April 2021 - ChimeraX-users - RBVI Mailing Lists

specify pseudobonds
by Ruchika Bajaj 17 Apr '21

17 Apr '21

Hi Elaine I am using the contact tool from the structure analysis tool. It is giving me a few pseudobonds and I want to delete a few of them for the picture I am working on. I also tried checking the pseudobond command. So, could you please help me in specifying pseudo bonds and how to delete or hide specified pseudobonds in the figure, instead of all of them. Thanks a lot !! Regards Ruchika

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Exporting DNA Molecules from Chimera X
by AQUILINA Matthew 15 Apr '21

15 Apr '21

Dear ChimeraX users, I’ve recently started using ChimeraX to produce rendered 3D models of DNA nanostructures. I do this through the following process: * Prepare nanostructure as a PDB file. * Import this into ChimeraX. * Arrange visualization settings such as nucleotide representation shape, width etc. * Export .x3d file into Blender for downstream processing. However, there is one issue - the 3D models exported by ChimeraX aren’t grouped into individual objects per nucleotide, so I am not able to easily select nucleotides and colour them in according to their type (A, T, G or C). With the older version of Chimera, these nucleotides are exported as individual objects, but then are given identical names with randomized IDs. This means that setting the nucleotide types is a long manual process of clicking on each resulting nucleotide and naming them individually. Does anyone know of a way to export a 3D model of a DNA structure which also exports the IDs of each nucleotide? This would greatly speed up the process for me to produce and render a DNA structure. Many thanks for your help! Best wishes, Matthew Aquilina -- Matthew Aquilina Precision Medicine PhD Student College of Medicine and Veterinary Medicine & School of Engineering | University of Edinburgh Profile<https://www.ed.ac.uk/profile/matthew-aquilina> | LinkedIn<https://www.linkedin.com/in/matthewaq/> | Twitter<https://twitter.com/matt_aqui> [cid:3C793866-9668-486C-B3DC-D0346CD79675@Home] Mary Brück Building | Colin Maclaurin Rd | EH9 3DW | Scotland | UK The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. Is e buidheann carthannais a th’ ann an Oilthigh Dhùn Èideann, clàraichte an Alba, àireamh clàraidh SC005336.

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MCCOY - coloring a map by local resolution - Rnd 2
by McCoy, William 14 Apr '21

