeraX e-mail list chimerax-users(a)cgl.ucsf.edu that you can use if you have other issues/questions about ChimeraX specifically. Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Mar 18, 2019, at 12:13 PM, Moustafa, Ibrahim M. <ria2(a)psu.edu> wrote: > > Hi Pranav, > > Not sure about ChimeraX but in Chimera you can use 'colorkey' command line: > > colorkey x1,y1 x2,y2 value1 color1 value2 color2.... > > example: > colorkey 0.1,0.1 0.11,0.5 3.0 blue 4.0 cyan 5.0 green 6.0 yellow 7.0 orange 8.0 red > > You can use the colors and their values from the output of local resolution map. > > > Ibrahim > From: Chimera-users <chimera-users-bounces(a)cgl.ucsf.edu> on behalf of Pranav Shah <p.shah.lab(a)gmail.com> > Sent: Monday, March 18, 2019 2:56 PM > To: chimera-users(a)cgl.ucsf.edu BB > Subject: [Chimera-users] color key in chimera X > > Hi, > I have a isosurface rendering that I have colored by radius as well as > local resolution. I want to now place a colour key in the image to > indicate the relevance of the colors. Is there a way to achieve this > in ChimeraX? If not, is there a way to easily port the commands to > Chimera? > > Cheers, > Pranav > -- > Pranav Shah > Postdoctoral Research Fellow.

1 0

Volume Rendering Issue
by Scott, Brandon L. 15 Mar '19

15 Mar '19

I am trying to set the thresholds to properly display volumetric fluorescence data, and for some reason, when viewed from the side, i.e. xz or yz projection, the volume goes black. I've attached two images (top view and side view) with not changes to anything else by positioning, and this can be seen clearly in the rotation video I attached. I guess my question is, is this a bug, or is it acting as it was intended? Thanks for the help, -Brandon [cid:1b1e95a3-2efc-477f-925e-74b92b367f68] [cid:56f70b34-d199-466f-a578-76fde802d5ec] ____________________ Brandon Scott, PhD SDSMT, Nanoscience

3 2

OpenGL error running ChimeraX under VNC on CentOS 7
by Tom Goddard 14 Mar '19

14 Mar '19

Hi Alexis, ChimeraX is crashing in the OpenGL graphics driver (libGL.so.1) when the Qt window toolkit is trying to use it. This is certainly an OpenGL graphics problem with your VNC setup. Sometimes VNC is run mirroring an actual display connected to the server computer you are connecting to, and sometimes it displays a virtual desktop, for example, when connecting to a server that has no physical display. ChimeraX will very likely work if VNC is mirroring an actual display on the server, but will almost surely fail if it is using a virtual desktop on the server. This is because OpenGL rendering only works to a physical display directly connected to the computer running the app (ChimeraX). I think there have been efforts to send the OpenGL commands to another computer and have that client computer's graphics card render, but that is a very obscure capability, and I have only heard of it failing, never saw it work. Tom > On Mar 14, 2019, at 10:40 AM, Alexis Rohou wrote: > > Hi Tom, > > I am attempting to get ChimeraX running on a CentOS7 workstation with a > nice discrete GPU card for running ISOLDE. Unfortunately, I am having no > luck so far. Tristan Croll, who is helping me get started with ISOLDE, > suggested I send you directly this report and ask for guidance. > > Some details: > - I installed the daily CentOS7 RPM from yesterday (13-March-2019) > - I am connecting to this workstation using a VNC server/client. I do > not have physical access to the workstation, at least not any time soon > - Starting the binary under gdb gives the error & stack trace copied below > - it could be that this is just related to OpenGL over VNC not working > properly. If you suspect this is true, could you suggest some test I > could run to confirm this is the case? > > Any other hints would be most welcome! > > Thanks, > Alexis > > >> WARNING: QOpenGLShader::compile(Vertex): failed >> WARNING: QOpenGLShader::compile(Fragment): failed >> WARNING: Could not link shader program: >> "" >> >> Program received signal SIGSEGV, Segmentation fault. >> 0x00007fffe6e6a013 in ?? () from /usr/lib64/nvidia/libGL.so.1 >> Missing separate debuginfos, use: debuginfo-install >> ucsf-chimerax-daily-2019.03.13-1.el7.x86_64 >> (gdb) bt >> #0 0x00007fffe6e6a013 in () at /usr/lib64/nvidia/libGL.so.1 >> #1 0x00007fffe54e268a in () at >> /usr/lib64/nvidia/libnvidia-glcore.so.340.107 >> #2 0x00007fffe6eac1a0 in () at /usr/lib64/nvidia/libGL.so.1 >> #3 0x00007fffe0e4fc6f in () at >> /opt/UCSF/ChimeraX-daily/lib/python3.7/site-packages/PyQt5/Qt/lib/libQt5Gui.so.5 >> #4 0x00007fffe0df1842 in () at >> /opt/UCSF/ChimeraX-daily/lib/python3.7/site-packages/PyQt5/Qt/lib/libQt5Gui.so.5 >> #5 0x00007fffe0df2143 in >> QPlatformBackingStore::composeAndFlush(QWindow*, QRegion const&, >> QPoint const&, QPlatformTextureList*, QOpenGLContext*, bool) () at >> /opt/UCSF/ChimeraX-daily/lib/python3.7/site-packages/PyQt5/Qt/lib/libQt5Gui.so.5 > > >

1 0

MOL2 import
by Marco J. Müller 14 Mar '19

14 Mar '19

Dear ChimeraX Team, when I try to load structure outputs of docking runs in .mol2 format into ChimeraX, it fails to load them, while the same can be imported by Chimera successfully. After a bit of playing around I found that the following section is relevant and fails in this format: @<TRIPOS>MOLECULE MYCOOLMOLECULE 57 62 1 SMALL USER_CHARGES The problem seems to be that ChimeraX requires explicit definitions of /#features/ and/#sets/ in the third line (apart from /#atoms #bonds #substructures/), while they are typically omitted in most programs. So the following lines could be imported: @<TRIPOS>MOLECULE MYCOOLMOLECULE 57 62 1 0 0 SMALL USER_CHARGES Can this case be addressed in a future version of ChimeraX? Thank you in advance, Marco -- Marco J. Müller PhD student Technische Universität Braunschweig Institute of Medicinal and Pharmaceutical Chemistry https://www.tu-bs.de/pharmchem Beethovenstr. 55 | 38106 Braunschweig | Germany

2 3

How can I use command crosslinks with bonds?
by Jun Ha Song 04 Mar '19

04 Mar '19

Dear RBVI, I want to use few command lines that are exclusively available for pseudobonds. The problem is that my model is consisted of markers and links, and there seems like no possible way for me to simply transfer bonds into pseudobonds. What commands like *crosslinks histogram *provide seems way to good for it to be limited for pseudobonds only. Is there a technical reason why such command is only applicable with pseudobonds? Can commands in Chimera/ChimeraX that work with pseudobonds easily be adapted to work with bonds, or is that too much of technical difficulty? If it is not feasible, is there a way to turn bonds into pseudobonds? Best, Junha Song.

3 2

matchmaker RMSD in ChimeraX
by Tom Goddard 04 Mar '19

04 Mar '19

> From: Martin Moncrieffe <mcm35(a)cam.ac.uk> > Date: March 4, 2019 at 1:15:06 AM PST > To: Tom Goddard > Subject: matchmaker in ChimeraX > > Hi Tom, > > Is it possible to get the rmsd as a function of residue position when using mm in ChimeraX? I’ve turned on the verbose flag and can see the residues used to match but not their respective rmsd’s. >

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Can we draw arrows in ChimeraX?
by Steve Chou 28 Feb '19

28 Feb '19

Dear ChimeraX team, I need to draw straight and curved arrows to show the straight and twisting forces on the molecules. See the attached images (cropped from ChimeraX interface) for details. Does ChimeraX have the functionality to do this? Steve -- Steve Chou

2 3

equivalent to "define"?
by Alexis Rohou 28 Feb '19

28 Feb '19

Hi there, Having looked through the docs a few times, I'm pretty sure I know the answer, but here goes... Is there a ChimeraX equivalent to define <https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/define.html> in Chimera 1? Or any other facility to draw geometric shapes (I'm particularly interested in calculating and drawing planes)? Cheers, Alexis

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Re: [chimerax-users] Color palettes for planes and solid data?
by Tom Goddard 28 Feb '19

28 Feb '19

Hi Oli, The single plane you are showing is the “solid” style, no different from if multiple planes are shown. You can use brightness value 1 for each color if you want, but it needs to be specified, it does not default to 1 (that usually is not what people want when using solid style rendering of more than 1 plane since it would be totally opaque). Also normally single planes are shown as partially transparent in both Chimera 1 and ChimeraX. Tom > On Feb 28, 2019, at 12:34 PM, Oliver Clarke <olibclarke(a)gmail.com> wrote: > > I’m also unclear why for an opaque plane it is necessary to set a brightness for each map value - surely a color palette with simple color,value pairs would be fine if there is no transparency issue as there is with a 3D solid representation? > > Oli > >> On Feb 28, 2019, at 3:06 PM, Tom Goddard <goddard(a)sonic.net> wrote: >> >> Hi Oli, >> >> To set the colors of different map values use the volume command >> >> volume #1 level 0,0 color white level 10,.9 color blue level 70,1 color green >> >> This says map value 0 has brightness 0 and color white, map value 10 has brightness 0.9 (on a 0 to 1 scale) and color blue, map value 70 has brightness 1 and color green. That is for using the “volume” or “plane” style as shown in the volume viewer panel. >> >> When you instead try to color a clipped map surface, your second screenshot has the surface threshold set to -10 while your map values range -.1 to .15 so you see just a cube surface — not sure what you are doing that for. In your third screen snapshot it looks better, but the colors are streaks on the clipped surface because the cap surface mesh subdivision is not fine. In Chimera you can set the cap subdivision in the Surface Capping dialog, but there currently is no control of the cap mesh subdivision in ChimeraX. Instead you could just crop the map either setting its bounds with the volume command “region” option or easier by using the crop mouse mode. Then the face of the cropped box will use a mesh that matches the map resolution and coloring should be ok. >> >> Tom >> >> >>> On Feb 28, 2019, at 11:35 AM, Oliver Clarke <olibclarke(a)gmail.com> wrote: >>> >>> Hi, >>> >>> Would it be possible to add support for more convenient coloring of solid representation data and planes of density maps? E.g. by specifying a color palette? Apologies if this already exists and I’m just not finding it! >>> >>> I would like to be able to make nice looking slices of a density map, without surface contours, colored by density value (e.g. attached). This can be a good way of showing disordered regions of a EM reconstruction. >>> >>> Currently, when a density map is loaded as a plane or solid represntation in Chimera, there is no way to automatically assign a predefined palette, and the defaults do not convey much information (at least for typical EM maps - example attached). >>> >>> Also, when I attempt another way to do this, coloring the surface by map value and then clipping the surface, the results are odd, unlike in Chimera (see attached at different contours). >>> >>> Cheers >>> Oli >>> >>> <Screen Shot 2019-02-28 at 2.34.47 PM.png><Screen Shot 2019-02-28 at 2.32.03 PM.png><Screen Shot 2019-02-28 at 2.25.00 PM.png><Screen Shot 2019-02-28 at 2.26.03 PM.png> >>> _______________________________________________ >>> ChimeraX-users mailing list >>> ChimeraX-users(a)cgl.ucsf.edu >>> Manage subscription: >>> http://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users >> > >

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Re: [chimerax-users] Color palettes for planes and solid data?
by Tom Goddard 28 Feb '19

