- ChimeraX-users - RBVI Mailing Lists

3D stereo lighting is not the same as mono
by Kenneth Satyshur 26 May '20

26 May '20

I am using version 1.0 in Centos7 with Nvidia 3D glasses and K4000 video card. I do all my work in 3D stereo. Especially density fitting. I noticed that the lighting is different in mono vs stereo mode. When i go to stereo mode with camera stereo the image is in stereo but the "full" lighting is on and the image is very dark with shadows. If I switch to 'simple' it is bright and has weak shadowing. Switching to 'soft' the image is flat black and can only be seen with white background but contains no atoms. I think this is a bug. But a Great improvement in rendering of images. thanks kas p.s. old chimera does stereo very well on my system Linux kenworkathome 3.10.0-1127.el7.x86_64 #1 SMP Tue Mar 31 23:36:51 UTC 2020 x86_64 x86_64 x86_64 GNU/Linux Kenneth A. Satyshur, M.S., Ph.D. Senior Scientist, Department of Bacteriology: College of Ag and Life Sciences; Departments of Bio Molecular Chemistry, Neuroscience, Oncology, and Carbone Cancer Center: School of Medicine and Public Health; and the School of Pharmacy University of Wisconsin-Madison Madison, Wisconsin, 53706 608-215-5207

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Recreating views
by Martin Montgomery 22 May '20

22 May '20

Hi, I have a session file that contains everything I need to make figures for a paper. With pymol, I saved the get_view matrix in a text file for each view which meant that with one session file I could easily recreate the views if I needed to go back and tweak a figure. In ChimeraX, the closest way that I found to replicate this was to use named views. Am happy to supply a session file if it helps also happy to be educated if there is a better way of doing this, especially as now the ChimeraX session files can get rather large. Cheers MGM Martin G Montgomery Senior Scientist ATP Synthase Group MRC Mitochondrial Biology Unit University of Cambridge The Keith Peters Building Cambridge Biomedical Campus Hills Road Cambridge Great Britain CB2 0XY www.mrc-mbu.cam.ac.uk <http://www.mrc-mbu.cam.ac.uk/>

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Save/restore scene?
by Oliver Clarke 20 May '20

20 May '20

Hi ChimeraX-ers, Is there currently an equivalent of the "scene" command from Chimera? It was super helpful to be able to quickly switch between different (and often complex) representations of a molecule. I know the view command for saving and restoring orientations, and the "name" command for saving selections, but I can't find an equivalent of scene. I'm guessing it's not yet implemented, but count me as one vote for porting it over after 1.0 is out the door, it was super helpful in Chimera! Cheers Oli

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Feature suggestion - show color code in picker?
by Oliver Clarke 19 May '20

19 May '20

Hi, I love the color editor in ChimeraX, it is much nicer than the one in Chimera and is super useful! One minor suggestion - would it be possible to add a dynamically updated label showing in the editor the current color code? This sometimes shows up in the log but not always, and it is useful to have easily copy-able for use in scripts and aliases. Cheers Oli

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Cartoon smooth loops chimX
by Dominik Hrebík 19 May '20

19 May '20

Hi all! Is there any possibility to smooth loops in cartoon representation in ChimeraX? I can't find it in the user guide. Something similar to pymol's cartoon_smooth_loops,1: https://pymolwiki.org/index.php/Cartoon_smooth_loops Best, Dominik -- ################################## Dominik Hrebik Laboratory of Structural Virology CEITEC, Masaryk University Kamenice 5 / A35 Brno, 625 00, Czech Republic Phone: +420 549 49 7764 <%2B420%20549%2049%207756> ##################################

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Focus in ChimeraX
by Luca Pellegrini 18 May '20

18 May '20

Hi, What is the ChimeraX equivalent to the Focus command in Chimera? I have selected a portion of a structure, and would like to bring it into focus without dragging it into view. Also Focus would automatically set the selection as the pivot point. Best wishes, Luca Luca Pellegrini, PhD Department of Biochemistry University of Cambridge Cambridge CB2 1GA lp212(a)cam.ac.uk

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Turntable rotation
by Scott, Brandon L. 16 May '20