14 Apr '21

Dear Elaine and other Chimera support staff, Thank you for your explanation. Unfortunately, my problem is that I cannot find the tool "Surface Color" in ChimeraX-1.1.1. Here is a screenshot of what I see when I look for it with both .mrc files loaded. From the hyperlink that you provided (https://rbvi.ucsf.edu/chimerax/docs/user/tools/surfacecolor.html) it appears that I could also access "Surface Color" from "Depiction" within tools, but I also cannot find "Depiction" as an option. Is there somewhere else that I should be looking for the "Surface Color" tool? Thanks ahead of time for the help. Sincerely, Bill McCoy William H. McCoy IV, MD, PhD Research Instructor in Medicine Department of Medicine, Division of Dermatology Washington University School of Medicine Saint Louis, MO 63110 The materials in this email are private and may contain Protected Health Information. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone at (314) 540-1512 or by return email. ________________________________ From: Elaine Meng <meng(a)cgl.ucsf.edu> Sent: Tuesday, April 13, 2021 6:47 PM To: McCoy, William <mccoyw(a)wustl.edu> Cc: Elaine Meng <meng(a)cgl.ucsf.edu> Subject: Re: [chimerax-users] coloring a map by local resolution * External Email - Caution * I just sent the question to the whole list already, right above my response (below), so you didn't need to do it.... the reason I gave the address is for your future reference and future correspondence. The moderator is deleting the duplicate question so that people don't have to read the same exact question again. Elaine > On Apr 13, 2021, at 4:40 PM, Elaine Meng <meng(a)cgl.ucsf.edu> wrote: > > >> On Apr 13, 2021, at 4:17 PM, William.H.McCOy.IV(a)cgl.ucsf.edu wrote: >> >> I can't get the following from relion 3.1 to work: The output is a file called LocalRes/polished/relion_locres.mrc that may be used in UCSF chimera to color the Postprocess/polished/postprocess.mrc map according to local resolution. # This is done using Tools -> Volume data -> Surface color, and then select by volume data value and browse to the resmap file. > > Dear William, > We have a mailing list that is recommended for asking questions, chimerax-users(a)cgl.ucsf.edu (CC'd on this message). > <https://www.rbvi.ucsf.edu/chimerax/docs/contact.html> > > Coloring by local resolution is a fairly common task and I don't know of any reason it wouldn't work. It is not clear what you mean by not working. If you are more specific with your question, we can give more targeted answers. > > First you have to open both mrc files in ChimeraX. Say you opened the map that you want to show as a surface as model #1 and the map with locres values for coloring as model #2. Then in Volume Viewer, you can adjust the isosurface level of map #1 and hide the isosurface of map #2 (or you can hide it using Model Panel, same thing). In Surface Color you would choose the (already open) models: the surface to color is model #1, you want to color it by "volume data value," and the map with values to use for coloring is #2. You can see the help for the tool by clicking its Help button, or view the copy on our website here: > > <https://rbvi.ucsf.edu/chimerax/docs/user/tools/surfacecolor.html> > > I hope this helps, > Elaine > ----- > Elaine C. Meng, Ph.D. > UCSF Chimera(X) team > Department of Pharmaceutical Chemistry > University of California, San Francisco > > > > > > _______________________________________________ > ChimeraX-users mailing list > ChimeraX-users(a)cgl.ucsf.edu > Manage subscription: > https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users ________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.

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coloring a map by local resolution
by Elaine Meng 13 Apr '21

13 Apr '21

> On Apr 13, 2021, at 4:17 PM, William.H.McCOy.IV(a)cgl.ucsf.edu wrote: > > I can't get the following from relion 3.1 to work: The output is a file called LocalRes/polished/relion_locres.mrc that may be used in UCSF chimera to color the Postprocess/polished/postprocess.mrc map according to local resolution. # This is done using Tools -> Volume data -> Surface color, and then select by volume data value and browse to the resmap file. Dear William, We have a mailing list that is recommended for asking questions, chimerax-users(a)cgl.ucsf.edu (CC'd on this message). <https://www.rbvi.ucsf.edu/chimerax/docs/contact.html> Coloring by local resolution is a fairly common task and I don't know of any reason it wouldn't work. It is not clear what you mean by not working. If you are more specific with your question, we can give more targeted answers. First you have to open both mrc files in ChimeraX. Say you opened the map that you want to show as a surface as model #1 and the map with locres values for coloring as model #2. Then in Volume Viewer, you can adjust the isosurface level of map #1 and hide the isosurface of map #2 (or you can hide it using Model Panel, same thing). In Surface Color you would choose the (already open) models: the surface to color is model #1, you want to color it by "volume data value," and the map with values to use for coloring is #2. You can see the help for the tool by clicking its Help button, or view the copy on our website here: <https://rbvi.ucsf.edu/chimerax/docs/user/tools/surfacecolor.html> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco

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Re: [chimerax-users] ChimeraX reading cube files
by Elaine Meng 10 Apr '21