28 Feb '19

Hi Oli, There is no capability to automatically use a palette and min/max range of map values that sets the levels and colors. That might be useful although when I have done this by hand I think equally spaced colors rarely produces what I want. The cryosparc image you attached is a good example of the color spacing not producing a very informative view. At any rate, if you want this feature in ChimeraX use the Help / Report a Bug… menu entry which is also for requesting features. I just tried setting the map threshold below the lowest value in the map and clipping in Chimera 1 and it only clips a cube for me. So I’m not sure what you mean when you say that works in Chimera 1. The streaks when you color the clipped and capped surface are because the cap is composed of triangles and only the vertices of the triangles are colored and the triangles are very long and skinny. Read about the Surface Capping mesh subdivision option in Chimera 1 if you want more explanation of it. ChimeraX does not yet support the cap subdivision, but if you follow my previous suggestion it is an alternative method that can work. Tom > On Feb 28, 2019, at 12:31 PM, Oliver Clarke <olibclarke(a)gmail.com> wrote: > > Hi Tom, > > Yes I know it is possible to do manually, thank you, but it requires quite a lot of futzing about with brightness/color pairs to get nice looking results. I was wondering if it would be possible to add support for palettes, with color thresholds automatically distributed between a minimum and a maximum, so that one can for example color a map slice with a rainbow palette between a minimum and a maximum density value (e.g. as per the density slices from cryosparc that I attached to the previous email). > > Re the cube, I set the threshold to -10 so that when I clip the map, it exposes a face that I can color by density value. I do this in Chimera and it works as expected without altering anything, here I just see streaks. I’m still unclear why I just see streaks on the clipped face no matter the threshold - this doesn’t seem to be the intended behavior? > > Oli > >> On Feb 28, 2019, at 3:06 PM, Tom Goddard <goddard(a)sonic.net> wrote: >> >> Hi Oli, >> >> To set the colors of different map values use the volume command >> >> volume #1 level 0,0 color white level 10,.9 color blue level 70,1 color green >> >> This says map value 0 has brightness 0 and color white, map value 10 has brightness 0.9 (on a 0 to 1 scale) and color blue, map value 70 has brightness 1 and color green. That is for using the “volume” or “plane” style as shown in the volume viewer panel. >> >> When you instead try to color a clipped map surface, your second screenshot has the surface threshold set to -10 while your map values range -.1 to .15 so you see just a cube surface — not sure what you are doing that for. In your third screen snapshot it looks better, but the colors are streaks on the clipped surface because the cap surface mesh subdivision is not fine. In Chimera you can set the cap subdivision in the Surface Capping dialog, but there currently is no control of the cap mesh subdivision in ChimeraX. Instead you could just crop the map either setting its bounds with the volume command “region” option or easier by using the crop mouse mode. Then the face of the cropped box will use a mesh that matches the map resolution and coloring should be ok. >> >> Tom >> >> >>> On Feb 28, 2019, at 11:35 AM, Oliver Clarke <olibclarke(a)gmail.com> wrote: >>> >>> Hi, >>> >>> Would it be possible to add support for more convenient coloring of solid representation data and planes of density maps? E.g. by specifying a color palette? Apologies if this already exists and I’m just not finding it! >>> >>> I would like to be able to make nice looking slices of a density map, without surface contours, colored by density value (e.g. attached). This can be a good way of showing disordered regions of a EM reconstruction. >>> >>> Currently, when a density map is loaded as a plane or solid represntation in Chimera, there is no way to automatically assign a predefined palette, and the defaults do not convey much information (at least for typical EM maps - example attached). >>> >>> Also, when I attempt another way to do this, coloring the surface by map value and then clipping the surface, the results are odd, unlike in Chimera (see attached at different contours). >>> >>> Cheers >>> Oli >>> >>> <Screen Shot 2019-02-28 at 2.34.47 PM.png><Screen Shot 2019-02-28 at 2.32.03 PM.png><Screen Shot 2019-02-28 at 2.25.00 PM.png><Screen Shot 2019-02-28 at 2.26.03 PM.png> >>> _______________________________________________ >>> ChimeraX-users mailing list >>> ChimeraX-users(a)cgl.ucsf.edu >>> Manage subscription: >>> http://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users >> > >

1 0

Color palettes for planes and solid data?
by Oliver Clarke 28 Feb '19

28 Feb '19

Hi, Would it be possible to add support for more convenient coloring of solid representation data and planes of density maps? E.g. by specifying a color palette? Apologies if this already exists and I’m just not finding it! I would like to be able to make nice looking slices of a density map, without surface contours, colored by density value (e.g. attached). This can be a good way of showing disordered regions of a EM reconstruction. Currently, when a density map is loaded as a plane or solid represntation in Chimera, there is no way to automatically assign a predefined palette, and the defaults do not convey much information (at least for typical EM maps - example attached). Also, when I attempt another way to do this, coloring the surface by map value and then clipping the surface, the results are odd, unlike in Chimera (see attached at different contours). Cheers Oli

1 0

Missing features in ChimeraX
by Tom Goddard 26 Feb '19

26 Feb '19

Hi Junha, Glad to hear you are trying VR with ChimeraX. Per-model clipping in ChimeraX is done with the clip command, or with the clipping mouse modes, atom radii are set with the size command, visibility is set with the show/hide commands, color is set with the color command, there are volume tracer mouse modes, and saving marker files should work, although you hit some bug and should press the Report a Bug… button when you get that traceback. ChimeraX does not have the selection inspector window yet. ChimeraX uses a different window toolkit Qt while Chimera used Tk so it requires all new code to move any graphical user interface from Chimera to ChimeraX. ChimeraX is a completely new program, modernizing every component of the 20-year-old design of Chimera so even moving commands from Chimera to ChimeraX requires substantial work. If you don’t find ChimeraX ready for your use, of course you should continue to use Chimera. We expect ChimeraX to replace Chimera in a few years. You might want to spend an hour skimming Elaine’s thorough ChimeraX documentation to understand what is in ChimeraX, including many new features like virtual reality that are not in Chimera. Tom > On Feb 26, 2019, at 2:03 AM, Jun Ha Song wrote: > > Tom, > > I recently got HTC Vive, and therefore started using ChimeraX. I have to say; the VR functionality is amazing. The ability to VR alone is sufficient reason for me to move over to ChimeraX. > > However, I noticed that key, crucial, irreplaceable features are (as far as I am aware) non-existent on ChimeraX. Below are function/tools that exist in Chimera that I use (literally) everyday, and I am wondering if these function/tools can also be implemented on ChimeraX or not. > > - per-model clipping (mclip) > - inspect selection (ability to change atom/bond/surface radius, visibility, color) > - volume tracer (ability to save markerset or atom/bond as .cmm) > > If the circumstance is so that implementing these onto ChimeraX is not feasible, then I must remain with Chimera until similar tools become available on ChimeraX. > > Also, is there any particular reason why all the tools of Chimera are not copied onto ChimeraX? Is ChimeraX trying to be another program that is different from Chimera? > > > > As for "ability to save .cmm", I tried saving atom/link using command > > save E:\LBNL\Stereocilia\ChimeraX_Markerset.cmm format markers models #1 > > but I got error saying that > > NotImplementedError: Slices are not implemented. > File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\markers\cmmfiles.py", line 39, in markerset_as_xml > rgb = tuple(r/255 for r in m.color[:3]) > See log for complete Python traceback. > > is this a simple bug during development, or have I typed wrong command? > > Best, > Junha Song.

1 0

How to zoom into a spot that is not located in the center gradually and straightly?
by Steve Chou 24 Feb '19

24 Feb '19

Dear ChimeraX team, Thanks for your fast and detailed responses to my questions! If a spot is in the center of view, we can zoom into the spot through a straight line. If it's not, it's really difficult to get there through a straight line. I tried something like this in a "movie" script, but it's still not straight. ========= move y -20 zoom 1.25 wait 2 move y -20 zoom 1.25 wait 2 move y -20 zoom 1.25 wait 2 ========= Is there a way to zoom into a spot that is not in the center of view through a straight line. Steve -- Steve Chou

2 7

Can we change the lighting gradually in ChimeraX?
by Steve Chou 20 Feb '19

20 Feb '19

Dear ChimeraX team, Is it possible to change the lighting gradually in ChimeraX, e.g., from "soft lighting" to "lighting simple"? This sounds weird, but makes sense if we want to change the lighting method in a movie. Thanks in advance! Steve -- Steve Chou

2 1

help with chimerax wildcards
by Michael Lawrence 20 Feb '19

20 Feb '19

Hi, I am trying to use wild cards in chimerax but they appear not to work. I type the command color @N* blue and get as response Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' or a keyword All I am trying to do is color all nitrogens blue. Version 0.5 (2018-02-05) running on macOS Sierra v10.12.6 what am I doing wrong? thanks Mike Lawrence

2 2

Blank lines in pseudobond files
by Tom Goddard 19 Feb '19

19 Feb '19

I made ChimeraX ignore blank lines and comment lines starting with “#” in pseudobond (.pb) files. Tom > On Feb 15, 2019, at 3:02 PM, Steve Chou wrote: > > Hi Elaine, > (1) I tried to read the pseudobonds from a file (.pb) , > ========================= > #1/A:13@NE2 #1/A:704@O > #1/A:13@NE2 #1/A:502@MG > #1/A:13@NE2 #1/A:501@PB > > #2/A:13@NE2 #2/A:704@O > #2/A:13@NE2 #2/A:502@MG > #2/A:13@NE2 #2/A:501@PB > ========================= > the program reported an error. > ============================= > ValueError: not enough values to unpack (expected 2, got 0) > File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-packages/chimerax/read_pbonds/readpbonds.py", line 27, in read_pseudobond_file > aspec1, aspec2 = line.split()[:2] > See log for complete Python traceback. > ============================= > > (2) Then I tried to add distances on the ChimeraX terminal > ============================= > distance #1/A:13@NE2 #1/A:704@O > distance #1/A:13@NE2 #1/A:502@MG > distance #1/A:13@NE2 #1/A:501@PB > > distance #2/A:13@NE2 #2/A:704@O > distance #2/A:13@NE2 #2/A:502@MG > distance #2/A:13@NE2 #2/A:501@PB > ============================= > I was able to see the distance labels in the two structure. And I saw an new model (name: distances; ID:3) show up in the "Models" panels. Then I ran morphing again. The Mg and water molecules moved, but still didn't move together with the protein. > Steve > > On Fri, Feb 15, 2019 at 11:31 AM Elaine Meng <meng(a)cgl.ucsf.edu <mailto:meng@cgl.ucsf.edu>> wrote: > Hi Steve, > Yes, if those are the correct specifiers for atoms in your structure. You'd make a plain text file with name *.pb with lines like that and open it. > > You don’t have to read in pseudobonds from a file, however. If not too many, probably easier just to add distance monitors. > <http://rbvi.ucsf.edu/chimerax/docs/user/commands/distance.html <http://rbvi.ucsf.edu/chimerax/docs/user/commands/distance.html>> > <http://rbvi.ucsf.edu/chimerax/docs/user/selection.html#context <http://rbvi.ucsf.edu/chimerax/docs/user/selection.html#context>> > > Elaine > > > On Feb 14, 2019, at 9:49 PM, Steve Chou <stevezchou(a)gmail.com <mailto:stevezchou@gmail.com>> wrote: > > > > Hi Elaine, > > Thanks for your detailed explanation! > > What's the format of the pseudobond file? Should it look like this? > > =============================== > > #1/A:13@NE2 #1/A:502@MG > > =============================== > > All the best, > > Steve > > > > On Thu, Feb 14, 2019 at 7:43 PM Elaine Meng <meng(a)cgl.ucsf.edu <mailto:meng@cgl.ucsf.edu>> wrote: > > Hi Steve, > > Actually I’m surprised the Mg and water were included (even if present at both ends) because I thought they had to be tethered by a bond or pseudobond (like a distance measurement) to the biopolymer chain, as described here under “Atoms in Common”: > > > > <http://rbvi.ucsf.edu/chimerax/docs/user/commands/morph.html#pairing <http://rbvi.ucsf.edu/chimerax/docs/user/commands/morph.html#pairing>> > > > > For the case where composition changes, you could add in a fake Mg ion and water to the structure that’s missing them, but you’d have to decide where to put them. Also it was my understanding that they had to be tethered to the biopolymer chain (e.g. add distance measurement, which can then be hidden), but maybe that requirement has changed, or the Mg does already have a metal-coordination pseudobond to the biopolymer. > > > > Or if you don’t care if the Mg or water move during the morph, you could just display those atoms from the original model (that was input to morphing) even though they are not present in the trajectory. > > Elaine > > ----- > > Elaine C. Meng, Ph.D. > > UCSF Chimera(X) team > > Department of Pharmaceutical Chemistry > > University of California, San Francisco > > > > > On Feb 14, 2019, at 12:51 PM, Steve Chou <stevezchou(a)gmail.com <mailto:stevezchou@gmail.com>> wrote: > > > > > > Thanks, Elaine! > > > You command "rainbow structures" works beautifully. > > > There is "a Mg ion" and "a water molecule" in the two conformations. > > > (1) If the two conformations have exactly the same compositions (by shifting the structure), the "Mg ion" and the "water molecule" do not follow the same path as the protein. They move but separate from the protein. > > > (2) If the two conformations have slightly different compositions, the "Mg ion" and the "water molecule" do not show up in the morphed pdb ensemble. > > > Is there a way to morph the specific components properly? > > > Steve > > > > > > > > > > > > > _______________________________________________ > > Chimera-users mailing list: Chimera-users(a)cgl.ucsf.edu <mailto:Chimera-users@cgl.ucsf.edu> > > Manage subscription: http://www.rbvi.ucsf.edu/mailman/listinfo/chimera-users <http://www.rbvi.ucsf.edu/mailman/listinfo/chimera-users> > > > > -- > Steve Chou > > > _______________________________________________ > Chimera-users mailing list: Chimera-users(a)cgl.ucsf.edu <mailto:Chimera-users@cgl.ucsf.edu> > Manage subscription: http://www.rbvi.ucsf.edu/mailman/listinfo/chimera-users <http://www.rbvi.ucsf.edu/mailman/listinfo/chimera-users>

