- ChimeraX-users - RBVI Mailing Lists

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

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

04 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

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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

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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

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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

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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

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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

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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

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