16 May '20

I would like to create an animation where the camera is spun around at a constant azimuthal angle so the object appears to spin on a tabletop. Currently, when I use roll, when it spins to the backside I see underneath the model rather than remaining on top. Any help is greatly appreciated. -Brandon ____________________ Brandon Scott, PhD CZI Imaging Scientist, Research Assistant Professor SDSMT, Nanoscience and Nanoengineering

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Re: [chimerax-users] transition from Chimera
by Tom Goddard 15 May '20

15 May '20

Hi Jerome, Putting that "open instructions,html" in your startup preferences is a nice way to show an HTML interface that could have links that execute commands in ChimeraX. I had not thought of that use. Tom > On May 15, 2020, at 1:37 AM, MUTTERER Jerome (IBMP) <jerome.mutterer(a)ibmp-cnrs.unistra.fr> wrote: > > Hi Tom, > Thank you very much for your answers. > I didn't try the drag and drop emulation approach, but I confirm the "remotecontrol rest" option at startup works nicely. > I added the following 2 lines to the Favorites>Settings...>Startup tab > > remote rest start port xxxxx > open instructions.html > > and it makes it easy to operate. > Thanks a lot! > > Jerome > > > De: "Tom Goddard" <goddard(a)sonic.net> > À: "MUTTERER Jerome, IBMP" <jerome.mutterer(a)ibmp-cnrs.unistra.fr> > Cc: chimerax-users(a)cgl.ucsf.edu > Envoyé: Mardi 12 Mai 2020 20:14:39 > Objet: Re: [chimerax-users] transition from Chimera > > Hi Jerome, > > We don't have the chimerax --send option to open files in an already running ChimeraX, although we plan on adding it. > > I have two ideas for how to do this in current ChimeraX. One is to use the remotecontrol command to tell ChimeraX to accept commands via http. In ChimeraX I enable this with command > > remote rest start port 58123 > > Then http requests can run commands in ChimeraX. The http url can be entered in a web browser or from a script. From a script you could use curl or wget programs, for example, > > curl http://localhost:58123/run?command=open+/Users/goddard/Downloads/ChimeraX/P… <http://localhost:58123/run?command=open+/Users/goddard/Downloads/ChimeraX/P…>.cif > > You could make ChimeraX alway enable http requests by putting the "remote..." command in ChimeraX Settings/Preferences under the Startup tab "Execute these commands at startup". > > The other idea I have is simpler but did not work in my test. ChimeraX accepts files dragged and dropped on the application. On macOS (and probably Linux and Windows) I should be able to run a shell command that says drop this file on ChimeraX. On Mac the shell command looks like > > % open -a /Applications/ChimeraX.app ~/Downloads/ChimeraX/PDB/1a0m.cif > > That worked for starting ChimeraX and showing the first file. But when I run it again to open a different it merely raised ChimeraX and did not open the new file. That is a bug. I've made a bug report for it. I don't know the equivalent commands on Linux and Windows and whether the would work. > > Tom > > > On May 12, 2020, at 1:50 AM, Jerome Mutterer <jerome.mutterer(a)ibmp-cnrs.unistra.fr <mailto:jerome.mutterer@ibmp-cnrs.unistra.fr>> wrote: > > Dear all, > I'm trying to transition from Chimera to ChimeraX, but my workflow relies on passing scripts to an open, with GUI, instance of Chimera using --send > https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/options.html#send <https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/options.html#send> > > I see that this is not described here: > https://www.rbvi.ucsf.edu/chimerax/docs/devel/apps/ChimeraX/ChimeraX.html <https://www.rbvi.ucsf.edu/chimerax/docs/devel/apps/ChimeraX/ChimeraX.html> > > Is that still available somehow in ChimeraX? > Thanks for any input. > Sincerely, > Jerome. > > -- > Jerome Mutterer > CNRS - Institut de biologie moléculaire des plantes > 12, rue du Général Zimmer > 67084 Strasbourg Cedex > www.ibmp.cnrs.fr <http://www.ibmp.cnrs.fr/> > > _______________________________________________ > ChimeraX-users mailing list > ChimeraX-users(a)cgl.ucsf.edu <mailto:ChimeraX-users@cgl.ucsf.edu> > Manage subscription: > https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users

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Stuck on one XML-RPC command
by Mungo Carstairs (Staff) 14 May '20