10 Apr '21

> On Apr 10, 2021, at 7:54 AM, Carles Serrat Jurado <carles.serrat-jurado(a)upc.edu> wrote: > > Dear Elaine, > Thank you very much for your help. These instructions will certainly be very important for my work. > > There is still something that is not clear to me. My cube files, produced by the NWChem package, include information about the differential density. This appears by default when I open one of these files with the VESTA visualization software (https://jp-minerals.org/vesta/en/) Here I attach the 10 cube files I sent to you just converted to tif images after opening them with VESTA. As you can see, it is not the position of the atoms what evolves, as you already observed, but the differential charge density. > > I don’t know why ChimeraX does not produce the differential densities. If it would do it, then following your kind indications I could make now a movie to see that evolution (I have thousands of cube files to see a quite long time evolution - 5 femtoseconds, actually :-), which is what I am looking for. > > Again, I sincerely thank you for your answers and indications. I understand that probably ChimeraX is not able to read this information from my cube files. > > Best regards, > Carles > > PS: Please no worries about the data I am sending, it is not private so to say, these are tests I am doing at the moment. > PS2: I subscribed to the ChimeraX mailing list, but I don’t manage yet to answer there and attach files, please be free to share my mails however. Dear Carles, From your first message, I mistakenly thought you only wanted to see the atomic coordinates, so I ignored the density part. The instructions I sent before were how to make an atomic trajectory. If the atoms don't change position, then you can ignore most of those long instructions and just make one atomic model and keep showing it at the same time you show the changing density. For example, just open the attached PDB file, carles1.pdb. By default, ChimeraX does show the density from the cube files... that is the blob you see as soon as you open the file. If you mean that you want to see the densities as a series that changes over time, you just need to use the "open" command "vseries" option to tell ChimeraX that it is a volume series. For example, you previously sent a folder containing 10 files named density_subgs.0000030000.cube .... density_subgs.0000039000.cube (numbering increments of 1000). In ChimeraX, the following command opens the 10 files as a single volume series (time series): open [folder location]/density*cube vseries true Now you have a slider to play the series, or you can use the "vseries" command. Screen shot below. <https://rbvi.ucsf.edu/chimerax/docs/user/commands/vseries.html> More about atomic trajectories and volume series: <https://rbvi.ucsf.edu/chimerax/docs/user/trajectories.html> The blob is probably bigger than what you are used to seeing in Vesta. This is just the contour level. To change contour level, you can move the vertical bar on the volume viewer (density map) histogram that automatically appears when you open the data in ChimeraX. <https://rbvi.ucsf.edu/chimerax/docs/user/tools/volumeviewer.html> Your cube files are signed data, so there are two vertical bars, one for the positive contour level and one for the negative contour level. You can drag either bar, and change the color by then clicking on the small color square above the histogram. In the attached screenshot I made the negative one greenish and the positive one magenta. I only see a very small change in these densities as I play the 10 frames. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > > >> On Apr 10, 2021, at 3:10 AM, Elaine Meng <meng(a)cgl.ucsf.edu> wrote: >> >> Hi Carles, >> Attached is the PDB file from step #3 that you can open as a trajectory as described in step #4. >> Best, >> Elaine >> >> <carles-atomic.pdb> >> >> >> >>> On Apr 9, 2021, at 6:07 PM, Elaine Meng <meng(a)cgl.ucsf.edu> wrote: >>> >>> Dear Carles, >>> It took me a couple of days to try that recipe script on your data, sorry about the slow reply. Now I realize there are a few extra steps to convert your data to a trajectory (e.g. with slider to play as movie), so I thought I should share the details with the list: >>> >>> (1) In ChimeraX, I opened