- ChimeraX-users - RBVI Mailing Lists

Session Initiation Error
by Alexander Julian 22 Apr '21

22 Apr '21

Good morning, I am currently trying to create a python script that hides atoms and shows ribbons in a .pdb file. However, I am getting an error while trying to initialize a session. I've been trying to debug the problem to the best of my ability, but I am unable to figure out the issue. My code: ``` import chimerax.core.session as cxsession session = cxsession.Session('name') ``` My error: ``` File "./test.py", line 15, in <module> session = cxsession.Session('name') File "/opt/UCSF/ChimeraX/lib/python3.7/site-packages/chimerax/core/session.py", line 437, in __init__ self.app_name = app_name File "/opt/UCSF/ChimeraX/lib/python3.7/site-packages/chimerax/core/session.py", line 508, in __setattr__ if not name.startswith('_') and self.snapshot_methods(value, base_type=StateManager) is not None: File "/opt/UCSF/ChimeraX/lib/python3.7/site-packages/chimerax/core/session.py", line 535, in snapshot_methods from .serialize import PRIMITIVE_TYPES File "/opt/UCSF/ChimeraX/lib/python3.7/site-packages/chimerax/core/serialize.py", line 42, in <module> from ._serialize import msgpack_serialize_stream, msgpack_deserialize_stream, PRIMITIVE_TYPES ImportError: libpython3.7m.so.1.0: cannot open shared object file: No such file or directory ``` I look forward to your assistance. Best, Alexander -- *Alexander T. Julian* PhD Student, Department of Biology, Microbiology Bachelor of Science, Biomedical Engineering, Cell and Tissue Specialization 2021 Master of Advanced Study, Chemical Engineering 2021 Illinois Institute of Technology Chicago, IL 60616 *Phone (727)-735-7104*

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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 14 Apr '21

14 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 10 Apr '21

10 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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Re: [chimerax-users] Displaying silhouette around specific visual elements
by Tom Goddard 01 Apr '21