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Fwd: [Chimera-users] Can ChimeraX morph between two surfaces?
by Steve Chou 16 Feb '19

16 Feb '19

Hi Elaine, (1) I tried to read the pseudobonds from a file (.pb) , ========================= #1/A:13@NE2 #1/A:704@O #1/A:13@NE2 #1/A:502@MG #1/A:13@NE2 #1/A:501@PB #2/A:13@NE2 #2/A:704@O #2/A:13@NE2 #2/A:502@MG #2/A:13@NE2 #2/A:501@PB ========================= the program reported an error. ============================= ValueError: not enough values to unpack (expected 2, got 0) File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-packages/chimerax/read_pbonds/readpbonds.py", line 27, in read_pseudobond_file aspec1, aspec2 = line.split()[:2] See log for complete Python traceback. ============================= (2) Then I tried to add distances on the ChimeraX terminal ============================= distance #1/A:13@NE2 #1/A:704@O distance #1/A:13@NE2 #1/A:502@MG distance #1/A:13@NE2 #1/A:501@PB distance #2/A:13@NE2 #2/A:704@O distance #2/A:13@NE2 #2/A:502@MG distance #2/A:13@NE2 #2/A:501@PB ============================= I was able to see the distance labels in the two structures. And I saw an new model (name: distances; ID:3) show up in the "Models" panels. Then I ran morphing again. The Mg and water molecules moved, but still didn't move together with the protein. Steve On Fri, Feb 15, 2019 at 11:31 AM Elaine Meng <meng(a)cgl.ucsf.edu> wrote: > Hi Steve, > Yes, if those are the correct specifiers for atoms in your structure. > You'd make a plain text file with name *.pb with lines like that and open > it. > > You don’t have to read in pseudobonds from a file, however. If not too > many, probably easier just to add distance monitors. > <http://rbvi.ucsf.edu/chimerax/docs/user/commands/distance.html> > <http://rbvi.ucsf.edu/chimerax/docs/user/selection.html#context> > > Elaine > > > On Feb 14, 2019, at 9:49 PM, Steve Chou <stevezchou(a)gmail.com> wrote: > > > > Hi Elaine, > > Thanks for your detailed explanation! > > What's the format of the pseudobond file? Should it look like this? > > =============================== > > #1/A:13@NE2 #1/A:502@MG > > =============================== > > All the best, > > Steve > > > > On Thu, Feb 14, 2019 at 7:43 PM Elaine Meng <meng(a)cgl.ucsf.edu> wrote: > > Hi Steve, > > Actually I’m surprised the Mg and water were included (even if present > at both ends) because I thought they had to be tethered by a bond or > pseudobond (like a distance measurement) to the biopolymer chain, as > described here under “Atoms in Common”: > > > > <http://rbvi.ucsf.edu/chimerax/docs/user/commands/morph.html#pairing> > > > > For the case where composition changes, you could add in a fake Mg ion > and water to the structure that’s missing them, but you’d have to decide > where to put them. Also it was my understanding that they had to be > tethered to the biopolymer chain (e.g. add distance measurement, which can > then be hidden), but maybe that requirement has changed, or the Mg does > already have a metal-coordination pseudobond to the biopolymer. > > > > Or if you don’t care if the Mg or water move during the morph, you could > just display those atoms from the original model (that was input to > morphing) even though they are not present in the trajectory. > > Elaine > > ----- > > Elaine C. Meng, Ph.D. > > UCSF Chimera(X) team > > Department of Pharmaceutical Chemistry > > University of California, San Francisco > > > > > On Feb 14, 2019, at 12:51 PM, Steve Chou <stevezchou(a)gmail.com> wrote: > > > > > > Thanks, Elaine! > > > You command "rainbow structures" works beautifully. > > > There is "a Mg ion" and "a water molecule" in the two conformations. > > > (1) If the two conformations have exactly the same compositions (by > shifting the structure), the "Mg ion" and the "water molecule" do not > follow the same path as the protein. They move but separate from the > protein. > > > (2) If the two conformations have slightly different compositions, the > "Mg ion" and the "water molecule" do not show up in the morphed pdb > ensemble. > > > Is there a way to morph the specific components properly? > > > Steve > > > > > > > > > > > > > _______________________________________________ > > Chimera-users mailing list: Chimera-users(a)cgl.ucsf.edu > > Manage subscription: > http://www.rbvi.ucsf.edu/mailman/listinfo/chimera-users > > -- Steve Chou -- Steve Chou

2 5

ChimeraX equivalent to ribinsidecolor
by Lukas Kater 15 Feb '19

15 Feb '19

Hi, is there a way to change the color of the inside of helices? Something like "ribinsidecolor" in chimera. see an example here (second picture from top): https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/ribstyles.html Thanks for any feedback! Lukas

2 1

Can ChimeraX morph between two surfaces?
by Steve Chou 15 Feb '19

15 Feb '19

Dear ChimeraX team, 1. Can ChimeraX morph between two surfaces (surfaces generated from two PDBs, not maps)? 2. During morphing, can the color also change gradually from one color (one conformation colored in red) to another color (another conformation colored in blue)? 3. The following command works if #1 has only one chain. morph #2 #1/L frames 10 When there are several chains in #1, ChimeraX stopped with an error (ValueError: models have different number of chains). Thanks in advance! Steve -- Steve Chou

2 5

bug report: hide with silhouettes
by Alexis Rohou 11 Feb '19

11 Feb '19

Hi Elaine, ChimeraX team, When silhouettes is set to true, hiding all models causes a bug whereby the display panel is not responsive / redrawn. As far as I can tell other parts of the GUI are still working. Below is a minimal reproducer. Attached are screenshots of what I'm seeing when silhouettes true (bug) or silhouettes false (no bug). I am running this on MacOS 10.13.6 on a MBP with graphics "Intel Iris Plus Graphics 650 1536MB" (sorry not sure what might be relevant here), and the Chimera version is: UCSF ChimeraX version: 0.8 date: 2018-12-17 22:26:30 UTC branch: v0.8 commit: 412d62d1949722ed7f52b3e515ec0f3b70b6b7af Python: 3.6.4 Obviously there's a workaround to avoid this but this caught me a few times in the last couple of days and it'd be nice to not have to watch out for it because the only solution I've found so far is to quit ChimeraX and start again. Cheers, Alexis PS. here's the reproducer: open pdb:1tbq set silhouettes true # Hide stuff hide #!1 models # Wait a bit (alternatively stop here and return to interactive use before doing the next step) wait 100 # print version out version verbose # Try to show it again. This should work (and does if silhouettes false) show #!1 models

3 4

volume zone - unexpected behavior when newMap false
by Alexis Rohou 11 Feb '19

11 Feb '19

Hello, I've been playing with volume zone and having good fun, but... I've noticed that if I set newMap to false, then the invert option is ignored (behavior is as though invert is false, even when I specify invert true). When newMap is set to true, or not set at all, the invert option has the effect I expected from reading the documentation. Am I missing something? Hopefully description above is unambiguous but let me know if you need step-by-step. Cheers, Alexis

3 4

Can ChimeraX add noise (Brownian-like motion) in morphing?
by Steve Chou 11 Feb '19

11 Feb '19

Dear ChimeraX support, When morphing from one structure to another unaligned structure, ChimeraX follows a smoothly curved path? Can it add noise (Brownian-like motion) to the path? All the best, Steve -- Steve Chou

2 3

equivalent to "move cofr"
by Alexis Rohou 08 Feb '19

08 Feb '19

Hello, Switching to ChimeraX, I find myself looking for an equivalent to "move cofr <https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/move.html#cofr>". Is there one? The use case is: I'm working on a particular part of a map & structure, I open a structure of a homologuous domain from the PDB, but its coordinates are way off, and I want to move it to the region I'm working on without having to zoom out and drag it. My apologies if this is in the documentation somewhere, I'm still finding my way around. Cheers, Alexis

2 2

Output motion prickle magnitude
by Scott, Brandon L. 08 Feb '19

08 Feb '19

Using the measure motion command I am able to generate the prickles on the surfaces correctly, which is great for visualization. Is it possible to write the magnitude of those prickles, and the index to a file so we can do further analysis on the distributions? Cheers, -Brandon ____________________ Brandon Scott, PhD SDSMT, Nanoscience

2 1

How to align two molecules using a subset of atoms in ChimeraX?
by Steve Chou 08 Feb '19

08 Feb '19

Dear ChimeraX support team, I tried the following command first - it worked well. ================== match #1/A to #2/A ================== Then I tried to align the two molecules using parts of them - it didn't work and complained that "No chains in reference structure PROT.pdb #2 compatible with BLOSUM-62 similarity matrix." ================== matchmaker #1/A:10-20@CA to #2/B:10-20@CA ================== System Info: ================== Platform: Linux-3.10.0-862.el7.x86_64-x86_64-with-redhat-7.5-Maipo ChimeraX version: 0.9 (2019-02-05) ================== Thank a bunch! Steven -- Steve Chou

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How to re-define the secondary structure info in ChimeraX?
by Steve Chou 08 Feb '19

08 Feb '19

Dear ChimeraX developers and users, In Chimera, I can use the following commands to redefine the secondary structure info. ============================ setattr r isHelix false : setattr r isSheet false : setattr r isSheet true :8-12,16-21 setattr r isHelix true :55-61,78-92 ============================ What's the ChimeraX equivalent? By the way, I can also delete the hydrogen atoms using "delete element.H" in Chimera. Is there an equivalent in ChimeraX? Many thanks in advance! Steve -- Steve Chou

2 1

Bio-Formats with ChimeraX?
by Matthew Akamatsu 08 Feb '19

08 Feb '19

Hi, I just started using ChimeraX to render and save 3D time lapse microscopy data as a high-performance replacement of Fiji. I am wondering how flexible ChimeraX can be in opening different TIF-derived file formats - particularly hyperstacks (multi color, multi Z, multi time). Other desired formats would be proprietary formats like .nd2 and .sld . Bio-Formats does all of this in an open-source manner - how feasible would it be to have bio-formats type functionality in ChimeraX? Thanks, Matt

2 3

VR in ChimeraX and Dell Visor
by Lewandowski, Jozef 24 Jan '19

24 Jan '19

Hi, Has anyone tested Dell Visor for VR in ChimeraX? If yes are there any issues you have run into? I am assuming that the experience should be similar to what Tom has described for Samsung Odyssey but I would appreciate if anyone had specific feedback on this particular piece of hardware. Thanks, Józef

2 1

color by conservation
by George Ghanim 17 Jan '19

17 Jan '19

Hello, Is it possible to color amino acids by conservation from an alignment file? Thanks, George Ghanim —— PhD Student Rio Lab Molecular and Cellular Biology, University of California Berkeley

2 1

ChimeraX crashes from time to time on Lenovo Y530
by Yehuda Halfon 02 Jan '19

02 Jan '19

Hi All, I bought a new laptop, Lenovo Y530 which has GTX 1050Ti as well as the intel 8750H which has UHD 630 and 16 GB of ram with windows 10. Chimerax is installed on m.2 drive. Sometimes, without any correlation it freezes and crashes, when I restart the error in the picture. All the drivers are updated. I run chimerax with the GTX as the GPU. I think it's something with the dual GPUs, is there a fix for it? I tried both 0.7 and the new 0.8 (not daily). On my other laptop, an old Macbook pro it run perfectly. Thanks, Yehuda Halfon

3 2

Movie recording error
by Carlos Escalante 21 Dec '18

21 Dec '18

Dar all, Trying to make a morphing movie. Everytime I run it, it comes out with the following error: Unknown command: coordset #3 1,21 And there is no sign that is recording. The same error occurred when I created the morphing, but it did created the morphing. Also, if I try to change anything and run the command again, it says ‘already recording a movie’ Any suggestions? Thank you Carlos R. Escalante Assistant Professor Department of Physiology and Biophysics VCU School of Medicine 1220 East Broad Street MMRB 2040 Richmond VA 23298 carlos.escalante(a)vcuhealth.org 804-628-1202

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version 0.7
by jingdong cheng 21 Dec '18

21 Dec '18

Hello, Could you provide me the older version 0.7? I tried the new 0.8, it is good, fixed a lot of bugs, but it runs super slow slow. It is better to change back to 0.7, but on your website I can’t find it anymore. Cheers! Merry Christmas! Jingdong

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FW: hi
by Williams, Joanne 21 Dec '18