14 May '20

Any XML-RPC fans who can help me with this please? This label command works in the PyMOL command line: label 4zho//A/36/CA 4zho//B/36/CA, "hello world" How do I format an equivalent XML-RPC request? I've tried <methodCall> <methodName>label</methodName> <params> <parameter> <value>4zho//A/36/CA 4zho//B/36/CA</value> </parameter> <parameter> <value>"hello world"</value> </parameter> </params> </methodCall> but get back a fault response XML message with <class 'SyntaxError'>:invalid syntax (<string>, line 1) I have also tried encoding the " as %22, or omitting the quotes, same result. Any ideas please? 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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Stereo and VR support
by Gökhan Tolun 13 May '20

13 May '20

Hi, Would it be possible to make the graphics window undockable, too, Like the other ones? This would allow the use of stereo monitors with SBS and tb support, which does not work currently with menus, etc. surrounding the graphics window. Also, will you implement DTI stereo as in Chimera? By the way, if theres a way of making ISOLDE work in VR, thatd be great! Thanks, Gökhan

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pyqtchart
by Anthony James Schaefer 13 May '20

13 May '20

Hello, I'm interesting in using pyqtchart (https://pypi.org/project/PyQtChart/) as an alternative to matplotlib for some plots in my bundle (I like the default style better, it resizes better - small things like that). If I list pyqtchart as a dependency in my bundle_info.xml like ... <Dependencies> <Dependency name="pyqtchart"/> </Dependencies> ... a new version of PyQt5 gets installed in the directory where bundles get installed. The QChart module from pyqtchart gets installed in this new PyQt5 package. I can't use the QChart module because it's not in the PyQt5 that ChimeraX uses. Is there anything I can do with my bundle to get it to install a usable pyqtchart? Thanks, Tony

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wrong version in download
by Christine Gee 13 May '20

13 May '20

Dear ChimeraX I downloaded what was supposed to be chimeraX 0.5 from your site, and 0.1 instead. I have an older mac with an older OS (10.11.6) and would like the last version that was developed for it. Can you please let me know where I can download 0.5? Also does it work with isolde? Regards Christine Dr Christine Gee Research Specialist Kuriyan Lab HHMI/Molecular and Cell Biology/QB3 527 Stanley Hall MC 3220 University of California, Berkeley Berkeley, CA 94720-3220 Lab Phone: 510 643 0164 Cell: 510 230 7891 Email: christinelgee(a)berkeley.edu <mailto:christinelgee@berkeley.edu>

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Manual segmentation in ChimeraX
by Pattana Jaroenlak (Michael) 13 May '20

13 May '20

Hello, I saw the twitter post from ChimeraX on segmentation of EM serial images ( https://twitter.com/ucsfchimerax/status/1260425173238415360?s=12) It was very beautiful. I have serial section EM images. I am wondering that can I do manual segmentation on ChimeraX? Some cellular features on my images can not be picked up by thresholding or watersheding. Thank you PJ -- *Pattana (Michael) Jaroenlak, PhD* Bhabha & Ekiert Labs Skirball Institute of Biomolecular Medicine New York University School of Medicine *Email: pattana.jaroenlak(a)nyulangone.org <pattana.jaroenlak(a)nyumc.org>, p.jaroenlak(a)gmail.com <p.jaroenlak(a)gmail.com>*

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Renaming chain IDs
by Fahrenkamp, Dirk 12 May '20

12 May '20

Hi ChimeraX team. I am happily using chimeraX along with ISOLDE for modelling. Lately, I am running into issues with complexes having too many chains to be handled by the standard .pdb format which is why I am using .cif now. Is there a smooth way/command to rename chain IDs and change _entity.pdbx_description _struct_asym.entity_id accordingly? Thanks! Kind regards, Dirk -- Dr. rer. nat. Dirk Fahrenkamp UKE Hamburg Zentrum für experimentelle Medizin Institut für Struktur- und Systembiologie/ CSSB Centre for Structural Systems Biology c/o Deutsches Elektronen-Synchrotron DESY Notkestraße 85, Building 15 3.OG D-22607 Hamburg Telefon:+49 (0) 40 8998-87657 Dirk.Fahrenkamp(a)cssb-Hamburg.de www.cssb-hamburg.de

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transition from Chimera
by Jerome Mutterer 12 May '20