01 Apr '21

Hi Gustavo, Glad you noticed the smoothness of the surface. I made it smoother than the default. The surface came from the molmap command which computes a density map from the atomic model. That command uses a density map grid spacing of 1/3 the requested resolution by default, but I specified an extra option that used a grid spacing 1/8 of the resolution: open 2gbp molmap #1 8 gridSpacing 1 Also if you are doing this with a big molecule (100,000 atoms) the density map created may be very large and may be shown subsampled so the surface looks coarser. Make sure to set the "step" to 1 in the Volume Viewer panel so that it uses the full resolution of the computed map instead of step 2 which would use only every other grid point. One more pro tip about that image composition example. It only worked nicely because the atomic structure was completely behind the surface, so I could layer the surface on top. If part of the atomic model was behind and part in front (for example with a cryoEM map surface), then the layering would not work well -- the composite image would have the surface in front everywhere. Elaine's selection highlight approach can handle that situation with correct occlusions but the edging is not as nice as silhouettes. Tom > On Mar 31, 2021, at 1:00 PM, de Miranda Seabra, Gustavo <seabra(a)cop.ufl.edu> wrote: > > Hi Tom, > > This looks beautiful! Just one tangential question: How do you get such a smooth surface? Can you share the exact commands you gave? > > Thanks! > > -- > Gustavo Seabra > Assistant Scientist > Center for Natural Products, Drug Discovery and Development (CNPD3) > Department of Medicinal Chemistry > College of Pharmacy > University of Florida, Gainesville, FL, USA > From: ChimeraX-users <chimerax-users-bounces(a)cgl.ucsf.edu <mailto:chimerax-users-bounces@cgl.ucsf.edu>> on behalf of Tom Goddard <goddard(a)sonic.net <mailto:goddard@sonic.net>> > Sent: Tuesday, March 30, 2021 8:55 PM > To: Andre LB Ambrosio <andre(a)ifsc.usp.br <mailto:andre@ifsc.usp.br>> > Cc: ChimeraX Users Help <chimerax-users(a)cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>> > Subject: Re: [chimerax-users] Displaying silhouette around specific visual elements > > [External Email] > Hi Andre, > > If you are willing to go to a little trouble you can get silhouettes on an atomic model beneath a transparent surface that has no silhouettes. You first save an image of the atomic model with silhouettes with no surface, then save an image of the transparent surface with no atomic model and no silhouettes, then overlay the second image on the first in a photo editor like Gimp. Below is Elaine's example done this way. The command to save the surface image with transparency for overlaying is "save transpsurf.png transparentBackground true". > > Tom > > Overlay of two images. > > > Atomic model image > > > Transparent surface image > > >> On Mar 30, 2021, at 3:11 PM, Andre LB Ambrosio <andre(a)ifsc.usp.br <mailto:andre@ifsc.usp.br>> wrote: >> >> Dear Elaine, that is excellent! It is the visual effect I was looking for indeed. >> Thank you very much for this and thank you Tom for the very detailed response and for the feature request ticket. >> Andre. >> >> Em ter., 30 de mar. de 2021 às 15:59, Elaine Meng <meng(a)cgl.ucsf.edu <mailto:meng@cgl.ucsf.edu>> escreveu: >> Hi Andre, >> Sometimes you can approximately "fake" this effect by using the selection outline. It is not the same, however, as silhouettes; it will only go around the outside perimeter of the selected item(s). For example, if I have a molecule inside a map surface, I can make the surface transparent, select the atomic structure, and make the selection outline color black etc. as in these commands, resulting in the appearance in the attached image. >> >> open 2gbp >> molmap protein 8 >> trans 70 >> view >> set bgColor white >> select @* >> graphics selection color black >> >> I hope this helps, >> Elaine >> ----- >> Elaine C. Meng, Ph.D. >> UCSF Chimera(X) team >> Department of Pharmaceutical Chemistry >> University of California, San Francisco >> >> >> >> >>> On Mar 25, 2021, at 8:23 PM, Tom Goddard <goddard(a)sonic.net <mailto:goddard@sonic.net>> wrote: >>> >>> Hi Andre, >>> >>> It is not currently possible to display silhouettes on some models and not others. >>> >>> Several people have wanted this but I think it is complex to achieve. The silhouettes show boundaries where the depth in the entire scene changes abruptly. In order to have per-model silhouettes the ChimeraX GPU shader programs would need to compute an additional depth buffer separately for each model. Also the silhouette edges are not currently drawn at a specific depth. If per-model silhouettes were supported a stick model with silhouettes beneath a transparent surface needs to draw the silhouettes under the transparent surface so knowing the depth of the silhouette edge becomes important. When not using silhouettes the shader programs need to not compute the extra per-model depth buffers otherwise it would slow down rendering even when not being used. Adding these additional complexities to already complex graphics rendering shader programs have so far made this feature out of reach for our one graphics rendering developer (me). >>> >>> I made a feature request for per-model silhouette edges and perhaps in the future we will find a simpler way to implement it that makes it feasible. >>> >>> https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/4420 <https://urldefense.proofpoint.com/v2/url?u=https-3A__www.rbvi.ucsf.edu_trac…> >>> >>> Tom >>> >>>> On Mar 25, 2021, at 10:09 PM, Andre LB Ambrosio <andre(a)ifsc.usp.br <mailto:andre@ifsc.usp.br>> wrote: >>>> >>>> Dear all, >>>> >>>> I wonder if it's possible to display silhouettes selectively in the same figure; for instance, displaying silhouettes only on structure representation (around sticks, spheres, cartoons and so on), but not around the maps or volumes that surround them. >>>> Many thanks in advance, >>>> >>>> Andre >>>> _ >> >> >> -- >> Andre LB Ambrosio >> Associate Professor, IFSC/USP - Brazil >> www.ifsc.usp.br/alba <https://urldefense.proofpoint.com/v2/url?u=http-3A__www.ifsc.usp.br_alba&d=…> >> _______________________________________________ >> 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://urldefense.proofpoint.com/v2/url?u=https-3A__plato.cgl.ucsf.edu_mai…>

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Displaying silhouette around specific visual elements
by Andre LB Ambrosio 31 Mar '21

