- ChimeraX-users - RBVI Mailing Lists

Dome projection camera mode
by Tibor Füzik 10 Apr '19

10 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

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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

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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

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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>

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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

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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.

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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

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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 > > >

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