21 Dec '18

From: mosbah amine <aminemosbah(a)hotmail.com> Date: Thursday, December 20, 2018 at 11:24 AM To: "chimerax(a)cgl.ucsf.edu" <chimerax(a)cgl.ucsf.edu> Subject: hi dear colleague trying to download chimiraX , no way to get to the right page !!! would you please send me the zip file , i agrre to licesing requarements also i have a windows10 for compatibility regards Dr mosbah amine TN

2 1

scale bar in chimerax
by Xu Jingwei 13 Dec '18

13 Dec '18

Hi, I recently installed the ChimeraX in my centos 7 and it is really powerful software to make beautiful figures. I really like it! However, one question before I setup for figures is how could I make a scale bar in ChimeraX? I did not find the relative information in the web. Could you please help me about that? I am really appreciated for that. Best, Jingwei ETH Zürich Dr. Jingwei Xu Postdoc Institute of Molecular Biology & Biophysics Department of Biology HPK D17 Otto-Stern-Weg 5 8093 Zürich, Switzerland

2 2

Dual GPU VR support
by Lewandowski, Jozef 11 Dec '18

11 Dec '18

Hi, A quick question. Does implementation of VR in ChimeraX support dual GPU? Or dual GPU would give no advantage? Thanks, Józef

2 1

transparentBackground doesn't seems to work on save
by Yehuda Halfon 09 Dec '18

09 Dec '18

Hi all, We are trying to save an image without a background using save image filename format png transparentBackground true but we get the error: transparentBackground expected key word. What are we doing wrong? Thanks, Yehuda Halfon

2 2

Incrementing value in perframe
by Scott, Brandon L. 09 Nov '18

09 Nov '18

I am attempting to use the measure convexity on each frame, and seem to have a mismatch between the frame number which goes from [0 - (N-1)] and the volume child which goes from [1 - N]. Is there a way to augment the $1 value to be $1+1? Attached are the command calls. This displays the convexity properly on the called frame: vseries play #1 jumpTo 1; measure convexity #1.2 smoothingIterations 12 palette cyan-gray-maroon range -1,1; The does not display it because of the mismatch: movie record; perframe "vseries play #1 jumpTo $1; measure convexity #1.$1 smoothingIterations 12 palette cyan-gray-maroon range -1,1;" range 1,200; wait 200; movie encode C:\Users\LLSM\Desktop\Convexity.mp4 quality highest framerate 25 Thanks in advance. -Brandon ____________________ Brandon Scott, PhD SDSMT, Nanoscience

2 1

Render images in nogui mode
by Lukas Pravda 07 Nov '18

07 Nov '18

Hi all, I was wondering if there is a way how to generate images from linux terminal. I’ve come across a couple of very old posts in the mailing list stating that this was not possible at that time. So, I wonder if anything has changed. If I use cif files only, chimerax gives “Unable to render images to save them” message. If I try to include volumetric data from cryo-EM overlaid on the structure I get an exception during opening a *.map file. Please see the script below. The exception is in the attachment Best, Lukas open emd_8909.map volume #1 color white transparency 0.7 level 0.1 step 1 zoom 1.2 open 6ds5.cif set bgColor white hide selAtoms show selAtoms ribbons color bychain ribbons light full light shadow true save image default.png width 1600 height 1600 supersample 5 transparentBackground true turn y 90 save image y.png width 1600 height 1600 supersample 5 transparentBackground true turn z 90 save image z.png width 1600 height 1600 supersample 5 transparentBackground true

3 2

chimeraX questions on representation
by Dr. Eddie 16 Oct '18

16 Oct '18

Hi, I have a few small n00b questions that would really help me along. 1) How do I change the "ball scale" property in chimeraX using a command for the sphere representation? 2) When I do "select protein" (which is represented as a cartoon) it highlights it but clicking on any of the buttons to change the representation does nothing. I need to click first on the show atoms and then I can click on those but many of the H are not connected (for LYS I have two white dots floating above the carbon with no bond to them, but a bond to other C's and it is only for one CH3 group, the other is fine). This is true in all three representations. How do I fix this? 3) Can I increase the resolution in VR? 4) After clocking on the label tool with a VIVE controller and using it, how to I change it back to the original mode so I can scale the model (using both triggers)? Thank you very much for your help! Eddie

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Re: [chimerax-users] chimeraX questions on representation
by Eric Pettersen 16 Oct '18

16 Oct '18

Hi Eddie, ChimeraX (and Chimera for that matter) connect atoms in standard residues using a connectivity template. Therefore the atoms have to have standard names. Some hydrogens in your file don’t have their PDB-standard names, and therefore wind up unconnected. I have committed a fix for this — if there are unconnected hydrogens after the template pass then Chimera(X) does an additional connect-by-distance pass. A second problem with the file is that it uses ATOM records for everything, including solvent, ions, and the lipid bilayer. ATOM records are for polymeric residues and imply connectivity between consecutive residues with the same chain ID. Therefore the non polymeric components of the file should have been using HETATM records. I have attached an edited version of your file with appropriate HETATM records. It should work much better in tomorrow’s fixed build. —Eric > On Oct 16, 2018, at 11:31 AM, Dr. Eddie <eackad(a)gmail.com> wrote: > > Thanks for the help! As for the pdb, I've attached it. It shows fine in vmd and pymol. > Thanks, > Eddie > > On Tue, Oct 16, 2018 at 1:19 PM Eric Pettersen <pett(a)cgl.ucsf.edu <mailto:pett@cgl.ucsf.edu>> wrote: >> On Oct 15, 2018, at 8:35 PM, Elaine Meng <meng(a)cgl.ucsf.edu <mailto:meng@cgl.ucsf.edu>> wrote: >> >> I don’t know why your H’s are disconnected specifically, but it’s almost surely some issue with the input file. > > If you provided the input file, we might be able to offer advice on how to get ChimeraX to handle it better. One thing you might try sight unseen is to remove the LINK/CONECT records in the file (assuming it’s a PDB file). > > —Eric > > Eric Pettersen > UCSF Computer Graphics Lab > > > > > > > -- > Eddie > <popc.3a4.ionf.pdb>

2 1

Question about measuring the distance of helix axis
by ze li 16 Oct '18

16 Oct '18

Dear ChimeraX supporting team: I try to measure the distance between two helix axises, but in the "distance" command there is only atom-to-atom usage in Chimera X. Is there any command and plugin for this function, such as in Chimera? Thank you. Best,

3 2

symmetric function from different template in chimera x
by Alexei Hernandez 09 Oct '18

09 Oct '18

Good morning, I am currently utilizing chimera x for different modeling features. Right now I am trying to use the symmetric option for a file created by a peer of mine titled ppar.pdb. I added the file here and trying to use the sym function by using the template of a close protein blast result, one called 3DZU, also added it. I want to use the template of the 3dzu to create a structure for ppar. I am confused as to which command line to use out of all of them and if it is possible to use 3dzu as a template for the ppar file created. Could you please help me with the command line. Have a nice day... Alexei Hernandez

2 1

Re: [chimerax-users] [Chimera-users] FW: Contributing to ChimeraX ?
by Tom Goddard 01 Oct '18

01 Oct '18

Hi Nicholas, The ChimeraX OBJ reader is all in Python with source code included in the distribution. Windows chimerax/bin/lib/site-packages/chimerax/wavefront_obj Linux chimerax/lib/python3.6/site-packages/chimerax/wavefront_obj Mac ChimeraX.app/Contents/lib/python3.6/site-packages/chimerax/wavefront_obj The ChimeraX git repository is here https://www.rbvi.ucsf.edu/trac/ChimeraX/browser <https://www.rbvi.ucsf.edu/trac/ChimeraX/browser> I don’t think the repository can be cloned due to access restrictions, but here is some info about that and you can try and see if it works. https://www.cgl.ucsf.edu/chimerax/docs/devel/conventions.html Tom > On Oct 1, 2018, at 7:52 AM, Williams, Joanne wrote: > > > > From: Nicholas Yue > Date: Sunday, September 30, 2018 at 3:40 AM > To: "chimerax(a)cgl.ucsf.edu <mailto:chimerax@cgl.ucsf.edu>" <chimerax(a)cgl.ucsf.edu <mailto:chimerax@cgl.ucsf.edu>> > Subject: Contributing to ChimeraX ? > > Hi, > > I took ChimeraX for a spin and when I save out to OBJ, the geometries looks connected up wrongly. > > I was hoping I can take a look at the source code to attempt to fix it myself. > > I see git being mentioned in the documentation. Is there a git repo I can clone and contribute to? > > If I need to sign any documents before contributing, let me know :-) > > I have other geometry format I'd like to write out to and also I am hoping to write out quads rather than triangles for use with OpenSubdiv in rendering software like RenderMan, Arnold, Mantra etc. > > Cheers > -- > Nicholas Yue > Graphics - Arnold, Alembic, RenderMan, OpenGL, HDF5 > Custom Dev - C++ porting, OSX, Linux, Windows > http://au.linkedin.com/in/nicholasyue <http://au.linkedin.com/in/nicholasyue> > https://vimeo.com/channels/naiadtools <https://vimeo.com/channels/naiadtools>_______________________________________________ > Chimera-users mailing list: Chimera-users(a)cgl.ucsf.edu <mailto:Chimera-users@cgl.ucsf.edu> > Manage subscription: http://www.rbvi.ucsf.edu/mailman/listinfo/chimera-users <http://www.rbvi.ucsf.edu/mailman/listinfo/chimera-users>

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Re: [chimerax-users] [Chimera-users] chimerax mesh commands doesn't work
by Elaine Meng 20 Sep '18

20 Sep '18

Hi Yehuda, I don’t think you are doing anything wrong; in ChimeraX, the lineThickness option doesn’t work for me either, although it works fine in Chimera on the same computer — we will look into it. Sorry for the inconvenience and thanks for reporting, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco P.S. there is a chimerax-users(a)cgl.ucsf.edu mailing list too <http://rbvi.ucsf.edu/chimerax/docs/contact.html> > On Sep 20, 2018, at 4:56 AM, Yehuda Halfon <yehuda.halfon(a)weizmann.ac.il> wrote: > > Hi all, > I wanted to use chimeraX to use some commands on mesh display. > Some works like meshLightning but others like lineThickness doesn't > I use volume #1 lineThickness 10 (or any other integer) but nothing seems to change. What am I doing wrong? > Yehuda Halfon

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Ca trace
by v.kalienkova＠bioc.uzh.ch 19 Sep '18

19 Sep '18

Dear all, I was wondering, is there an option to just show a Ca trace in ChimeraX? If yes, can one modify the width of it? Thanks a lot in advance, Valeria

2 2

Forward of moderated message
by chimera-users-bounces＠cgl.ucsf.edu 17 Sep '18

17 Sep '18

3 2

ChimeraX - Color by Electrostatic Potential
by Maurício Menegatti Rigo 14 Sep '18

14 Sep '18

Hi, is there a way to color the protein surface according to Electrostatic Potential, just like we do with Chimera ("Electrostatic Surface coloring" under "Tools"). The input potential file was calculated with Delphi. Thanks in advance, Maurício Menegatti Rigo, *Ph.D.* Brazil

2 2

Saving obj file
by Donghyun Park 13 Sep '18

13 Sep '18

Dear ChimeraX-users, I have a question about saving the scene as obj file. In the traditional Chimera, I was able to generate obj file with texture by simply clicking 'save' button. I tried to save obj file simply by typing *save ~/Desktop/file.obj . *I generated obj file but it does not show texture - basically black &white. I was hoping to find some more information on the user guide but I did not find much. Could somebody please help me with this problem? Thank you, Raphael

2 1

Thank you for your free vector icons.
by Moira Ames 12 Sep '18

12 Sep '18

Hi, I hope this email finds you well. Thank you for making this page: https://www.cgl.ucsf.edu/chimerax/docs/embedded.html I recently passed my thesis with a lot of aid from that resource page. It has helped us tremendously. May I ask if you are still updating the page? If you are, I would like to repay you by way of recommending an additional resource which could be a good addition to it. Here it is: https://www.webhostingsecretrevealed.net/free-icons/. <https://www.webhostingsecretrevealed.net/free-icons/> I hope you find it useful and helpful as well. Best Regards, Moira Ames *Graduating student from University of St. Thomas*

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Apply dust command to entire timeseries
by Scott, Brandon L. 10 Sep '18

10 Sep '18

I am attempting to remove small connected components from my timeseries volumes. The surface dust command works well for this, but it only works on one time point at a time, is there a way to script this, or use in conjunction with the vseries play command to apply this to each timepoint? Thanks, -Brandon ____________________ Brandon Scott, PhD SDSMT, Nanoscience

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Re: [chimerax-users] invert selection in ChimeraX
by Yashar Sadian 10 Sep '18

10 Sep '18

2 1

Re: [chimerax-users] [Chimera-users] ChimeraX and crosslinks visualization
by Tom Goddard 05 Sep '18