31 Mar '21

Dear all, I wonder if it's possible to display silhouettes selectively in the same figure; for instance, displaying silhouettes only on structure representation (around sticks, spheres, cartoons and so on), but not around the maps or volumes that surround them. Many thanks in advance, Andre

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Re: [chimerax-users] [Chimera-users] Debug
by 안예림 30 Mar '21

30 Mar '21

As soon as I start Chimera, the error message appears. I don't know how to report a bug to you. help me -----Original Message----- From: "Eric Pettersen"<pett(a)cgl.ucsf.edu> To: "안예림"<cp7617(a)naver.com>; Cc: <chimera-users(a)cgl.ucsf.edu>; Sent: 2021-03-30 (화) 03:36:23 (GMT+09:00) Subject: Re: [Chimera-users] Debug You should start Chimera and immediately use Help→Report A Bug to send a bug report to us, with a short description of the problem like you provided here. That will automatically provide us with many details about the machine you are using and the version of Chimera you are running. We can carry on from there, since I imagine this problem is only affecting you and therefore other people on this mailing list wouldn't want to get mail about all the details of this problem. --Eric Eric Pettersen UCSF Computer Graphics Lab On Mar 28, 2021, at 10:28 PM, 안예림 <cp7617(a)naver.com> wrote: Hi I have tried to make a movie of MD simulation by Chimera. I could be done one time, then for other MD’s it exits abnormally with the code -1073741819. Even I have decreased the size of .xtc file, it exits abnormally yet. Please check my capture picture. I have reinstalled chimera, but the problem did not resolve.What should I have to do ? I need your assistant. Thanksbe <20210329_142325.png>_______________________________________________ Chimera-users mailing list: Chimera-users(a)cgl.ucsf.edu Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users

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xchimera multiscale model
by Ana Sofia Ramos 29 Mar '21

29 Mar '21

Hi, I am having some difficulties in using xchimera, and I would like to ask you if you could help me. I want to make a representation of a virus-like nanoparticle using the pdb 1HQK. I have searched in the tutorial of xchimera but I could not find the general instructions, but I found them in the tutorial of chimera (multiscale model), however, the options are not present in my installation xchimera (and also in my installation of chimera). Then, I thought that maybe you could tell me how to make it in xchimera. Thank you very much for your attention. Kind regards, Ana

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Rotate PDB file around euler angles in ChimeraX
by Vorländer,Matthias Kopano 26 Mar '21

26 Mar '21

Dear all, So, I am working with a tomogram and refined subtomogram average and would like fit all copies of the molecule, represented as a pdb file, back into the tomogram at all positions where it was found. In practice this means to translate the pdb file to specific coordinates of a reference volume (tomogram) and then rotate it around 3 euler angles defined in a relion star file. I figured out the translation part (thanks to your help), but for the rotation I could only find this script (https://plato.cgl.ucsf.edu/trac/chimera/attachment/wiki/Scripts/eulermove.py) for chimera which allows to rotate a volume around the euler angles and then resample the transformed volume and save it. While a workaround would be to do the operation with the volume in chimera, then fit the pdb file in the transformed volume, and then save the transformed pdb file, and then load everything back in chimera, the manual fitting of the pdb would become very laborious for several hundred copies. So ideally, I would like to adapt the eulermove.py script that I linked to i) work in ChimeraX and ii) work with pdbs instead of volumes. Unfortunately I have zero coding experience… Any help would be much appreciated! Best, Matthias

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RR distance maps
by William S Wang 26 Mar '21

26 Mar '21

Is there implementation of RR distance maps from chimera?

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generating icosahedron from pentamer
by Moustafa, Ibrahim M. 26 Mar '21

26 Mar '21

Dear all, I want to generate icosahedral structure from a pentamer (chains A-E). When I use the command: sym #1 i,222 coordinateSystem #2 center #2 It generated 5 copies, icosahedron for each chain. What I'd like to build is just 12 copies of the pentamer in an icosahedral sym. How to do that in ChimeraX? Thanks, Ibrahim

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Custom Palette
by Abhilash Padvannil 26 Mar '21

26 Mar '21

Hi, I am wondering if there is a way to create custom palettes for use in ChimeraX. Please suggest. Thanks Regards Abhilash.

