- ChimeraX-users - RBVI Mailing Lists

Re: [chimerax-users] [Chimera-users] .dae export for ChimeraX
by Tom Goddard 02 Dec '21

02 Dec '21

Hi Byrne, I agree, OBJ and STL are very limited compared to Collada and GLTF. OBJ is supported by almost every 3D model program and STL is commonly used for 3D printing (single color) which is why they are in ChimeraX. GLTF is definitely the best option in ChimeraX for your case. There appear to be lots of programs that convert GLTF to Collada and the other direction too. But I have not tried any of them so don't have any recommendation. Let us know if you find one that works well -- other ChimeraX users may have the same need. A major stumbling block exporting 3D models from ChimeraX (or Chimera) is that they use vertex colors, while most of the non-biology 3D model world uses texture colors, and will simply ignore vertex colors losing all your color information. That example I linked to in the last email describes a relatively new ChimeraX feature to export texture colors (for limited cases, e.g. discrete colors only). Another common problem exporting molecular models for use in other software is that the file size and number of triangles is too large for the application that you want to use them in, often tens of millions of triangles or hundreds of Mbytes to Gbytes in size. The example also shows how to tell ChimeraX to limit the number of triangles. https://www.rbvi.ucsf.edu/chimerax/data/texture-may2021/export_3d.html Tom Model from gltf export from linked ChimeraX example > On Dec 2, 2021, at 2:04 PM, Byrne Pedit <bpedit(a)comcast.net> wrote: > > Hello Tom, > > Thanks for the response. I tried the GLTF export, not recognizable by Xcode (the development platform for iOS and Mac OS). The only ChimeraX file options I’ve found to be openable are OBJ and STL. These are, however, problematic and unusable. > > But your hint of using GLTF as an intermediary offers an avenue for exploration, it’s not a format I’ve used. I see it supports scene graph hierarchy, absent with OBJ and STL( exported from ChimeraX anyway) so this is promising. Now to find a converter. > > The GLTF export link is informative, it may help further refine my approach. Interestingly, the molecule you’ve chosen for demo purposes appears to be the one, or a variant thereof, I’ve been testing with! > > Thanks again, > > Byrne > > >> On Dec 2, 2021, at 12:30 PM, Tom Goddard <goddard(a)sonic.net <mailto:goddard@sonic.net>> wrote: >> >> Hi Byrne, >> >> We have long been interested in adding Collada format export of scenes from ChimeraX. Here is the feature request for that >> >> https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/485 <https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/485> >> >> But our scene export in ChimeraX has focused on GLTF format, as that has been the most requested. Here is an example showing GLTF export from ChimeraX (including texture colors). >> >> https://www.rbvi.ucsf.edu/chimerax/data/texture-may2021/export_3d.html <https://www.rbvi.ucsf.edu/chimerax/data/texture-may2021/export_3d.html> >> >> ChimeraX also exports OBJ, STL, X3D, VTK as shown in the save command docs >> >> https://rbvi.ucsf.edu/chimerax/docs/user/commands/save.html#formats <https://rbvi.ucsf.edu/chimerax/docs/user/commands/save.html#formats> >> >> Can you make use of GLTF files? If not, a quick solution might be to convert ChimeraX GLTF files to Collada with third-party software. >> >> Tom >> >>> On Dec 2, 2021, at 10:41 AM, Byrne Pedit via Chimera-users <chimera-users(a)cgl.ucsf.edu <mailto:chimera-users@cgl.ucsf.edu>> wrote: >>> >>> ChimeraX is awesome and definitely superior to the original but for the inability to export as .dae (Collada). Is that possibly on the to-do list? This is important for those of us (just me?) writing interactive molecular apps for devices. It is the only satisfactory path I’ve found between a PDB file and SCNNodes/Scenes in iOS. (See the iOS app ‘BioMole’, free, if interested in an application.) >>> _______________________________________________ >>> Chimera-users mailing list: Chimera-users(a)cgl.ucsf.edu <mailto:Chimera-users@cgl.ucsf.edu> >>> Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimera-users <https://www.rbvi.ucsf.edu/mailman/listinfo/chimera-users> >>> >> >