your 10 cube files, and then I used the python file in the ChimeraX recipe to create 10 atomic models. >>> <https://rbvi.github.io/chimerax-recipes/gaussian_cube_atoms/gcatoms.html> >>> >>> (2) Then I saved the 10 atomic models as a single PDB file (using ChimeraX menu: File... Save), File type PDB, relative to the first atomic model. Doesn't matter which one you choose as the "relative to" model, however. >>> >>> (3) Then I was going to open that single PDB file as a trajectory. However, there is a bug in the saving that currently prevents it. The bug puts "END" after each atomic structure in the file. So I first needed to text-edit the PDB file to remove all of the "END" lines (but not "ENDMDL"). >>> >>> **I will send you the resulting PDB file in a separate message in case it is private data.** >>> >>> (4) In ChimeraX, I closed all the other models and then opened the new edited multi-model PDB file with the "coordsets" option to make it into a trajectory, for example, command: >>> >>> open carles-atomic.pdb coordsets true >>> >>> However, 10 frames of the trajectory all look exactly the same to me, but far as I know that is a correct conversion of the data from the 10 cube files you sent me. >>> >>> When the bug is fixed (#4487 <https://plato.cgl.ucsf.edu/trac/ChimeraX/ticket/4487>), step #3 would not be necessary. >>> >>> I hope this helps, >>> Elaine >>> ----- >>> Elaine C. Meng, Ph.D. >>> UCSF Chimera(X) team >>> Department of Pharmaceutical Chemistry >>> University of California, San Francisco >>> >>> >>>> On Apr 7, 2021, at 9:33 AM, Anthony James Schaefer <tony.schaefer(a)uga.edu> wrote: >>>> >>>> ChimeraX does actually store the atom info in the cube file. Someone asked about this a while ago, and it was mentioned that there's some limitation where the stuff for opening volume data can't load atomic structures or something. I can't find the thread, but Tom Goddard wrote a script to load those atoms into ChimeraX: https://rbvi.github.io/chimerax-recipes/gaussian_cube_atoms/gcatoms.html >>>> >>>>> >>>>>> On Apr 7, 2021, at 7:25 AM, Carles Serrat Jurado <carles.serrat-jurado(a)upc.edu> wrote: >>>>>> >>>>>> Dear Elaine, >>>>>> >>>>>> I am writing because I have problems to plot a cube file with ChimeraX. I would greatly appreciate your assistance. Here I send the only figure I get when I open the cube file with ChimeraX. Also I attach what I would more expect, which is obtained with the software VESTA. >>>>>> >>>>>> My ultimate goal is to make a movie with using different frames. I also send a zipped file with the frames, so that you can see the kind of cube files I am working on. >>>>>> >>>>>> Thank you very much in advance for your support. >>>>>> >>>>>> Best regards, >>>>>> >>>>>> Carles >>>>>> >>>>>> <ChimeraX.png> >>>>>> >>>>>> <VESTA.png> >>>>>> <cube_files.zip> >>>>>> —————————-————————— >>>>>> Prof. Carles Serrat (PhD) >>>>>> Department of Physics >>>>>> UPC - Polytechnic University of Catalonia >>>>>> Colom 11, 08222 - Terrassa >>>>>> Phone: +34 93 739 8137 >>>>>> Mobile: +34 696 738 728 >>>>>> https://donll.upc.edu >>>>>> ——————————————————- >>>>> >>>>> >>>>> _______________________________________________ >>>>> ChimeraX-users mailing list >>>>> ChimeraX-users(a)cgl.ucsf.edu >>>>> Manage subscription: >>>>> https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users >>>>> >>>> >>>> >>>> _______________________________________________ >>>> ChimeraX-users mailing list >>>> ChimeraX-users(a)cgl.ucsf.edu >>>> Manage subscription: >>>> https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users >>>> _______________________________________________ >>>> ChimeraX-users mailing list >>>> ChimeraX-users(a)cgl.ucsf.edu >>>> Manage subscription: >>>> https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users >>> >>> >>> _______________________________________________ >>> ChimeraX-users mailing list >>> ChimeraX-users(a)cgl.ucsf.edu >>> Manage subscription: >>> https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users >>> >> > > —————————-————————— > Prof. Carles Serrat (PhD) > Department of Physics > UPC - Polytechnic University of Catalonia > Colom 11, 08222 - Terrassa > Phone: +34 93 739 8137 > Mobile: +34 696 738 728 > https://donll.upc.edu > ——————————————————- > > > > > > > > > > > > > > > > >