05 Sep '18

Hi Pascal, I enhanced the ChimeraX select command so you can select the crosslinks in a length range. Then you can color the selected ones. For example, select #1.1 minimumLength 30 color sel red select #1.1 minimumLength 5 maximumLength 10 color sel yellow sel #1.1 min 10 max 15 color sel blue The minimumLength and maximumLength options will be in tonight’s ChimeraX builds (available around 5 AM Pacific time). Tom > On Sep 1, 2018, at 2:57 AM, Pascal Albanese wrote: > > Dear Support Staff, > > first of all many thanks for developing Chimera! > > I'm using ChimeraX to integrate CryoEM and crosslinking MS data.I think that some features might be further implemented (or maybe are already there but i don't know how to use them): > > - Is it possible to load different sets of distances/crosslinks (like with different IDs)? > - is it possible to color code the distances with a cutoff (like red if >30 for instance)? > - The histogram and network is a nice feature, but it would be nice if there were some grouping based on the distances (i.e.: 1 to 5 A; 5 to 10 A, 10 to 15 A... etc), and then you can click on the column representing your distances class to select them (so you can make a subgroup, or delete them, or edit them etc...) > > that's it, maybe something can be done writing the code but unfortunately it's not my job. > > Thanks a lot and looking forward to hear from you, > > Cheers, > Pascal > > -- > Pascal Albanese, PhD > Post-doc, Politecnico di Torino > Dipartimento DISAT, > BioSolar Lab@Environment Park > > Via Livorno 60 > > 10144 Torino > > _______________________________________________ > Chimera-users mailing list: Chimera-users(a)cgl.ucsf.edu > Manage subscription: http://www.rbvi.ucsf.edu/mailman/listinfo/chimera-users

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Re: [chimerax-users] [Chimera-users] ChimeraX and crosslinks visualization
by Elaine Meng 04 Sep '18

04 Sep '18

Hi Pascal, Many features are are still in development, so although we can easily imagine useful features (and we welcome your suggestions), many are not yet implemented. Yes, you can load different sets of crosslinks. The “pseudobond” input format is just plain text specifiying pairs of atoms. <http://rbvi.ucsf.edu/chimerax/docs/user/pseudobonds.html> <http://rbvi.ucsf.edu/chimerax/docs/user/commands/open.html#atomic> Then you can specify the different models (input file -> model) in the “crosslinks histogram” command by their numbers as shown in the Models panel, e.g. crosslinks hist #1.3 crosslinks hist #3 <http://rbvi.ucsf.edu/chimerax/docs/user/commands/crosslinks.html#histogram> Currently there isn’t color-by-length or selection-by-length, sorry. The interaction with the histogram that you may already have seen is that passing the cursor over the columns of the histogram temporarily enlarges the corresponding-length pseudobonds and hides the others. There isn’t control over how wide the histogram bars are. Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco P.S. there’s a chimerax-users mailing list CC’d on this message which you can send to and/or join > On Sep 1, 2018, at 2:57 AM, Pascal Albanese <pascal.albanese(a)polito.it> wrote: > > Dear Support Staff, > > first of all many thanks for developing Chimera! > > I'm using ChimeraX to integrate CryoEM and crosslinking MS data.I think that some features might be further implemented (or maybe are already there but i don't know how to use them): > > - Is it possible to load different sets of distances/crosslinks (like with different IDs)? > - is it possible to color code the distances with a cutoff (like red if >30 for instance)? > - The histogram and network is a nice feature, but it would be nice if there were some grouping based on the distances (i.e.: 1 to 5 A; 5 to 10 A, 10 to 15 A... etc), and then you can click on the column representing your distances class to select them (so you can make a subgroup, or delete them, or edit them etc...) > > that's it, maybe something can be done writing the code but unfortunately it's not my job. > > Thanks a lot and looking forward to hear from you, > > Cheers, > Pascal

1 0

FYI: Model.id_string API change
by Eric Pettersen 22 Aug '18

22 Aug '18

For those of you writing code in ChimeraX, in case you’re using Model.id_string you should know that as of tomorrow’s build, Model.id_string is a property instead of a function. —Eric Eric Pettersen UCSF Computer Graphics Lab

1 0

question about chimerax
by Fang, Fei 14 Aug '18

14 Aug '18

Hi, This is Fei from University of Pittsburgh. Here is a question about chimera x. By introducing two structures into the chimera x, how can I move the one structure over so that they're no longer covering each other? Thanks. Best, Fei

3 6

Export a scene from Chimera and into ChimeraX?
by Oliver Clarke 06 Aug '18

06 Aug '18

Hi, I love the new visualization features in ChimeraX, but I also really like the depth of functionality available in the original Chimera. I understand that ChimeraX has been rebuilt from the ground up and therefore can’t be expected to support importing sessions from Chimera1. However, Chimera1 is also able to export static scenes - e.g. as COLLADA or VTK format. Would it be possible to add an import function for these scenes in ChimeraX, so we can create a static scene just the way we like it in Chimera1, and then render it with e.g. ambient occlusion etc in ChimeraX? Alternatively/additionally, would it be possible to add an export function for molecular surfaces to ChimeraX? One of the major improvements in ChimeraX (at least for my work) is that it has a robust and fast surface calculation function that works on large, multi chain structures. Would it be possible to export these surfaces (e.g as MRC format) so they could be imported into Chimera1? Cheers Oli

2 3

Setting the bgColor transparent in ChimeraX
by bertrand beckert 03 Aug '18

03 Aug '18

Dear all, I have now been trying to use ChimeraX as a replacement for Chimera for making really nice images for publication. So far I have to say I really liked the rendering! definitely a really nice work! However I was really wondering how to get the background transparent... In Chimera we were able to set the background transparent as preference which is actually really useful... any idea how we can to do it in ChimeraX? Any help would be highly appreciated! Best Bertrand

2 1

Transparency and Scaling factor in ChimeraX
by Christoph Bachmann 31 Jul '18

31 Jul '18

Dear ChimeraX team First of all, great piece of software. It's a lot more userfriendly than pyMol or VMD. But it is hard to find information, since most is still for the old Chimera. I'm struggeling to get transparency in saved pngs to work. I've tried it on a PC and a Mac with no luck. This is strange since both computers support transparency and I regularly work with that feature so it can't be a hardware problem. My main question is how to get absolute sizes of the molecules. I'm currently making an illustration with different molecules, from small to large and I want their size to be displayed as accurate as possible (so a carbon atom in one molecule is exactly as big as the one in another molecule). I'm sure there is an easy way but I haven't found anything so far. If I would load them all into ChimeraX their sizes are represented correctly, but that's just too much for the computer. So, thanks in advance for your help. Best wishes Christoph Bachmann University Basel - Switzerland

2 1

How to not build bundles/use wheel?
by Yuri 25 Jul '18

25 Jul '18

I am trying to build on FreeBSD. It calls the module 'bundle_builder', which calls 'wheel'. How to only do a regular python build, and not call 'wheel'? Thanks, Yuri

3 3

Volume isosurface transparency
by Zack Gainsforth 24 Jul '18

24 Jul '18

Hi, I’m fairly new to ChimeraX so forgive me if I’m a bit ignorant in this question. I have volumes acquired by tomographic reconstruction of STEM/EDS data (elemental composition in an electron microscope). I want to visualize several elements together as different colors representing phases. In some cases, the boundary is fairly obvious and can be represented with an isosurface. When I try to set the transparency of the isosurface so I can see the objects inside it, it simply turns darker color rather than transparent. As an example, here is a silicon isosurface obscuring the other volumes inside it: I’m setting the transparency using the colors dialog box: For comparison, if I make the isosurface invisible to show the objects inside: If instead I use the transparency command: volume #5 transparency 50 The isosurface turns black: My question is: am I doing this incorrectly? Thanks, Zack Gainsforth Space Sciences Laboratory, UC Berkeley 7 Gauss Way Berkeley, CA 94720 zackg(a)ssl.berkeley.edu

2 1

Re: [chimerax-users] I suggest the addition of a "Automatic Styling (Smart Initial Display)" button
by Eric Pettersen 20 Jul '18

20 Jul '18

Hi Jean-Yves, The latest builds of ChimeraX have a “Presets” menu with an entry (“Original Look”) which allows you to easily return to the initial depiction of a model. —Eric Eric Pettersen UCSF Computer Graphics Lab > Greetings, > > > thank you for your quick reply about the "non-bug" request relating to the initial display and the explanation. After your reply I searched more intensely in the documentation and indeed found page help:user/autostyle.html with these details about the number of chains. > > > As I am preparing to demonstrate ChimeraX in the department (tutorial I find that some inherent aspect of the Automatic Styling (Smart Initial Display) is very quickly lost. e.g. simply by clicking on the "Show atoms" button in the Molecular display toolbar and then the "Hide atoms". > > > I found commands for selection at http://www.rbvi.ucsf.edu/chimerax/docs/user/commands/atomspec.html <http://www.rbvi.ucsf.edu/chimerax/docs/user/commands/atomspec.html> which are useful and one can reconstruct the initial display. > > > As I example I am using myoglobin (1mbo.) The molecule opens as a ribbon, heteroatoms as stick models, the iron ion as sphere, and AA close to the ligands as sticks as well. > > Simply pressing the "Show atoms" button will display all water molecules as small spheres. > > But now if I click "Hide atoms" only the ribbon is left. > > > Yesterday I tried to find a way to select heteroatoms in general and use the sel ~ sel selection inversion found on the pipermail<http://plato.cgl.ucsf.edu/pipermail/chimerax-users/2017-December/000169.html <http://plato.cgl.ucsf.edu/pipermail/chimerax-users/2017-December/000169.html>> but that was not the best solution. > > > Today I could reconstruct the initial display with these commands if all I did was to toggle the "Show atoms" and "Hide atoms" buttons: > > > show ions > > show ligand > > select ligand:<3.8 & protein > > show selAtoms > > > For novices this is a bit complicated to understand. > > > Therefore I would like to suggest the addition of a "Automatic Styling (Smart Initial Display)" button, perhaps at the First position in the Molecular display toolbar. > > > I firmly believe that this would avoid lots of frustration for many new users! > > > P.S. One more thing: would it be possible to Copy from the built-in browser to Paste elsewhere as I am trying to do with the email address? > > > Sincerely, > > Jean-Yves Sgro

1 0

Hardware for VR of volume data
by Tom Goddard 11 Jul '18

11 Jul '18

Hi Bernard, VR is not going to handle large volumes no matter what hardware you buy. To avoid causing nausea current VR headsets use 90 frames/second graphics updating. That is in two eyes, so the effective graphics frame rate needed is 180 frames/second. By comparison on a flat panel display it is routine to show a very large volume at 10 frames per second and this causes no problem. So VR requires about 20 times the rendering speed of visualization on a conventional display. So here are some ideas of what you can expect. Some recent 3d light microscopy I was looking at in VR is 4K by 2K by 31 z planes with 3 channels — and it rendered fast enough with VR on a GTX 1080 and also on a Quadro P6000. Comparing to your 2K cubed example my data was equivalent to about 2k x 2k x 186, or about 1/10th the size. I haven’t benchmarked volume rendering so I don’t actually know at what size graphics is too slow — I should test this. But I suspect this is close to the limit. For molecular structure display, 100,000 atoms with very coarsely triangulated spheres works in VR but is near the limit. For surface and triangle rendering the limit is about 2-5 million triangles depending on which high-end graphics card before frame drops start causing flicker. For molecules showing 2.4 million atoms of HIV capsid 3j3q is fine on a desktop display but is not going to work in VR. With that in mind I would recommend a GTX 1080 Ti graphics card with a high-end CPU, maybe 64 Gbytes of memory, definitely get a high-end SSD drive or two as the data transfer rates of about 3 Gbytes/second are very handy for large data compared to the 100 Mbytes/second of spinning drives — the whole system would be about $4-5k. You could spend more but you won’t get any better performance. The main VR performance bottleneck is going to be in the software if you use ChimeraX. Unfortunately it does color blending and mapping data values to colors and cropping on the CPU instead of the GPU which is painfully slow, tens of seconds to adjust brightness on the above-mentioned 3-channel light microscopy. I expect to put the blending and color lookup on the GPU in ChimeraX over the next 12 months. Tom > On Jul 10, 2018, at 12:48 PM, Heymann, Bernard (NIH/NIAMS) [E] wrote: > > Hi > > I'm interested in acquiring a PC with capabilities to use ChimeraX for 3D VR visualization of large volumes (2k cube). What is the best configuration (CPU, GPU, VR hardware) for around a $5-10k budget? > > Bernard > > > > > > _______________________________________________ > Chimera-users mailing list: Chimera-users(a)cgl.ucsf.edu > Manage subscription: http://www.rbvi.ucsf.edu/mailman/listinfo/chimera-users >

1 0

pdb and map colors
by Andrey Feklistov 25 Jun '18

25 Jun '18

My question is about ChimeraX 0.6: is it possible to highlight different parts of a pdb (based on the protein sequence) with different colors and then color a corresponding map accordingly. I can't find an option 'Sequence' like in the old Chimera, is it possible to do this from a command line? Thanks!