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Making New Bonds between two molecules in ChimeraX
by Steven Truong 25 Mar '21

25 Mar '21

Dear ChimeraX Admins and Elaine, Hello, I was wondering if ChimeraX now has a “bond” command. I saw an inquiry like this in the mailing list archives (https://www.rbvi.ucsf.edu/pipermail/chimerax-users/2020-April/001029.html) but it seems like bond is still not an official functionality. When I switched over to Chimera and tried using the “bond” command, I get the error “Cannot form covalent bond joining two molecules,” even though I’ve saved all of the molecules into one PDB file. Is it because Chimera still sees these two sub-models as un-joinable? My command looks something like: "bond #0:61.A@ND2 #0.1:1222.X@C1”. For further context, we are trying to script orienting/bonding residues to glycans. We’ve been able to figure out aligning and orienting the glycans quite well with the scripts alone (.py scripts), but it seems like we’ll have to find another way to make bonds between the proteins/glycans. Do you have any suggestions? Ideally, we’d also keep as much of the pipeline in ChimeraX, but if it’s necessary, we could further pursue the ChimeraX+Chimera route. Thank you for your help! Many thanks, Steven Truong sdt45(a)cam.ac.uk<mailto:sdt45@cam.ac.uk> Cambridge University

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SwissSidechain equivalent for ChimeraX
by Madeline Grace Rollins 24 Mar '21

24 Mar '21

Hi all, I would like to mutate a serine residue to phosphoserine for one of the proteins I am working with. I have used SwissSidechain in Chimera to do this in the past, but I was wondering if there is an equivalent module like SwissSidechain but for ChimeraX? I tried downloading the SEQCROW bundle for structure editing, but I couldn't find the same range of sidechain derivatives. If not, can you use SwissSidechain in ChimeraX? I apologize in advance if this question has been asked already. Thank you, Madeline

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Questions about focal length of camera in ChimeraX
by Bin Shi 24 Mar '21

24 Mar '21

Thanks very much for your software so that I can specify the camera position and then take a snapshot. However, I can't find the information on the focal length of the virtual camera. I am using mono (default) – monoscopic with perspective (apparent size decreasing with distance from the viewer), and I didn't see any details about the camera intrinsics. Regards, Bin ----------------------------------------------------------------------------------------------- Department of Materials Science and Engineering, University of Toronto Email: binmse.shi(a)mail.utoronto.ca

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Re: [chimerax-users] VR Support
by Tom Goddard 24 Mar '21