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Re: [chimerax-users] [Chimera-users] .dae export for ChimeraX
by Tom Goddard 02 Dec '21

02 Dec '21

Hi Byrne, We have long been interested in adding Collada format export of scenes from ChimeraX. Here is the feature request for that https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/485 <https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/485> But our scene export in ChimeraX has focused on GLTF format, as that has been the most requested. Here is an example showing GLTF export from ChimeraX (including texture colors). https://www.rbvi.ucsf.edu/chimerax/data/texture-may2021/export_3d.html ChimeraX also exports OBJ, STL, X3D, VTK as shown in the save command docs https://rbvi.ucsf.edu/chimerax/docs/user/commands/save.html#formats Can you make use of GLTF files? If not, a quick solution might be to convert ChimeraX GLTF files to Collada with third-party software. Tom > On Dec 2, 2021, at 10:41 AM, Byrne Pedit via Chimera-users <chimera-users(a)cgl.ucsf.edu> wrote: > > ChimeraX is awesome and definitely superior to the original but for the inability to export as .dae (Collada). Is that possibly on the to-do list? This is important for those of us (just me?) writing interactive molecular apps for devices. It is the only satisfactory path I’ve found between a PDB file and SCNNodes/Scenes in iOS. (See the iOS app ‘BioMole’, free, if interested in an application.) > _______________________________________________ > Chimera-users mailing list: Chimera-users(a)cgl.ucsf.edu > Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimera-users >

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coloring clipped surface only separately
by Y. Mutum 02 Dec '21

02 Dec '21

Hi Elaine and Team My question relates on how we can color the 'clipped surface only' using a different color independently. This is without messing up the color of the outer surface of the model. Suppose the outer surface of the pdb-model has been colored by hydrophobicity (mlp). Then, I slice the model using the 'side view' tool. Now, using the 'surface cap' command, I can get a clipping plane which is colored 'bychain'. However, if I try to color the clipped surface using a different color, the entire hydrophobicity surface is no longer there. These are my commands below. Is there a way to color the clipped surface by a different color? If not is there a way around? The commands I have used are: >>> open 6g2j; hide all; >>> color #1 green; color /B-G,I,Q,P,R,W,q yellow; Then using the side view tool, clip the surface of the model to get a slice. I am trying to clip in the plane containing Chain D and B. >>> mlp #1; >>> surface cap true; Then, I can get a clipping plane colored by-chain. If I then type >>>color zone #1 near #1 distance 5 Then, I can get the clipped surface to change its color but this messes up the hydrophobicity of the outer surface. Thus, 1. Is there a way to color the clipped surface separately, while not messing up with the outer surface coloring (hydrophobity in this case)? 2. Suppose I want to remember this clipping plane for another ChimeraX session and would like to avoid the manual clipping using the 'Side view'. Using command line, is there a way to get back to the clipping plane? Similar to 'camera matrix' command, but, with the 'sectioned plane' also included. Thanks Yaikhomba

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measuring rotation between two homologous PDB models
by Y. Mutum 28 Nov '21

28 Nov '21

Hi Elaine and ChimeraX Team My query relates to measuring rotation between two subunits from homologous models in ChimeraX. Here, I have first aligned the two models on one of sub-domains of these multi-domain complex. Then, without moving the models, the plan is to calculate the rotation in another domain, between the 2 models, apart from measuring the translational shift. So, * Align Chain /L,M (model #1, PDB:6g2j ) and Chains /5,4 (model #2, PDB:6rfr). * Calculate rotation of Chain /F (model #1, PDB:6g2j) and Chain /B (model #2, PDB:6rfr). I am using the following commands: -- open 6g2j; open 6rfr; -- match #1/L,N to #2/5,4 pair ss; -- measure rotation #1/F toModel #2/B coordinateSystem #1/F showAxis true showSlabs true; The log report is: Position of 6g2j #1 relative to 6rfr #2 in 6g2j #1 coordinate system: Matrix rotation and translation 0.80441124 0.40360431 -0.43591986 67.76279700 0.18783349 0.52334489 0.83116106 -121.82969657 0.56359661 -0.75047565 0.34517410 202.31442783 Axis -0.83978100 -0.53070022 -0.11456502 Axis point 0.00000000 87.13355460 206.39866592 Rotation angle (degrees) 70.33834463 Shift along axis -15.42901832 Thus, ChimeraX is calculating a rotation of ¬70 degrees, which is clearly the case. The visual inspection suggests, that the rotation should be no more than ~15-20 degrees. I am not sure where I am going wrong. Could you please help? Thanks Yaikhomba