12 May '20

Dear all, I'm trying to transition from Chimera to ChimeraX, but my workflow relies on passing scripts to an open, with GUI, instance of Chimera using --send https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/options.html#send I see that this is not described here: https://www.rbvi.ucsf.edu/chimerax/docs/devel/apps/ChimeraX/ChimeraX.html Is that still available somehow in ChimeraX? Thanks for any input. Sincerely, Jerome. -- Jerome Mutterer CNRS - Institut de biologie moléculaire des plantes 12, rue du Général Zimmer 67084 Strasbourg Cedex www.ibmp.cnrs.fr

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Map "Blobs" tool - Generate objects?
by Christophe Leterrier 11 May '20

11 May '20

Hi, I started using ChimeraX for visualization and quantification of 3D microscopy images. The "blob" tool is particularly impressive to semi-automatically segment objects of interest and measure their characteristics. However, I could not find a way to generate an independent object from the picked blobs. This makes the quantification process unreproducible as it is not possible to store the blobs in the session or automatically measure all the picked blobs. Am I wrong in the intent of the tool, or is there a way to do this? Thank you, -- Christophe Leterrier NeuroCyto lab INP CNRS UMR 7051 Aix Marseille University, France

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ChimeraX on Twitter
by Tom Goddard 08 May '20

08 May '20

For ChimeraX news, tips, tricks and special features meet us on Twitter @UCSFChimeraX. https://twitter.com/UCSFChimeraX <https://twitter.com/UCSFChimeraX> Tom, Eric, Elaine, Greg, Conrad, Scooter, Tom -- the UCSF ChimeraX team.

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How to display crystal packing?
by Guillaume Gaullier 08 May '20

08 May '20

Hello, Today I was trying to display a crystal packing from a PDB entry in ChimeraX, but could not find how to do this. I read the documentation for the sym command https://www.cgl.ucsf.edu/chimerax/docs/user/commands/sym.html ; but either I didn’t get it, or this is not the adequate command for what I am trying to do. What I want to do is the equivalent of PyMOL’s "Action / generate / symmetry mates / +/- one unit cell and within… Å", which is different from the biological assembly the sym command can generate from the PDB annotation. When working with crystallographic data, ISOLDE displays molecules related to the working model by crystallographic symmetry, so displaying the crystal packing seems doable in ChimeraX. Or is it one of ISOLDE’s additions? It would be wonderful if someone could help me with this (it is one of the last few things I need on a regular basis, that I still don’t know how to do in ChimeraX). Thank you in advance, Guillaume

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preview ChimeraX 1.0!
by Elaine Meng 07 May '20

07 May '20

The ChimeraX 1.0 (!!) release candidate is now available: <http://www.rbvi.ucsf.edu/chimerax/download.html> Please, please try it out and report any issues that you find, as we plan to make the production release by the end of the month. To report issues, use the ChimeraX menu: Help... Report a Bug <http://www.rbvi.ucsf.edu/chimerax/docs/contact.html> For what's new, see the Change Log: <https://www.rbvi.ucsf.edu/trac/ChimeraX/wiki/ChangeLog> Thanks! Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco

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Problems with making movie in chimerax
by Nandish Kumar Khanra 07 May '20

07 May '20

Hello all, I want to make a movie of a multi-domain protein between two functional states using Chimerax. One domain undergoes drastic conformational change while there is virtually no structural change in another domain. I did the following steps to make the movie. * Aligned two models using matchmaker, mm #1 to #2 pair ss ss false * make morph morph #1,2 frames 100 play false cartesian true * make movie movie record size 1000,1000 coordset #3 wait 100 movie encode output ~/Desktop/movie1.mp4 quality higher framerate 25 roundTrip true The stationary domain of two functional states aligned perfectly after structural alignment, but I do see motions in that domain in the movie. Am I doing anything wrong? Is there a way to overcome this? Thanks, Nandish

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Script to color zone a map according to the underlying model
by Caroline Stone 07 May '20

