- ChimeraX-users - RBVI Mailing Lists

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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Re: [chimerax-users] Assistance: ChimeraX save scene
by Guillaume Gaullier 19 Oct '20

19 Oct '20

Hi Priyanka, Sorry for this late reply. I am copying the chimerax-users list (if you had sent your last email to the list, somebody else would maybe have answered you earlier; also a good idea to communicate through the list because all emails are archived and that sometimes enables people to find answers to their questions directly by searching the archives). Regarding you question about colors: in ChimeraX, the command "color list" will print in the log a list of colors with their names. Color names made of more than one word are listed twice: spelled with and without a space. I just checked that if you spell color names as they are listed by this command, it works. So, in your case, try spelling it "royalblue" with no space. Regarding your second question, I think this should work, but I am not quite sure what you are trying to do: volume zone #1 nearAtoms sel range 2 newMap true minimalBounds false in which #1 is your main map (so not necessarily #1 in your session, use the correct model number for your map as seen in the model panel) and sel is a selection of the atoms of interest (in your case "/A" for chain A), "range 2" is how many angstroms away from the model atoms you want to perform the map cut-out (I put 2 arbitrarily; try different values and use what you think is best for what you are trying to do), "newMap true" tells it to generate a new object for this map cut-out (it should show up in the model panel after you run the command) and "minimalBounds false" tells it to keep the same box size as your original map (if set to true instead, it will choose the minimal box size that encloses your map cut-out; not sure which one you need, but keeping the same box size should be safe). Once you have this, you can write this map cut-out to a file with the following command: save /path/to/your/new/map.mrc models #2 (replace #2 by the correct object identifier for your new map, as reported in the model panel). I hope this helps, Guillaume > On 16 Oct 2020, at 03:31, Priyanka Abeyrathne <pabeyrat(a)gmail.com> wrote: > > Hi Guillaume, > > Thank you so much for your assistance. I am going to use it soon and if I happened to have questions I will let you know. > > I have two other questions to clarify with you. > > 1. I used the following commands to color the pdb > seq chain /A > Then I highlighted the chain A > color sel blue > > I can see the chain A color is blue. Now ChimeraX has really nice color scheme. I tried to color chain A to royal blue (#4169E1 26,41,88). When I use the above commands > seq chain /A > highlighted the chain A > color sel royal blue > Didn't change the color blue to royal blue. Cod you please assist me how to fix theis? > > 2. pdb of the protein has three chains (A, B and C). I have a cryo-EM structure of the same protein. How can I extract only chain A density from cryo-EM structure. I think I have to use a segment map command. Could you please assist me how to do this in ChimeraX. > > Thank you so much. > Kind regards, > Priyanka > > > > On Mon, Oct 12, 2020 at 3:41 AM Guillaume Gaullier <guillaume(a)gaullier.org <mailto:guillaume@gaullier.org>> wrote: > Hi Priyanka, > > If what you need is a command that can restore the camera’s position to a previously saved state after you moved it, then this should be helpful: > > 1. set the scene the way you want it > 2. run command "view name myview" ("myview" can be any name); what this does is assign a name to the current view (camera settings) > 3. rotate or translate, move around, etc. > 4. run command "view myview", which should reset the camera settings to what they were when you did step 2 above > > I believe named views are saved with the session, so you should be able to use them even after you save and close, then reopen your .cxs file. > > You will find more details in the documentation, with command "help view". Also here: https://www.rbvi.ucsf.edu/chimerax/docs/user/commands/view.html#name <https://www.rbvi.ucsf.edu/chimerax/docs/user/commands/view.html#name> > > I hope this helps, > > Guillaume > > >> On 11 Oct 2020, at 22:10, Priyanka Abeyrathne <pabeyrat(a)gmail.com <mailto:pabeyrat@gmail.com>> wrote: >> >> Hi All, >> >> Is there a save scene command in ChimeraX? >> >> Thanks, >> Priyanka >> _______________________________________________ >> 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 <https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users> >

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Set transparency on DNA stubs
by Siyu Chen 16 Oct '20

16 Oct '20

Dear chimerax developers, I am writing to ask about an issue regarding to the transparency of DNA bases. I set the double strand DNA as stubs and colored cyan, and I wanted to set it as transparent (trans 70 tar c). However, it looks like only the DNA backbones become transparent, and the bases are still bright and solid. I even tried to throw in all possible targets into the 'trans' command (acrsbpfl) and got the same looking images. I am just wondering if this is because of the style or color that makes the bases look solid? Also, do you have other suggestions to get around this issue? Thanks in advance for your time and help! Best, Siyu Chen

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