October 2020 - ChimeraX-users - RBVI Mailing Lists

Worms?
by Boris Steipe 28 Oct '20

28 Oct '20

Worm plots is one of the still missing features. I probably have the following options (though I haven't actually tried any): - compute my own spline and place a dense string of spheres - compute my own spline and place alternating spheres and cones - place pseudoatoms and compute a surface with a small probe radius - wait until Chimera's worm plot arrives in ChimeraX. Or is there a better way? Thanks! Boris

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Set different colors for each letter like in chimera
by Siyu Chen 28 Oct '20

28 Oct '20

Dear chimerax developers, I was trying to color my labels in chimerax using commands, but it will be too tedious for me to create different labels for each letters, color them differently then align them by fine-tuning the x/y positions. I remember in chimera I was able to call out an window and within that, I can conveniently edit my texts and colors, and save it as a label file. Does chimerax still offer the similar function? Or if there is any equivalent way to achieve that easily? Thanks a lot for your help! Best, Siyu

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Using ChimeraX Modeller interface
by Moradkhan, Tiglath A 26 Oct '20

26 Oct '20

Hi My name is Tiglath and I'm trying to use ChimerX Modeller interface to build a dimer model of a protein I'm currently studying. I first tried to run a BLASP search to find templates but it seems that in ChimeraX, this works differently than in Chimera. In the user guide it says that if the query is a sequence whose structure hasn't been determined, then it's not necessary to specify particular chains. However, when I try running the BLAST search it doesn't do anything. It seems that it is necessary to specify a chain number. But how is this possible if I don't know the template for the target sequence? Am I missing something? Also, I'm a little bit unsure how the Modeller interface works for building dimers. I would be very glad for your help. Thank you Tiglath

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Markers from CMM
by Scott, Brandon L. 26 Oct '20

26 Oct '20

Hello all, When loading markers from a cmm file (example attached), is there a way to specify which submodel the marker goes to rather than it creating a new id? I've added the id_string to the cmm file when I created a new one which is the desired model. I hacked the following, which works, but there are hundreds of tracks so I would like to come up with an automated (and proper) way to do this. perframe "rename #2.$1 track_1 id #1.$2.2;" ranges 1,113 ranges 4,116 perframe "rename #2.$1 track_2 id #1.$2.3;" ranges 114,259 ranges 5,150 Brandon Scott, PhD CZI Imaging Scientist, Research Assistant Professor Nanoscience & Nanoengineering South Dakota Mines 501 E. Saint Joseph St., Rapid City, SD 57701 724.510.1253 | Brandon.Scott(a)sdsmt.edu<mailto:Brandon.Scott@sdsmt.edu> [South Dakota Mines]<https://www.sdsmt.edu/> [South Dakota Mines on Facebook]<https://www.facebook.com/SouthDakotaMines/>[South Dakota Mines on Instagram]<https://www.instagram.com/southdakotamines/>[South Dakota Mines on Twitter]<https://twitter.com/sdsmt>[South Dakota Mines on Snapchat]<https://www.snapchat.com/add/sdsmt>

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Re: [chimerax-users] ISOLDE on Chimerax on centos8.0
by chimera-users-owner＠cgl.ucsf.edu 23 Oct '20

23 Oct '20

Hi I have just recently installed Chimerax 1.1 on my centOS 8.0 workstation and am trying to install the ISOLDE bundle thru Toolshed but I get the message "no download available for Cimerax 1.1 on Linux." how do I get around this problem Cheers Shabir Najmudin

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Re: [chimerax-users] ChimeraX hardware recommendations
by Tom Goddard 21 Oct '20

