- ChimeraX-users - RBVI Mailing Lists

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 14 May '20

14 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 14 May '20

14 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 12 May '20

12 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 09 May '20

09 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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