24 Mar '21

Hi Gökhan, Your Nvidia RTX 3090 should give the best performance possible with current GPUs. There was a shortage of high-end graphics card in 2020 and supply continues to far outpace demand with popular cards priced 2 to 3 times their suggested retail price. For instance your RTX 3090 has a suggested price of $1500 but currently is priced over $3000. This may not improve until 2022 according to news reports. This may be the biggest problem in getting a new molecular visualization computer setup for VR. https://www.theverge.com/2021/3/23/22345891/nvidia-amd-rtx-gpus-price-scalp… <https://www.theverge.com/2021/3/23/22345891/nvidia-amd-rtx-gpus-price-scalp…> I have not tried the HP Reverb G2 virtual reality headset. I know people were excited about the 2160 by 2160 pixels per eye resolution -- for comparison a Valve Index headset has 1440 by 1600 pixels. But reports said the hand-controller tracking with the Reverb G2 was below current VR standards. ChimeraX and any SteamVR application will work with any hand controllers. I have used ChimeraX VR with other Windows Mixed Reality controllers with a Samsung Odyssey headset with no problems. I've also used it with various other controllers with no problem: Vive Pro, Vive, Oculus Rift S, Oculus Rift, Oculus Quest. ChimeraX won't take advantage of the many extra inputs on Valve Index hand controllers. Nanome is a VR molecular visualization application funded by venture capital -- so they of course will need to charge plenty of money once that VC money runs out. I expect they will mostly be aiming their features at pharmaceutical company needs. I don't know if Nanome has any atomic model refinement capabilities. Tom > On Mar 23, 2021, at 12:11 AM, <tolung.bio(a)gmail.com> <tolung.bio(a)gmail.com> wrote: > > Hi Tom, > > Thanks for the prompt response. > > My responses are below. > > Cheers, > > Gökhan > > > > From: Tom Goddard <goddard(a)sonic.net <mailto:goddard@sonic.net>> > Sent: Tuesday, 23 March 2021 5:49 PM > To: tolung.bio(a)gmail.com <mailto:tolung.bio@gmail.com> > Cc: Tristan Croll <tic20(a)cam.ac.uk <mailto:tic20@cam.ac.uk>>; ChimeraX Users Help <chimerax-users(a)cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>>; Simon Brown <simonb(a)uow.edu.au <mailto:simonb@uow.edu.au>>; James Bouwer <jbouwer(a)uow.edu.au <mailto:jbouwer@uow.edu.au>> > Subject: Re: [chimerax-users] VR Support > > Hi Gökhan, > > ISOLDE works in VR in a minimal way -- you can tug on atoms. Here's a little video showing that in ChimeraX 1.1. > > https://www.rbvi.ucsf.edu/chimerax/data/isolde-vr-mar2021/isolde_vr.mp4 <https://www.rbvi.ucsf.edu/chimerax/data/isolde-vr-mar2021/isolde_vr.mp4> > > I turned off depth cue and clipping with commands "light depthcue off" and "clip off" otherwise it clips to a slab which keeps moving as I move my head. I click a VR button on the ISOLDE panel tug atoms mouse mode icon to assign the VR button. I wouldn't say this makes ISOLDE usable in VR. For instance I don't have a way to move the roaming contour mesh region which normally stays in the middle of the screen. But it is enough to play around a bit. I was using a GTX 1080 Ti graphics card. Both the VR and ISOLDE molecular dynamics are running on the graphics card so this puts heavy demand on the card. For simulating just a region around a residue it was reasonably smooth. > > Thanks for the tips to get it to work with ISOLDE. I have a 3090 to play with (which recently replaced my trusty 1080) that should have significantly better performance than the 1080 Ti. Let’s see how it goes… > > I would like to make ISOLDE work well in VR. I think it is the perfect VR application where you really benefit from the best 3D perception possible and the 6-degree-of-freedom hand controllers for moving atoms around is much better suited than a mouse. > > ABSOLUTELY, and I cannot wait for that day that I’ve been waiting for since I started working on structures, to come… > > VR resolution has not been a major issue for use in molecular visualization. We have been using Vive Pro headsets that have adequate resolution for a few years now. A Valve Index headset is probably the best choice for molecular visualization right now. People also use Quest 2 with link cable. > > I have an HP Reverb G2 that recently replated my original HTC Vive. I am quite disappointed with it so far, and was wondering whether I should’ve gone for an Index. However, Index is not sold in Australia (and therefore would have required having one shipped from the US, which means no warranty here and expensive shipping). That was one of the reasons for going for the G2, and I have already used that warranty, since the first unit they sent died after minutes of first use! > > Do you think ChimeraX+ISOLDE should work with the WMR controllers that come with the G2, or is the current code specific to the Vive controllers? > > The big problem is it would take many developer years of effort to have decent user interfaces in VR. The furthest along on this for molecular visualization is Nanome -- you should check out their molecular VR. We continued to develop ChimeraX VR including multi-person VR. > > I have used Nanome’s one of the earliest versions, but it looks like they’re locking more and more of its features for free users based on my most recent try. ☹ Does it work as well as ChimeraX+ISOLDE in refining models? > > Tom > > > > >> On Mar 22, 2021, at 9:18 PM, <tolung.bio(a)gmail.com <mailto:tolung.bio@gmail.com>> <tolung.bio(a)gmail.com <mailto:tolung.bio@gmail.com>> wrote: >> >> Hello Tristan and the Chimera team, >> >> I have been using ChimeraX in VR: fantastic! >> >> However, ISOLDE was not working in VR, unfortunately. >> >> Is there a fix/workaround currently available to get ISOLDE running in VR? >> >> Is there ongoing work on making ISOLDE VR compatible? >> >> Also: 1) are there any advantages of using a Quadro card over a consumer-line card for ChimeraX VR? and 2) is there a recommended minimum system spec for getting high-enough frame rates in VR with large models? We are planning to put together a new system soon for molecular visualization and modelling, hence the questions. >> >> Now that there are VR headsets with high-enough resolution (such as the HP Reverb G2) that allow reading smaller text and finer details in VR, I am hoping that the molecular visualization and modelling software will start providing built-in easy-to-use support for these devices. I applaud ChimeraX team for leading in this space (no pun intended 😊). >> >> Best, >> >> Gökhan >> >> _______________________________________________ >> 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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Re: [chimerax-users] movie in ChimeraX
by Elaine Meng 24 Mar '21