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Exporting Measure and Color Blob data
by BINGHAM Dominic 25 Nov '21

25 Nov '21

Hello, I am wanting to get the volumetric data of several blobs in a manner I can easily export and analyse. I am using the Measure and Color Blobs tool and I can see the data I need. However, I have lots of models, with lots of blobs. That means me stopping and writing down the volume data each time I click is not very efficient. So is there anyway I can export all the volume data per each selected blobs per each image into one file? Thanks, Dominic Bingham

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Match the scale of OBJ and volume
by Roden Deng Luo 24 Nov '21

24 Nov '21

Hi, As shown in the screenshot, I have opened one volume and one obj. But they should have the same scale. How can I achieve this? Thanks, Roden -- This message and its contents, including attachments are intended solely for the original recipient. If you are not the intended recipient or have received this message in error, please notify me immediately and delete this message from your computer system. Any unauthorized use or distribution is prohibited. Please consider the environment before printing this email.

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Color volume series by per voxel variance?
by Oliver Clarke 24 Nov '21

24 Nov '21

Hi all, Is there any way in either Chimera or X to calculate the per voxel variance of a volume series, and then use that to color the individual voxels in each frame? When one has a series of volumes showing a subtle conformational change - lets say identified using cryoDRGN or 3D variability analysis in cryoSPARC - it would be nice to be able to visually highlight on the map the region that is changing the most, in some kind of quantitatively sound way. Often local changes are visually apparent when looking at the maps and rotating them around, but don't necessarily stand out in a movie of the whole volume. Coloring the series of maps (which are all on the same grid) by the variance of the density value at each voxel might be one way to visualize this. Is this possible? Cheers Oli

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ChimeraX import multiple positions of the same .pdb structure
by Frey, Lukas 23 Nov '21

23 Nov '21

Dear Elaine, I have an external file with a transformation matrix (orientation and translation) for a .pdb structure and I would like to apply the transformation in ChimeraX to a .pdb file. I’m aware that ChimeraX needs a matrix like [[1,1,1],[2,2,2],[3,3,3],[x,y,z]], where the first 3 columns are the orientation the last column the x,y,z translation positions. One can load a new orientation/translation into chimeraX with the „open“ command: https://rbvi.ucsf.edu/chimerax/docs/user/formats/positions.html in the command line of chimeraX I had to type in: open path-to-file/test.positions models #1 childModels true matchNames true my test.positions file is a .txt file containing the name of the .pdb structure and transformation matrix and I already loaded the .pdb structure before I applied the transformation matrix. Below you can find the input of the transformation matrix file, called text.positions: 6y2l.pdb,-0.6515591636522021,-0.6041757901381976,-0.45873987277293393,0.09148867345316551,-0.662890582358989,0.7431055769199559,-0.7530607405054541,0.44220774578318395,0.48718767500700594,30.0,20.0,30.0 If I apply the open command in chimera somehow it leads to a distortion of the .pdb protein structure. If I check the transformation position of the model with „view matrix“, then I have the following output: view matrix camera position: 0.94464,-0.25925,-0.20113,-578.87,-0.29451,-0.94014,-0.17144,1242.4,-0.14464,0.22118,-0.96445,-8143.8 model positions: #1,-0.65156,-0.60418,-0.45874,0.091489,-0.66289,0.74311,-0.75306,0.44221,0.48719,30,20,30,#1.1,1,0,0,0,0,1,0,0,0,0,1,0,#1.2,1,0,0,0,0,1,0,0,0,0,1,0 Somehow the transformation matrix is only applied to #1 but not to #1.1 and #1.2, do you have an idea what I have to change? If I save the transformation matrix of the distorted .pdb structure via the save command: save path-to-file/test_2.positions models #1 childModels true I have the following output: 6y2l.pdb,-0.651559163652,-0.604175790138,-0.458739872773,0.0914886734532,-0.662890582359,0.74310557692,-0.753060740505,0.442207745783,0.487187675007,30,20,30 metal coordination bonds,1,0,0,0,0,1,0,0,0,0,1,0 missing structure,1,0,0,0,0,1,0,0,0,0,1,0 The goal in the future is to load several positions (1 … 100) of the same .pdb structures. Best, Lukas Lukas Frey Visiting Postdoctoral Associate UMASS Medical School Worcester Grigorieff Laboratory