21 Oct '20

Hi Shaun, Apple will keep OpenGL graphics working well into the future. They switched to using their proprietary Metal graphics to run the macOS window system about 4 years ago, and deprecated OpenGL use, but that just means they aren't going to improve their OpenGL. Mac OpenGL drivers tend to crash when lots of graphics memory is used. We are considering using Vulkan instead of OpenGL maybe in a few years. Vulkan is an open standard and has been layered on top of Metal (called MoltenVK) and has native drivers on Windows and Linux. Also I have been testing Chimera and ChimeraX on the next macOS, called Big Sur, likely coming out in the next month. Both are working on Big Sur beta 10 released a week ago, although you need ChimeraX 1.1.1. We had to fix ChimeraX 1.1 on Big Sur because Apple changed how software finds the OpenGL library. Tom > On Oct 21, 2020, at 10:40 AM, Shaun Rawson <rawson(a)hkl.hms.harvard.edu> wrote: > > No worries, thanks for the response. As an aside to the initial question, are you expecting any issues with OpenGL for ChimeraX on Macs now that they are depreciating and pushing metal instead? > > Shaun > > On Wed, Oct 21, 2020 at 1:31 PM Tom Goddard <goddard(a)sonic.net <mailto:goddard@sonic.net>> wrote: > Oops, sorry for misspelling your name. > > Tom > > >> On Oct 21, 2020, at 10:30 AM, Tom Goddard <goddard(a)sonic.net <mailto:goddard@sonic.net>> wrote: >> >> Hi Shawn, >> >> You are right that a MacBook with i5 CPU and 16 GB memory and Intel graphics will work fine for ChimeraX including making movies. For large molecules, for example ribosome structures with several hundred thousands atoms, or large cryoEM maps, for example 512 x 512 x 512 and up you could benefit from faster AMD or Nvidia laptop graphics (MacBook Pro), and 32 GB of memory. Another thing to consider is to keep data and ChimeraX on an SSD drive, not a spinning drive. Today's SSD drives are 30 times faster reading data than spinning drives. All Mac laptops only come with SSD drives I believe, but it is good to have enough SSD drive space that your data (like lots of cryoEM maps) does not have to reside on an external drive. Usually 512 GB SSD will do, but again if you work with lots of large data 1 TB SSD could be helpful. >> >> Sorry our ChimeraX web site is unexpectedly down this morning due to some server upgrade issue. Should be back online later today. >> >> Tom >> >> >>> On Oct 21, 2020, at 7:50 AM, Shaun Rawson <rawson(a)hkl.hms.harvard.edu <mailto:rawson@hkl.hms.harvard.edu>> wrote: >>> >>> Hi Tom, >>> >>> Just a quick question on any hardware recommendations for running ChimeraX (primarily macbook based). We have a user who is particularly interested in generating animations in ChimeraX so I was wondering if you have any specific min/recommended specs for various functionality. >>> >>> It seems to me like the standard macbook config (i5, 16GB RAM, intel graphics) should be fine for day to day operations but maybe they would need to swap to a more powerful linux workstation for the heavy lifting. >>> >>> Apologies if this is available online - currently https://www.cgl.ucsf.edu/chimerax/ <https://www.cgl.ucsf.edu/chimerax/> gives a 403 error for me. >>> >>> Thanks, >>> >>> Shaun >> >

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Re: [chimerax-users] ChimeraX hardware recommendations
by Tom Goddard 21 Oct '20

21 Oct '20

Hi Shawn, You are right that a MacBook with i5 CPU and 16 GB memory and Intel graphics will work fine for ChimeraX including making movies. For large molecules, for example ribosome structures with several hundred thousands atoms, or large cryoEM maps, for example 512 x 512 x 512 and up you could benefit from faster AMD or Nvidia laptop graphics (MacBook Pro), and 32 GB of memory. Another thing to consider is to keep data and ChimeraX on an SSD drive, not a spinning drive. Today's SSD drives are 30 times faster reading data than spinning drives. All Mac laptops only come with SSD drives I believe, but it is good to have enough SSD drive space that your data (like lots of cryoEM maps) does not have to reside on an external drive. Usually 512 GB SSD will do, but again if you work with lots of large data 1 TB SSD could be helpful. Sorry our ChimeraX web site is unexpectedly down this morning due to some server upgrade issue. Should be back online later today. Tom > On Oct 21, 2020, at 7:50 AM, Shaun Rawson <rawson(a)hkl.hms.harvard.edu> wrote: > > Hi Tom, > > Just a quick question on any hardware recommendations for running ChimeraX (primarily macbook based). We have a user who is particularly interested in generating animations in ChimeraX so I was wondering if you have any specific min/recommended specs for various functionality. > > It seems to me like the standard macbook config (i5, 16GB RAM, intel graphics) should be fine for day to day operations but maybe they would need to swap to a more powerful linux workstation for the heavy lifting. > > Apologies if this is available online - currently https://www.cgl.ucsf.edu/chimerax/ <https://www.cgl.ucsf.edu/chimerax/> gives a 403 error for me. > > Thanks, > > Shaun

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(no subject)
by Kazan Ramy (M.) 20 Oct '20

20 Oct '20

Greetings to all, When opening a new molecule, ChimeraX automatically apply a color to my molecule. I know how to modify the colors, which is very fun especailly using the command line but also very time consuming for multi-chain molecules. I would like to impose a coloring scheme for a model by default, that way everytime I open the model the coloring is the same for the my molecule. I guess one way is to use the function key but this would be limited to a mixumum of twelve molecules and is atom-spec dependent so not very practical. Is there a way to permently save the information, maybe in the pdb file header/footer, or somewhere else? Ramy Kazan PhD Student

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cartoon style atom-spec
by Daniel Asarnow 20 Oct '20

20 Oct '20

Hi, When I use cartoon style with an atom spec, ChimeraX reports "expected a keyword" error. This is the "licorice" example from the documentation, which only works without an atom spec. car style protein modeh default arrows f xsect oval width 1 thick 1 car style #6/H protein modeh default arrows f xsect oval width 1 thick 1 Is my syntax wrong? Thanks, -da

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Access to git repository
by Tomris, I. (Ilhan) 19 Oct '20

19 Oct '20

Dear sir/madam, At the moment I am utitilizing ChimeraX to render 3D images of lightsheet data I have obtained (see attachment of 3D render). It is a pretty nice software package, although there is something I would like to implement into chimerax. A bounding box/outline box with gridpoints on it to indicate the size of the rendered volume, additionally I would also like to implement a scalebar of some sort. Hence I was wondering whether I could get access to the git repository so I could attempt to use the "Outline box" already present and put grid points on it? [cid:ab15abd2-e188-42fa-ae88-eedbeae317dd] Kind regards, Ilhan

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