2 1

Re: [chimerax-users] [Chimera-users] ChimeraX won't start on Ubuntu 16.04
by Greg Couch 22 Jun '18

22 Jun '18

(This is really a question for the chimerax-users mailing list, not the chimera-users one.) If you can wait a week or so, I'll have a ChimeraX .deb package for Ubuntu 16.04 (and another for 18.04). But to answer your question, you do not need a system-wide replacement of Qt5. libQt5core.so.5 is in CHIMERAX/lib/python3.6/site-packages/PyQt5/Qt/lib/libQt5Core.so.5, where CHIMERAX is where ChimeraX was installed. So add that directory to the LD_LIBRARY_PATH environment variable and rerun ldd on libqxcb.so. And please let me know what you find out so I can make sure the .deb package avoids that problem. Regards, Greg On 06/21/2018 10:34 AM, Petr Leiman wrote: > Dear ChimeraX users and Developers, > > ChimeraX v. 0.5 or 0.6 would not start on our stock Ubuntu 16.04 > machines. The error message is as follows: > > This application failed to start because it could not find or load the > Qt platform plugin "xcb" > in "". > > Available platform plugins are: eglfs, linuxfb, minimal, minimalegl, > offscreen, vnc, xcb. > > Reinstalling the application may fix this problem. > Fatal Python error: Aborted > > Current thread 0x000014f406ce7740 (most recent call first): > File > "/usr/local/lbbs/chimerax/current/lib/python3.6/site-packages/chimerax/ui/gui.py", > line 93 in __init__ > File > "/usr/local/lbbs/chimerax/current/lib/python3.6/site-packages/ChimeraX_main.py", > line 485 in init > File > "/usr/local/lbbs/chimerax/current/lib/python3.6/site-packages/ChimeraX_main.py", > line 788 in <module> > File "/usr/local/lbbs/chimerax/current/lib/python3.6/runpy.py", line > 85 in _run_code > File "/usr/local/lbbs/chimerax/current/lib/python3.6/runpy.py", line > 193 in _run_module_as_main > Aborted (core dumped) > > A few more errors while checking for missing libraries (ldd) of > ChimeraX-supplied libqxcb.so, libqxcb-glx-integration.so > or libqxcb-egl-integration.so > /usr/lib/x86_64-linux-gnu/libQt5Core.so.5: version `Qt_5.9' not found > /usr/lib/x86_64-linux-gnu/libQt5Core.so.5: version `Qt_5' not found > /usr/lib/x86_64-linux-gnu/libQt5XcbQpa.so.5: version > `Qt_5_PRIVATE_API' not found > /usr/lib/x86_64-linux-gnu/libQt5Gui.so.5: version `Qt_5' not found > /usr/lib/x86_64-linux-gnu/libQt5Gui.so.5 > > Do I need to do a system-wide replacement of Qt5 for a different > flavor (OpenGLES)? > > Thanks, > > Petr > > > _______________________________________________ > Chimera-users mailing list: Chimera-users(a)cgl.ucsf.edu > Manage subscription: http://www.rbvi.ucsf.edu/mailman/listinfo/chimera-users

3 3

Questions about ChimeraX and problems re-downloading Chimera
by Steven Douglas Aird 21 Jun '18

21 Jun '18

Dear Elaine, Is there a way in ChimeraX to specify colors for individual species of amino acids? I would like to color cysteine residues to illustrate disulfide bonds. There appears to be no ‘byresidue' or ‘byaminoacid’ command. Since I had formerly done this in Chimera, I sought to re-download that from: https://www.cgl.ucsf.edu/chimera/download.html This page has been unresponsive for hours and the download cannot be completed. Thanks for your help, as always. Sincerely yours, Steve Aird Steven D. Aird Technical Editor Faculty Affairs Office Okinawa Institute of Science and Technology Graduate University 1919-1 Tancha, Onna-son Kunigami-gun, Okinawa-ken Japan 904-0495 Phone: 098-982-3584 Cell: 080-4154-9504 Email: steven.aird(a)oist.jp<mailto:steven.aird@oist.jp>

2 1

Color clip plane
by Reza Khayat 15 Jun '18

15 Jun '18

Hi, I'm coloring a cryo-EM image reconstruction based on its local resolution. Thus, the image reconstruction will contain multiple colors. Is it possible to color the clipping plane the same as the underlying image reconstruction? Thanks. Best wishes, Reza Reza Khayat, PhD Assistant Professor Department of Chemistry City College of New York 85 Saint Nicholas Terrace, CDI 2.318 New York, NY 10031 http://www.khayatlab.org/ 212-650-6070

2 1

Deactivate model
by Reza Khayat 12 Jun '18

12 Jun '18

?Hi, Is it possible to deactivate a model like in Chimera? I wan to manually align a cryo-EM image reconstruction to another before using the fit command. The orientations are too different for fit to work. Thanks. Best wishes, Reza Reza Khayat, PhD Assistant Professor City College of New York Department of Chemistry New York, NY 10031

2 2

naming chain ids
by Andrew Macrae 06 Jun '18

06 Jun '18

To whom it concerns I am wondering if it is possible to change the names of the models in chimera X in a similar manner that was possible in chimera. When I split a large complex such as the ribosome it is nice to rename them so I don't need to memorize or reference the PDB what all the numbers and or letters mean. Thanks Cheers, Andrew MacRae

2 1

can now bundle user documentation with ChimeraX bundles
by Greg Couch 30 May '18

30 May '18

Starting with the next daily build, it is possible to have documentation for the tools and commands in the bundle automatically integrated into the User's Manual index. In the bundle_info.xml file, add the documentation to the DataFiles section, e.g.: <DataFiles> <DataFile>docs/user/commands/tutorial.html</DataFile> <DataFile>docs/user/tools/Tutorial_GUI.html</DataFile> </DataFiles> As you can see above, the documentation is in a directory hierarchy that matches the hierarchy of the builtin documentation. The file name for the tool should be the tool's name with underscore's replacing any spaces followed by .html. The file name for commands should be the the first word in the command name followed by .html. If help is asked for a subcommand, then a named reference is made to the subcommand, i.e., /command/.html#/subcommand/. -- Greg

1 0

Re: [chimerax-users] Question about Space navigator and ChimeraX
by Tom Goddard 29 May '18

29 May '18

Hi Rod, I just tried SpaceNavigator with the May 29, 2018 ChimeraX build on macOS 10.13.4 and it worked. Are you still getting the error that it cannot load _spacenavigator? Are you trying to use it on Mac or Windows or Linux? And does space navigator work with Chimera on that same machine? Tom > On May 29, 2018, at 12:17 PM, Tweten, Rodney K. (HSC) wrote: > > Hi Tom, > I downloaded the latest ChimeraX daily build (2018-05-29 02:45:16 PDT), but the space navigator still does not appear not work. Was it included in this build? Thanks! > > From: Tom Goddard <goddard(a)sonic.net> > Date: Friday, May 25, 2018 at 4:33 PM > To: "Tweten, Rodney K. (HSC)" <Rodney-Tweten(a)ouhsc.edu> > Cc: "chimerax-users(a)cgl.ucsf.edu" <chimerax-users(a)cgl.ucsf.edu> > Subject: [EXTERNAL] Re: [chimerax-users] Question about Space navigator and ChimeraX > > Hi Rod, > > Our Mac ChimeraX build machine did not have the Space Navigator library installed so it did not compile the module to use Space Navigator with ChimeraX. I've installed it on the build machine so hopefully tonight's build will have Space Navigator support. It works on my development machine. Thanks for reporting the problem. > > Tom > > > >> On May 25, 2018, at 11:02 AM, Tweten, Rodney K. (HSC) wrote: >> >> I have been using Chimera for some time and like it very much so I thought I would try ChimeraX, which has an undo button! However, I am unable to get the Space navigator to work with chimeraX. I keep getting that it can’t load space navigator (see attached screenshot). Can you tell me if I am doing something wrong here (likely) or if the use of the Space Navigator is not implemented yet. Thanks! >> >> <image001.png> >> >> Cheers, >> Rod Tweten, Ph.D. >> George Lynn Cross Professor >> "It's a great life if you don't weaken" >> >> Microbiology & Immunology >> BMSB-1053 >> 940 Stanton L. Young Blvd. >> The University of Oklahoma Health Sciences Center >> Oklahoma City OK 73104 >> USA >> >> >> _______________________________________________ >> ChimeraX-users mailing list >> ChimeraX-users(a)cgl.ucsf.edu <mailto:ChimeraX-users@cgl.ucsf.edu> >> Manage subscription: >> http://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users <https://urldefense.proofpoint.com/v2/url?u=http-3A__plato.cgl.ucsf.edu_mail…>

1 0

Question about Space navigator and ChimeraX
by Tweten, Rodney K. (HSC) 25 May '18

25 May '18

I have been using Chimera for some time and like it very much so I thought I would try ChimeraX, which has an undo button! However, I am unable to get the Space navigator to work with chimeraX. I keep getting that it can’t load space navigator (see attached screenshot). Can you tell me if I am doing something wrong here (likely) or if the use of the Space Navigator is not implemented yet. Thanks! [cid:image001.png@01D3F428.99CAA4A0] Cheers, Rod Tweten, Ph.D. George Lynn Cross Professor "It's a great life if you don't weaken" Microbiology & Immunology BMSB-1053 940 Stanton L. Young Blvd. The University of Oklahoma Health Sciences Center Oklahoma City OK 73104 USA Work phone: 405 271-1205 FAX: 405 271-3117 Skype: toxlab1 Email: rod-tweten(a)ouhsc.edu

2 1

info selection
by Wei Wang 14 May '18

14 May '18

Hello, After using ctrl-left click to select an atom, I use “info selection” as instructed in the manual. However I received the following error message: TypeError: 'str' object is not callable File "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/chimerax/list_info/util.py", line 50, in spec return o.atomspec() See log for complete Python traceback. If you wish to report this error, send mail to chimerax-bugs(a)cgl.ucsf.edu and describe what you were doing and include a copy of the contents of the log. Don't include any data you wish to remain private since a publicly viewable bug report will be created. If I use “info selection atom” then: info selection <help:user/commands/info.html#selection> atom Expected a keyword What am I doing wrong with? Please advice. Best, Wei

3 2

setattr m stickScale
by Wei Wang 14 May '18

14 May '18

Hello, I’m switching from Chimera1. I used to have “setattr m stickScale 0.6” to make whole stick representation “thinner”. Now in ChimeraX “stickScale” seems not available. Using “size stickRadius” looks similar to “setattr b radius” in Chimera1, but in this case the solvents radius are not changed. Is there a method to set all stick representation in the same arbitrary scale? Many thanks Wei

2 1

How to import chimera session to chimeraX
by Liz Kellogg 03 May '18

03 May '18

Hi all I love the graphics in chimera X, and I would like to render a scene I've set up in chimera. However, chimeraX doesn't seem to be able to open chimera session files. I tried exporting the chimera scene to different file format, such as vtk or wrl, but chimeraX can't seem to open those files either. Is there any way to open chimera sessions in chimeraX? Thanks a lot Liz

2 1

Re: [chimerax-users] spin movie error
by Sven Lange (PG Research) 02 May '18

02 May '18

Hi, I ran into the same error (related to _clock_gettime) today on macos 10.11, but found a workaround. I build ffmpeg using homebrew (brew -v install ffmpeg --with-fdk-aac --with-ffplay --with-freetype --with-libass --with-libquvi --with-libvorbis --with-libvpx --with-opus --with-x265) and then replaced the ChimeraX.app/Contents/bin/ffmpeg with the homebrew ffmpeg. Movies encoding now works in ChimeraX on my macos 10.11. Best wishes Sven The University of Dundee is a registered Scottish Charity, No: SC015096

1 0

mutitouch mac
by Edoardo Gianni 01 May '18

01 May '18

Hello, I was wondering if multitouch was available on chimerax for mac, or if you had plans to implement it in the future. Thanks and best wishes, Edoardo

3 3

Change the size of the model
by Shuto Araki 01 May '18

01 May '18

Dear Chimera X developers, I am trying to create a VR protein tour video by using the movie command. There is no problem and it works perfectly fine, but I was wondering if I could change the size of molecule models themselves so that, when the camera is inside a model, I can look around the inner structure of the model with the surface further placed. Right now, the model is so small that the surface feels too close to the camera when it is inside the model. Is it possible to change the size of a model with the coordinate being fixed? Thanks, Shuto