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Re: [chimerax-users] meshmol in chimeraX
by Tom Goddard 23 Nov '21

23 Nov '21

Hi Vijay, The meshmol command from Chimera which converts a surface mesh from wire edges to cylinder edges (making a fake molecule) is not yet in ChimeraX. But I can add it pretty easily, maybe tomorrow if time permits. Tom Icosahedral cage shown with wires and with meshmol cylinders > On Nov 18, 2021, at 2:38 PM, Vijay Reddy <reddyv(a)scripps.edu> wrote: > > Hi Tom, > > Greetings! Hope are staying safe and healthy. > > I am finally transitioning to chimeraX. > > Could you please tell me what is the equivalent of > > the chimera command “meshmol #26 6” in chimeraX > > Many thanks, > Vijay >

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Toolshed
by Moustafa, Ibrahim M. 23 Nov '21

23 Nov '21

Dear ChimeraX, Trying to install iSolde but toolshed page seems to be down! Is there another link to https://cxtoolshed.rbvi.ucsf.edu ? ChimeraX Toolshed<https://cxtoolshed.rbvi.ucsf.edu/> Resource for Biocomputing, Visualization amd Informatics (RBVI), and its precursor, the Computer Graphics Laboratory (CGL), develops cutting-edge interactive software tools and advanced web-based computational resources that provide integrated visualizations and analyses of molecular structures and related non-structural biological information. cxtoolshed.rbvi.ucsf.edu Thanks, Ibrahim Ibrahim M.Moustafa, Ph.D. Pennsylvania State University Biochemistry & Molecular Biology Dept. Millennium Science Complex University Park State College, PA16802 Phone: (814) 863 5940 Fax: (814) 865 7927

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Question about Chimerax
by JANE LEE 22 Nov '21

22 Nov '21

Hi, I was wondering how/if I could open saved session files from Chimera in Chimerax? Also, when I tried to open a protein in Chimera, it opened. But when I tried to open the same protein in Chimerax, it only showed up as atoms and I received the message "start residue of secondary structure not found." I was wondering if you have any suggestions for troubleshooting? Thank you! Regards, Jane

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ChimeraX AlphaFold2
by Ichcharisma 20 Nov '21

20 Nov '21

Hi ChimeraX Dev I wondering if I can run oligomer prediction on ChimeraX AlphaFold features. As we can do it with others colabfold version out there. Thank you

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Feature request: windowsize to be stored with session
by mailman-bounces＠cgl.ucsf.edu 18 Nov '21

18 Nov '21

From: Vorländer,Matthias Kopano <matthias.vorlaender(a)imp.ac.at <mailto:matthias.vorlaender@imp.ac.at>> Date: November 18, 2021 at 8:47:33 AM PST Dear all, I would like to suggest that the current windowsize is associated with a ChimeraX session. This is particularly useful when making figures in a reproducible manner (if I am not mistaken, when opening a .cxs file it will open it with the same windowsize that has been used for the last chimera session, rather than the one that was used when the session was created). I am aware that the windowsize can be specified in a script file. Thanks a lot for your consideration : ) Best, Matthias