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ChimeraX reading cube files
by Elaine Meng 09 Apr '21

09 Apr '21

Hi Carles, We recommend using the chimerax-users(a)cgl.ucsf.edu address (CC'd here) for questions about ChimeraX, unless you have attached data that needs to stay private. ChimeraX reads cube format but only as maps (e.g. density maps, electron localization functions, ...) with values on a grid. It does not read atomic coordinates from the cube format. This is a list of the atomic formats ChimeraX can read -- can you output any of those atomic formats instead of cube? (pdb, mol2, mol, sdf) <https://rbvi.ucsf.edu/chimerax/docs/user/commands/open.html#formats> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/open.html#atomic> You can see that "cube" is in the list for volume (map) formats, but not as an atomic format. <https://rbvi.ucsf.edu/chimerax/docs/user/commands/open.html#volume> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Apr 7, 2021, at 7:25 AM, Carles Serrat Jurado <carles.serrat-jurado(a)upc.edu> wrote: > > Dear Elaine, > > I am writing because I have problems to plot a cube file with ChimeraX. I would greatly appreciate your assistance. Here I send the only figure I get when I open the cube file with ChimeraX. Also I attach what I would more expect, which is obtained with the software VESTA. > > My ultimate goal is to make a movie with using different frames. I also send a zipped file with the frames, so that you can see the kind of cube files I am working on. > > Thank you very much in advance for your support. > > Best regards, > > Carles > > <ChimeraX.png> > > <VESTA.png> > <cube_files.zip> > —————————-————————— > Prof. Carles Serrat (PhD) > Department of Physics > UPC - Polytechnic University of Catalonia > Colom 11, 08222 - Terrassa > Phone: +34 93 739 8137 > Mobile: +34 696 738 728 > https://donll.upc.edu > ——————————————————-

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Surface caps only colored interactively
by Daniel Asarnow 09 Apr '21

09 Apr '21

Hi, I'm trying to generate a figure using several surfaces colored by map values. If I clip a surface, and then color it, the caps have the correct colors. However, when I do the same thing non-interactively, the caps are uncolored. Am I doing something wrong? view front.cut color sample #1.1 map #1.2 palette cyanmaroon range 2.25,7.0 #surface dust #1.1 size 100 save front_cut.png pixelSize 0.1 transparentBackground true Best, -da

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chimerax python module - LigParGen tutorial
by mdigennaro＠uliege.be 07 Apr '21

07 Apr '21

Dear ChimeraX users, I am trying to follow this tutorial to get the proper residues: http://zarbi.chem.yale.edu/ligpargen/gmx_tutorial.html I have found chimera (0.4.7) as pip module, but it's written in python2 and therefore no longer maintained. Is there a chimerax module I can import? Pychimera is also available and could install it with python2, but it also show compatibility problems with python3 Is DockPrep a separate module? I have found this thread on the chimera forum which doesn't really answer the question: http://plato.cgl.ucsf.edu/pipermail/chimera-users/2014-July/010115.html Generally, how do I get unknown/custom residues (from LigParGen in this case) for Gromacs input files. Thank you for your support Marco ------------------- Marco Di Gennaro University of Liege

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Use symmetry information in Isolde
by Sean Connell 06 Apr '21

06 Apr '21

Hello I have a naive question about using Isolde to build a model into a cryoEM map generated with symmetry (ie. D4). Basically I don't understand how to rebuild a chain and have the changes reflected in the symmetry related chains when using a cryoEM map. Is it possible to use, for example, a NCS file (like symmetry_from_map.ncs_spec) generated by phenix in order to get Isolde to build simultaneously the NCS related chains? Or is there another way build symmetry related chains into a symmetrical cryoEM map? Thanks for any tips you have.

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An issue about chimeraX
by 祗俊生 02 Apr '21

02 Apr '21

Dear expert： I used "chimeraX 1.1 for windows 10 64-bit" to make animation. As can be seen in the figure provided in the attachment, the labels of hydrogen bonding distance overlapped when I played the animation. However, when I used "Tools-Structure Analysis-Contacts" to show the labels of "Contacts", these labels did not exhibit the above-mentioned problem when I played the animation. I wonder how to solve the problem of the label overlap regarding hydrogen bonds because I want to make a movie to show all of the hydrogen bonds. Moreover, I want to download "chimeraX 1.0 for windows 10 64-bit", but I can't find the download address of the old version. Many thanks!

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