2 1

Equivalent of surface colour by radius in tools/Volume viewer of Chimera
by Shabih Shakeel 17 Apr '18

17 Apr '18

Hi, In ChimeraX, is there an equivalent of surface colour by radius in tools/Volume viewer of Chimera? I would like to colour an EM density map of a virus from its centre to the outside of the capsid with direct colour range in ChimeraX. Thanks. Regards, Shabih

2 3

Re: [chimerax-users] [Chimera-users] ConSurf script on ChimeraX
by Eric Pettersen 10 Apr '18

10 Apr '18

Hi Fabian, As a stopgap, you can color by bfactor by using a script I’ve attached. I’m attaching two scripts, one a generic color-by-bfactor that can be used for anything in the bfactor column. You would edit the values at the top of the script to choose low-high coloring or low-mid-high coloring, and what values to associate to what colors. The other script is tailored to ConSurf output in that it knows the nine ConSurf colors and colors only those residues whose bfactors are all equal and are integers in the range 1-9. You just open the ConSurf-generated PDB and then open the script (which runs it). I’ve attached an example output image (2gbp). —Eric > On Apr 10, 2018, at 12:26 AM, Fabian Glaser <fabian.glaser(a)gmail.com> wrote: > > Dear Eric, > > Thanks for your detail answer, so maybe the only thing it will be really useful now is to be able to color the residues with consurf colors in ChimeraX, with that I will be able to make figures for a paper, which is what I am after at this point. > > Of course we would be very happy to get a script for ChimeraX at some point that could be included in our output pages. > > Best, > > Fabian > > Fabian Glaser PhD > > 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, Israel > Web http://bku.technion.ac.il/ <http://bku.technion.ac.il/> > Tel +972 (0) 4 8293701 > > >> On 10 Apr 2018, at 1:59, Eric Pettersen <pett(a)cgl.ucsf.edu <mailto:pett@cgl.ucsf.edu>> wrote: >> >> Hi Fabian, >> ChimeraX is not backwards compatible with Chimera, so a Chimera session file cannot be opened in ChimeraX — such as what you tried to do below. We want to add a tool to Chimera that will write out a file that ChimeraX can read to restore the Chimera session as best it can, but we haven’t gotten there yet. >> Furthermore, although ChimeraX can display sequence alignments, its capabilities in that regard are currently much less than what Chimera offers. The features it lacks that ConSurf uses are: >> >> 1) Read Clustal ALN alignments >> 2) Show alignment headers >> 2b) Make header values available as residue attributes >> 3) Show Phylogeny trees >> 4) Color alignment/structures from coloring file >> >> To show ConSurf results in even bare bones form would require #1 and #4, and obviously #2 and #3 add a lot of value. So I’d say ChimeraX is not “ConSurf ready” yet. What I will do is open an “enhancement request” ticket in our bug database with you on the recipient list. As the above features get added I will update the ticket and at whatever point you feel it’s worthwhile you could work on getting ConSurf to deliver ChimeraX results. I would help with any questions or issues that popped up. Sorry I don’t have better news. >> >> —Eric >> >> Eric Pettersen >> UCSF Computer Graphics Lab >> >>> On Apr 8, 2018, at 7:56 AM, Fabian Glaser <fabian.glaser(a)gmail.com <mailto:fabian.glaser@gmail.com>> wrote: >>> >>> Hi, >>> >>> I would like to use Chimera ConSurf scripts in ChimeraX, but I get the following error when I try to run the script on ChimeraX >>> >>> ModuleNotFoundError: No module named 'cPickle' >>> >>> File "consurf_final_zn.py", line 1, in >>> >>> See log for complete Python traceback. >>> >>> If you wish to report this error, send mail to chimerax-bugs(a)cgl.ucsf.edu <mailto:chimerax-bugs@cgl.ucsf.edu> and describe what you were doing and include a copy of the contents of the log. Don't include any data you wish to remain private since a publicly viewable bug report will be created. >>> >>> Is this something that can be fixed or updated? >>> >>> More generally I would like to update ConSurf with a version of the script for ChimeraX, can you help me with that? >>> >>> Here is the beginning of the original chimera script >>> >>> import cPickle, base64 >>> try: >>> from SimpleSession.versions.v65 import beginRestore,\ >>> registerAfterModelsCB, reportRestoreError, checkVersion >>> except ImportError: >>> from chimera import UserError >>> raise UserError('Cannot open session that was saved in a' >>> ' newer version of Chimera; update your version') >>> checkVersion([1, 12, 41623]) >>> import chimera >>> from chimera import replyobj >>> replyobj.status('Restoring session...', \ >>> blankAfter=0) >>> replyobj.status('Beginning session restore...', \ >>> blankAfter=0, secondary=True) >>> beginRestore() >>> >>> def restoreCoreModels(): >>> from SimpleSession.versions.v65 import init, restoreViewer, \ >>> restoreMolecules, restoreColors, restoreSurfaces, \ >>> restoreVRML, restorePseudoBondGroups, restoreModelAssociations >>> molInfo = >>> >>> Thanks a lot, >>> >>> Best, >>> >>> Fabian >>> >>> Fabian Glaser PhD >>> >>> 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, Israel >>> Web http://bku.technion.ac.il/ <http://bku.technion.ac.il/> >>> Tel +972 (0) 4 8293701 >>> _______________________________________________ >>> Chimera-users mailing list: Chimera-users(a)cgl.ucsf.edu <mailto:Chimera-users@cgl.ucsf.edu> >>> Manage subscription: http://www.rbvi.ucsf.edu/mailman/listinfo/chimera-users <http://www.rbvi.ucsf.edu/mailman/listinfo/chimera-users> >> >

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Re: [chimerax-users] [Chimera-users] CjimeraX PDB save
by Eric Pettersen 02 Apr '18

02 Apr '18

Hi John, The PDB format only supports single-character chain IDs (one of the reasons for mmCIF format), so it is impossible to save structures with more than 36 chains in PDB format without losing chain information. A semi-workaround is to: 1) In ChimeraX: split the structure into multiple structures, one per chain (“split #1”) 2) Save those models into a multi-MODEL PDB file (“save ~/rib.pdb models #1”) 3) Read them into Chimera. 4) If there are <= 36 models, combine them into a single model (“combine” button of the Model Panel), otherwise you just have to work with them as separate models. —Eric Eric Pettersen UCSF Computer Graphics Lab > On Apr 2, 2018, at 2:29 PM, John Mercer, Ph.D. <jmercer(a)duke.edu> wrote: > > Hi Elaine, > > I load a ribosome mmcif file in ChimeraX and save it at as a PDB file. It loads and works fine in Chimera but all the chain identifiers have disappeared. Is there away to save a PDB file from ChimeraX that retains the identifiers? I am wanting to use the larger set of tools in Chimera when only mmcif files are available. > > Best, > -John > _______________________________________________ > Chimera-users mailing list: Chimera-users(a)cgl.ucsf.edu > Manage subscription: http://www.rbvi.ucsf.edu/mailman/listinfo/chimera-users

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morph and surfaces
by Giorgio Luciano 02 Apr '18

02 Apr '18

Hello ! I was looking at the script for morphing among structures that can be found here http://www.cgl.ucsf.edu/chimera/data/movie-howto-mar2012/movie_examples.html (*coordset #1 1,161). * I've tried to use the surfacecat command in the script in order to obtain a morph through volumes since my idea was to create the movie and then export all the surface perframe in order to use them in another 3d software. I've seen that surfcat can actually create volumes for all the surfaces included in the 1r7w but morph start does not seems to work among the surface created. I've seen also that it could be a solution to create density maps from the surface and them morph them using volume viewer but it seem quite an awkard solution (at least for me that I'm no expert :) I've tried to find the limitation of morph command but it does not report anything regarding surfaces. Any help is very appreciated. Sorry for the cross-posting

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I suggest the addition of a "Automatic Styling (Smart Initial Display)" button
by JEAN-YVES SGRO 29 Mar '18

29 Mar '18

Greetings, thank you for your quick reply about the "non-bug" request relating to the initial display and the explanation. After your reply I searched more intensely in the documentation and indeed found page help:user/autostyle.html with these details about the number of chains. As I am preparing to demonstrate ChimeraX in the department (tutorial I find that some inherent aspect of the Automatic Styling (Smart Initial Display) is very quickly lost. e.g. simply by clicking on the "Show atoms" button in the Molecular display toolbar and then the "Hide atoms". I found commands for selection at http://www.rbvi.ucsf.edu/chimerax/docs/user/commands/atomspec.html which are useful and one can reconstruct the initial display. As I example I am using myoglobin (1mbo.) The molecule opens as a ribbon, heteroatoms as stick models, the iron ion as sphere, and AA close to the ligands as sticks as well. Simply pressing the "Show atoms" button will display all water molecules as small spheres. But now if I click "Hide atoms" only the ribbon is left. Yesterday I tried to find a way to select heteroatoms in general and use the sel ~ sel selection inversion found on the pipermail<http://plato.cgl.ucsf.edu/pipermail/chimerax-users/2017-December/000169.html> but that was not the best solution. Today I could reconstruct the initial display with these commands if all I did was to toggle the "Show atoms" and "Hide atoms" buttons: show ions show ligand select ligand:<3.8 & protein show selAtoms For novices this is a bit complicated to understand. Therefore I would like to suggest the addition of a "Automatic Styling (Smart Initial Display)" button, perhaps at the First position in the Molecular display toolbar. I firmly believe that this would avoid lots of frustration for many new users! P.S. One more thing: would it be possible to Copy from the built-in browser to Paste elsewhere as I am trying to do with the email address? Sincerely, Jean-Yves Sgro

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Export as .obj
by Boris Chaumette 28 Mar '18

28 Mar '18

Dear colleagues, I am currently using ChimeraX and would like to save my file as a .obj I tried the following command line: save "ATPtest.obj" obj But model is expected. I don't understand how I can specify it to incorporate the whole figure. Thank you, Best, Boris Chaumette MD/PhD - postdoctoral researcher Laboratory of Guy A. Rouleau Montreal Neurological Institute McGill University Irving Ludmer Building 1033, Pine av. Room: 327 Montréal, Québec, H3A 1A1 Phone: +1 514-398-6821

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Matrixset equivalent
by Reza Khayat 15 Mar '18

15 Mar '18

Hi, Is there a matrixset (from Chimera) equivalent for ChimeraX? Thanks. Best wishes, Reza Reza Khayat, PhD Assistant Professor City College of New York Department of Chemistry New York, NY 10031

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VR mode not working
by Sebastian Poelsterl 13 Mar '18

13 Mar '18

Hi, I'm trying to view a PDB structure (2fha) in vr mode, but get the following error after executing 'vr on': An error occurred in drawing the scene. Redrawing graphics is now stopped to avoid a continuous stream of error messages. To restart graphics use the command "graphics restart" after changing the settings that caused the error. Traceback (most recent call last): File "C:\Program Files\ChimeraX-0.5\bin\lib\site-packages\chimerax\core\updateloop.py", line 61, in draw_new_frame view.draw(check_for_changes = False) File "C:\Program Files\ChimeraX-0.5\bin\lib\site-packages\chimerax\core\graphics\view.py", line 178, in draw r.draw_background() File "C:\Program Files\ChimeraX-0.5\bin\lib\site-packages\chimerax\core\graphics\opengl.py", line 677, in draw_background GL.glClear(flags) File "zr\accelerate\src\errorchecker.pyx", line 53, in OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError (src\errorchecker.c:1270) OpenGL.error.GLError: GLError( err = 1282, description = b'invalid operation', baseOperation = glClear, cArguments = (16640,) ) I'm using ChimeraX 0.5 with an Oculus Rift (1.24.0.545657), NVIDIA GeForce GTX 1060 (driver version 391.01) and SteamVR Version 2018-02-10 (1518226924) under Windows 10 (10.0.0.14393). Any suggestions would be appreciated. Thank you. Sebastian The Institute of Cancer Research: Royal Cancer Hospital, a charitable Company Limited by Guarantee, Registered in England under Company No. 534147 with its Registered Office at 123 Old Brompton Road, London SW7 3RP. This e-mail message is confidential and for use by the addressee only. If the message is received by anyone other than the addressee, please return the message to the sender by replying to it and then delete the message from your computer and network.