24 Mar '21

> On Mar 23, 2021, at 5:04 AM, Ruchika Bajaj <phd.ruchika(a)gmail.com> wrote: > > Hi Elaine > I am trying to figure out two things. Could you please help me with this? I would appreciate your help. > 1. I have two structures. The first one doesn't have a ligand and the second one has two ligands. I am trying to make a movie with these steps. 1) first structure, 2) two ligands are coming or flying in the picture, 3) then the 2nd structure with two ligands. However, when I am trying to make the morph between the first and second structure, it doesn't show any ligand. I did check the following link, where it discusses that both structures should have ligands to include it in the morph. So, my question is how should I include the ligand ? Could you please explain me with command usage? Thanks !! > <http://rbvi.ucsf.edu/chimerax/docs/user/commands/morph.html#pairing> > 2. I heard that frames/sec rate could be increased to smoothen steps in movies. I checked the maxFrameRate command. However, I don't know the usage. Could you please help me with that ? > Thanks a lot for your help !! Your prompt response would help me to proceed further. > Regards > Ruchika Hi Ruchika, Please send questions to chimerax-users(a)cgl.ucsf.edu (if you are using ChimeraX) or chimera-users(a)cgl.ucsf.edu (if using Chimera) rather than my individual address, or else they may not get answered. (1) as explained here <https://rbvi.ucsf.edu/chimerax/docs/user/commands/morph.html#pairing> morph only contains the atoms that are the same in both start and end structures. You can show ligands but because they are not included in the morph model, you have to display the ligand(s) from the original model (or an additional copy of the original model) along with the protein in the morph model. Moving them to different positions is even more complicated than showing/hiding. There is a Chimera tutorial that covers this, and what you would do with ChimeraX is similar except that ChimeraX "view" is used to save and restore positions instead of the Chimera commands "savepos" and "reset": <https://www.rbvi.ucsf.edu/chimera/data/tutorials/movies08/moviemaking.html> (2) if you mean you want more steps in the morph (more gradual change) then you would use the "frames" option in the morph command. Probably that is what you want. <https://rbvi.ucsf.edu/chimerax/docs/user/commands/morph.html#top> However, if you really mean you wanted movie framerate, then it is the "framerate" option of the "movie encode" command. <https://rbvi.ucsf.edu/chimerax/docs/user/commands/movie.html#encode> 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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VR Support
by tolung.bio＠gmail.com 23 Mar '21

23 Mar '21

Hello Tristan and the Chimera team, I have been using ChimeraX in VR: fantastic! However, ISOLDE was not working in VR, unfortunately. Is there a fix/workaround currently available to get ISOLDE running in VR? Is there ongoing work on making ISOLDE VR compatible? Also: 1) are there any advantages of using a Quadro card over a consumer-line card for ChimeraX VR? and 2) is there a recommended minimum system spec for getting high-enough frame rates in VR with large models? We are planning to put together a new system soon for molecular visualization and modelling, hence the questions. Now that there are VR headsets with high-enough resolution (such as the HP Reverb G2) that allow reading smaller text and finer details in VR, I am hoping that the molecular visualization and modelling software will start providing built-in easy-to-use support for these devices. I applaud ChimeraX team for leading in this space (no pun intended 😊). Best, Gökhan

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