07 May '20

Dear All, As an exercise in scripting, I am trying to write a script to imitate the appearance a published figure (from Toropova et al 2017). I would like to display a semi-transparent map which has been color zoned to match the underlying model in surface view. ChimeraX does everything in the script apart from the last two commands, in which I color zone the map, and then make it transparent. I don't get any errors in the log to give me a clue what to change. If I omit these last two commands from the script and then make them manually from the command line after the script is finished, it works. Is there something I can change that would allow me to include the final two commands in the script? Any pointers would be much appreciated. # ChimeraX script to imitate dynein 2 tail Toropova et al 2017 figure style # Adds custom colours to the ChimeraX session # Open model and set camera view and model rotation open 6RLB windowsize 775 775 view matrix camera -0.30533,0.56038,0.76991,623.53,0.82837,-0.24247,0.50499,467.83,0.46967,0.79195,-0.39016,-7.3434 models #1,1,0,0,0,0,1,0,0,0,0,1,0 # Work with model representation surface #1 set bgColor white lighting soft graphics silhouettes true # Define custom colours color name midblue #6b80b5 color name midgreen #a0c497 color name midyellow #f9ef87 color name midtomato #f97054 color name midmagenta #a4449b # Recolour model using custom colours defined above select #1/A; color sel midblue select #1/B; color sel skyblue select #1/C; color sel midtomato select #1/D; color sel midmagenta select #1/E/F; color sel midgreen select #1/G/H; color sel lightpink select #1/I-N; color sel midyellow select clear # Open map and modify color and transparency open emdb:4918 volume #2 step 1 volume #2 level 0.0172 surface dust #2 size 10 color zone #2 near #1 distance 15 volume #2 transparency 0.75 Best wishes, Caroline

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Silhouettes cause fill
by Daniel Asarnow 06 May '20

06 May '20

Hi, Is there any way to avoid this effect where silhouettes lead to an apparent flood fill? The helix in the upper left of this clip shows what I mean: [image: image.png] I was able to work around it a bit by making the silhouettes thinner than I'd like, and aggressively supersampling. It seems severe with any silhouette width greater than 1. Thanks and best, -da

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Re: [chimerax-users] Chimera X -showing electrostatic potential
by Elaine Meng 06 May '20

06 May '20

Dear Yi Shi, The structure is nice work, and worth showing off! We are fine so far... I hope you are well too. To color a surface by electrostatic potential in ChimeraX, currently you need to use a separate program to generate the electrostatic potential map, for example the APBS web server or the DelPhi web server mentioned/linked to the Chimera tutorial here: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/surfprop.html#es…> After you generate the map (e.g. a .dx file, .phi file, or .cube file) <http://rbvi.ucsf.edu/chimerax/docs/user/commands/open.html#volume> ... then you can open it in ChimeraX and use it for coloring the protein molecular surface with the ChimeraX "color electrostatic" command: <http://rbvi.ucsf.edu/chimerax/docs/user/commands/color.html#map> If you open a .cube file it will automatically show as isosurfaces. However, you can hide the isosurfaces such as by clicking the "eye" icon in the Volume Viewer panel, and then carry on with using the coloring command as mentioned above. Of course, you need to open the protein structure and then display the protein's molecular surface first, e.g. with the "surface" command, Actions menu, or Molecule Display icon. <http://rbvi.ucsf.edu/chimerax/docs/user/commands/surface.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 May 5, 2020, at 7:14 PM, Yi Shi <yi.shi(a)pitt.edu> wrote: > > Dear Elaine, > > Hope this finds you, your family and colleagues safe and well. > > We have a question about Chimera X software that you and your colleagues developed. Do you know how to show the electrostatic potential using Chimera X? Do we need some external software to do this? > > BTW, the software that you developed was amazing that we really enjoy it. And thanks a million for using our Nup84 hybrid structure for the cover of your paper in Protein Science. Absolutely beautiful work! > > Thanks in advance. > Yi > > Yi Shi Ph.D. > Assistant Professor > Department of Cell Biology > Program for Integrative Systems Biology > Pitt/ CMU Program in Computational Biology > University of Pittsburgh School of Medicine > BST3 9049 > 3500 5th Avenue > Pittsburgh PA 15213 > 412-383-3242 (office) > 412-383-3243 (lab) > www.shi-lab.org

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Scroll threshold step size
by Daniel Asarnow 04 May '20

04 May '20

Hi, Is it possible to adjust the step size when using alt + scrollwheel to change the contour level? I'd like to make it coarser for RSI reasons. Thanks, -da

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ubuntu 20.04
by Hua tiger 03 May '20

03 May '20

Please create a download and install package for ubuntu 20.04 Thank you very much. John

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