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Some core modules moving
by Eric Pettersen 07 Mar '18

07 Mar '18

Hi all, In the interest of making ChimeraX’s core smaller and less likely to need frequent updating (since it can’t be updated incrementally via the ToolShed), we will be moving some modules out of the core and into bundles, so those at least will be individually updatable via the ToolShed. Those core modules are atomic, map, surface, and ui. As of tomorrow’s daily build, you can and should use the the new import paths for these modules (e.g. from chimera.atomic import Atom rather than from chimerax.core.atomic import Atom). Old-style imports will continue to work for several months at least, at which time a warning will be raised if the import is still in use (but the import will work). Probably several months after that we will disable the old-style imports. One further note is that the MainToolWindow class can now be imported directly from the ui module, rather than from its gui submodule, so: from chimerax.ui import MainToolWindow is preferred over: from chimerax.ui.gui import MainToolWindow —Eric Eric Pettersen UCSF Computer Graphics Lab

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Surfaces & color by attribute
by Hernando J Sosa 06 Mar '18

06 Mar '18

Dear ChimeraX Is it possible to color a surface by atom/residue attribute (hydrohobicity, charge)? I know it is possible to do it in ucsf-chimera but unfortunately surface calculation does not work in chimera for the files I am working on. Thanks Hernando Hernando Sosa Dept. of Physiology and Biophysics Albert Einstein College of Medicine 1300 Morris Park Av. Bronx NY 10461 phone (718) 430-3456 FAX (718) 430-8819 email hernando.sosa(a)einstein.yu.edu<mailto:hernando.sosa@einstein.yu.edu>

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Cororing by B-factor
by Rajiv G Govindaraj 24 Feb '18

24 Feb '18

Hello, I am NOT able find the coloring atoms by bfactor in ChimeraX. I have a b-factor values range from negative to positive, and wants to color them from min to max(blue to red) as normal bfactor colors. Appreciated if you could tell me how it can be done in ribbons and surface using ChimeraX? Thank you. Regards, RJ

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ChimeraX user guide display issue
by Jerry Honts 20 Feb '18

20 Feb '18

Unlinked and linked text is *invisible* in user guide (and elsewhere in interface) because font color is *white* on white background. The apparently invisible text can be selected and displayed after copy and paste to another text field. Hyperlink underlines remain visible. Is this a CSS style sheet problem? Jerry E. Honts -- Jerry E. Honts, Ph. D. Associate Professor of Biology Drake University 2507 University Avenue Olin Hall 324 (office)

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open local pdb files "containing no atoms and bonds"
by Fekete Attila 15 Feb '18

15 Feb '18

Dear Colleagues, I have tried to open several local *.pdb files, but in each case I got the error: "Opened PDB data containing 0 atoms, 0 bonds and 0 coordinate sets", and a series of warnings (for each lines of the files) and ChimeraX doesn't show the structure. I have also tried different versions of ChimeraX (0.1/0.5 and even alpha releases, recently I'm using 0.5 under Ubuntu 16.04). I can open any online files (*pdb,*mmCIF) from the RCSB database, however if I download the same file, I got the above mentioned error message, so I have absolutely no clue to resolve the problem because I suppose this isn't related to pdb format issues but a bug can be somewhere in the softwere. I am really impressed by the visualization capabilities of ChimeraX so please help me if you can. Yours, Attila

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ChimeraX surface coloring
by Nadishka Jayawardena 14 Feb '18

14 Feb '18

Hi there, I recently installed ChimeraX and been trying to figure out a way to colour a cryo-EM map by radius- however, I couldn't find a way to get this done? Is this feature not implemented on ChimeraX as yet? Is there a way to colour the map by using a python script? Many thanks Nadishka P.S. Must say that this new version is a huge improvement!

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spin movie error
by Andrey Feklistov 05 Feb '18

05 Feb '18

Dear chimera X developers, upon trying to record a spin movie with a corresponding button I get an error: dyld: Symbol not found: _clock_gettime,Referenced from: /Volumes/ChimeraXInstaller 2/ChimeraX.app/Contents/bin/ffmpeg,Expected in: /usr/lib/libSystem.B.dylib Typing the command manually results in the same error. I remember that the feature used to work when I first tested ChimeraX last year. Thanks for any advice.. Andrey

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2dimage?
by Emmott, Ed 31 Jan '18

31 Jan '18

Hi, Is there (or likely to be in future) a 2d image feature, allowing you to overlay 2d graphics (.tif, .png) in the same way as the 2dlabel command (e.g. Xpos Ypos )? My use case is wanting to add additional 2d graphics (e.g. color bar or graphs) over a pdb structure prior to rendering images/generating movies. Whilst I can get ChimeraX to open the images easily e.g. (open "...test.tif"), they are acquiring edges (white background image on white background scene -> grey borders) I assume as a result of being interpreted as a 3d object. Otherwise loving the software! Thanks a lot, Ed Using ChimeraX build v0.5 (2018-01-12) Dr Edward Emmott Research Associate Slavov Lab Northeastern University 332 Mugar, 360 Huntington Ave. Boston, MA.

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Ignored bad PDB record found
by Maurício Menegatti Rigo 31 Jan '18

31 Jan '18

I don't understand, my .pdb file seems perfectly fine, but I keep getting this error: *Ignored bad PDB record found on line 1ATOM 1 N ASN A 1 61.433 13.168 52.787 1.00 69.56 N Ignored bad PDB record found on line 2ATOM 2 CA ASN A 1 62.543 13.695 51.962 1.00 69.56 C Ignored bad PDB record found on line 3ATOM 3 C ASN A 1 61.990 14.337 50.735 1.00 69.56 C Ignored bad PDB record found on line 4ATOM 4 O ASN A 1 60.999 13.878 50.167 1.00 69.56 O Ignored bad PDB record found on line 5ATOM 5 CB ASN A 1 63.479 12.547 51.555 1.00 69.56 C2610 messages similar to the above omitted* I can open it in Chimera, PyMol, VMD, among others. But in ChimeraX is always the same error. I'm working on Linux (Ubuntu 14.04) with ChimeraX version 0.5 (2018-01-24). Any help? Thanks in advance, Mauricio M Rigo, Ph.D

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Consultation about software use
by dejesusm＠sloankettering.edu 30 Jan '18

30 Jan '18

Good day. I am Miguel de Jesus, a graduate student in the lab of Morgan Huse at the Sloan-Kettering Institute, NY. We are embarking on a new project that may require some sophisticated analysis of morphology from time-series imaging data. I have encountered a recent paper (Fritz-Laylin et al., eLife 2017) that used UCSF ChimeraX to analyze lattice light sheet data on neutrophils. I suspect my project may benefit from the same tools, but I have no experience with computational or image analysis as of yet. Would it be possible for me to consult with someone from the dev team, perhaps over Skype or e-mail, to ask rather rudimentary questions about how I might be able to conduct analysis for the planned work? Thanks so much. Miguel DJ Miguel Francisco M. de Jesus Graduate Student (Huse Lab) Memorial Sloan Kettering Cancer Center Zuckerman Research Center, 417 E 68th Street, New York City, NY 10065, USA

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Cannot load Chimera X session
by Donghyun Park 29 Jan '18

29 Jan '18

Dear Chimera X users, I have trouble opening saved session in Chimera X. It loads my session for few seconds that shows following error messages: KeyError: 12 File "/private/var/folders/z_/sd6vflps0hs03gjrv5gt73yw0000gr/T/AppTranslocation/A86A6FCF-9B92-4C93-98CE-D4ADBB890140/d/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/chimerax/core/tools.py", line 333, in remove del self._tool_instances[tid] See log for Python traceback. Can anyone please help me? Thanks, Raphael Park

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Question regarding making movies & changing voxel size
by Donghyun Park 18 Jan '18

18 Jan '18

Dear Chimera X community, Currently, I am in a transition from the old Chimera to Chimera X. So far, I am very much enjoying Chimera X. 1) I was wondering if there's Chimera X equivalent of 'savepos' and 'movie recorder' . 2) Also, how can I change the voxel size in Chimera X? I tried to find answers in the User Guide but I couldn't find the right answer. I hope I can get some advice here. Thank you! Best, Raphael Park

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making color zone transparenct
by Yashar Sadian 06 Jan '18

06 Jan '18

Dear all Is there a command or a way to make a zone colored EM map transparent? -- Best, Yashar Sadian Christoph Mueller's group Structural and computational Biology Unit European Molecular Biology Laboratory (EMBL) Meyerhofstrasse 1 69117 Heidelberg, Germany Phone: 0049-6221-387-8496 Email: sadian(a)embl.de

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invert selection in ChimeraX
by Yashar Sadian 26 Dec '17

26 Dec '17

Hi is there a command to invert selection like in chimera? or simply hide whatever that is not selected -- Best, Yashar Sadian Christoph Mueller's group Structural and computational Biology Unit European Molecular Biology Laboratory (EMBL) Meyerhofstrasse 1 69117 Heidelberg, Germany Phone: 0049-6221-387-8496 Email: sadian(a)embl.de

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windows compatibility
by Sandrine Le Goff 19 Dec '17

19 Dec '17

Hi I would like to know if ChimeraX can be downloaded on a computer using windows 7 operating system Thanks a lot Best regards Sandrine Le Goff -- ___________________________________________ Sandrine VADON - LE GOFF Equipe Moali - Métalloprotéases et remodelage tissulaire Institut de Biologie et Chimie des Protéines UMR 5305 - Biologie Tissulaire et Ingénierie Thérapeutique - CNRS/Université de Lyon 7, passage du Vercors 69 367 LYON Cedex 07 FRANCE tel : 33(0)437652928

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Export formats
by Mike Goodstadt 11 Dec '17

11 Dec '17

Hi Tom, What formats are you planning to support for exporting scenes? Many thanks, Mike Goodstadt mikegoodstadt(a)gmail.com skype: mikegoodstadt +34 653 756 614

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Mapping local correlation between two maps
by Reza Khayat 07 Dec '17

07 Dec '17

Hi, Chimera allows one to map the CC between two maps onto a map and color the surface using the following commands: vop localCorrelation #0 #1 scolor #0 volume #2 cmap 0.6,red:0.7,white:1,blue I'm having difficulty executing the second command -mapping the values onto the first volume and assigning colors. Any help would be appreciated. Best wishes, Reza Reza Khayat, PhD Assistant Professor City College of New York Department of Chemistry New York, NY 10031

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activate model selectively
by Gabor PAPAI 29 Nov '17

29 Nov '17

Dear ChimeraX developers, I have a very naive question: how can I activate models selectively, like in Chimera? I would like to superimpose a density map with a pdb, but I don’t find how I can only activate and move the pdb. Thank you in advance for your help! Best regards, Gabor --- Gabor Papai IGBMC Integrated Structural Biology 1, rue Laurent Fries, Bp 10142 67404 Illkirch, France Tel: +33-3-69485288

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VR and optional functions
by Matthias Wolf 26 Oct '17

26 Oct '17

Hi Tom et al, Great job on chimeraX! The rendering engine is incredible. I have tried to view our cryo-EM volumes in VR with a new HTC Vive – it’s amazing and it works really well! ChimeraX supporting VR was one of the reasons for me to buy the Vive. Thank you! Now I haven’t used chimeraX before (I have used chimera since many years). I understand that the program is still work in progress. However, I am really missing some of the nice functions of chimera that make it so useful with a “clicky” interface - e.g. color surface by radius or by pdb properties, segmented isocontoured maps, clipping planes, subvolumes, combined shaded and wireframe surfaces, biological assembly, etc – I find these functions very useful and there don’t seem to exist any command line options for this, or I just haven’t studied them enough yet. Many of the existing menus in chimeraX have a fraction of the functionality of their sister program chimera. E.g. volume viewer, model panel, side view – I still have not figured out how to activate only one of several objects for rotation, when in chimera a click on the activate check box in the model panel does that (there is no active checkbox in the model panel of chimeraX and I couldn’t find a command to activate an object). It would be nice if one could simply grab an object in VR and rotate by itself it instead of the entire scene. Do you have a plan to add or port some of these beloved GUI functions from chimera into chimeraX? Could they be added by copying python modules from chimera? It would be great, if one could press a button in VR on the hand controller to display the menu and select functions “by virtual laser pointer”. This could preserve the development effort that went into the GUI design of chimera by reusing it in chimeraX as an identical projected 2D menu in VR and it would prevent having to take the goggles off for simple model adjustments. Best regards, Matthias

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Re: [chimerax-users] error when save sessions of chimeraX in Ubuntu
by Elaine Meng 19 Oct '17

19 Oct '17

> On Oct 18, 2017, at 2:07 AM, Yahui Yan <yahuiuk(a)gmail.com> wrote: > > Hi Elaine, > > I am a new user of chimeraX. I run it (the daily builds on 17th Oct 2017) in my Ubuntu system. All went well until I tried to save the session. An error message '[Errno 25] Inappropriate ioctl for device' popped out. Could you please give me some advice to fix it? Many thanks. > > Kind regards, > Yahui > Hi Yahui, I don’t know the answer, but I’m sharing it to the mailing list: chimerax-users(a)cgl.ucsf.edu … that is the recommended address for ChimeraX questions. Regards, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco

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