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Re: [chimerax-users] [Chimera-users] chimera, H-bonds
by Elaine Meng 18 Nov '21

18 Nov '21

> On Nov 18, 2021, at 11:37 AM, Rio Aquarius via Chimera-users <chimera-users(a)cgl.ucsf.edu> wrote: > > Dear Developer, > I have a specific task for ChimeraX. I want to show H-bonds and hide all amino acid residues. But when I hide amino acid residues, all H-bonds I need disappear. Is there a way to do what I want? Dear Rio, The H-bond displays are lines (pseudobonds) drawn between atoms. When you hide those atoms, the H-bonds are also hidden. I don't understand why you would want to display a bunch of lines in space without any atoms, as you won't be able to see most of the valuable information from the calculation. However, I will explain how to do it: In ChimeraX, there is no pseudobond option to display even when its atoms are hidden. The only way to make it look like the H-bond lines are shown when you can't see the atoms (and/or ribbons) is to make the atoms (and/or ribbons) 100% transparent with the "transparency" command. Example commands: open 2gbp hbonds reveal true transparency 100 target ar <https://rbvi.ucsf.edu/chimerax/docs/user/commands/transparency.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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getting sequences into the Structure Prediction
by Marc Pusey 17 Nov '21

17 Nov '21

Hi - I may be missing something very obvious, but... I am trying to input and use protein sequences for structure predictions using the AlphaFold feature of ChimeraX. I've not had any problems when the sequence can be obtained from a UniProt file, but several of the proteins I'm working with do not have such a file available. Additionally, there is going to come a time where I will want to see what the consequences are from making mutations to those sequences that are available from UniProt. The input gives the option of either Paste or UniProt, but I've not found a way to do a simple cut and paste to put in the sequence. I'm using a Mac running Mojave, version 10.14.6. Thanks! Marc Pusey -- Marc Pusey

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Viewing all frames of trajectory at once
by German Barcenas 17 Nov '21

17 Nov '21

Hello, I've made a trajectory of some similar frames that are stored as an .xtc file. I can upload this with my defined topology file (.pdb) and see each frame individually. Currently I can create a picture of each frame with the frame centered on some residue (SQA) with: perframe "save ~\snapshot_$1.png" frames 10;coordset #1 holdSteady /A:SQA This creates individual pictures for each frame which is nice. I was wondering how one makes a picture with all 10 frames superimposed on each other. I'd also like to change all but the 1st frame to be transparent. I'm aware of the transparent command, which I presume I'd apply to all frames except the 1st, but I'm not sure how to display all frames at once. I'm also struggling on the 1st frame only condition. This is my current attempt: perframe "transparency 0 ALL" frames 1;perframe "transparency 25 ALL" frames 9;coordset #1 holdSteady /A:SQA Thanks, -- German Barcenas Ph.D Candidate | Materials Science and Engineering Materials Modeling and Theory Group Boise State University

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Model info editing
by Eric Pettersen 16 Nov '21

16 Nov '21

Hi all, The current daily build (not 1.3 release candidate) has a new feature that may be of general interest. You can change the name/ID of a model in the Model Panel by double clicking on the corresponding field and entering a new value. --Eric Eric Pettersen UCSF Computer Graphics Lab

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Feature request regarding clipping planes
by Pranav Shah 15 Nov '21

15 Nov '21

Hi Team, Chimera has really nice clipping planes visibility and UX in comparison to ChimeraX. While it may take some effort to include the middle-click based riflling through planes shortcut, in the short term would it be possible to change the color of the clipping planes to a color that isnt gray? Currently, it is quite hard to see the clipping planes in the default view (see attached image). Best, Pranav -- Pranav Shah Postdoctoral Research Fellow. Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK

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Re: [chimerax-users] Any interest in reading ModelArchive metadata from mmCIF files?
by Tom Goddard 12 Nov '21

12 Nov '21

Hi Elaine, This is related but a little different from what Ben was asking. It is different because the template and scoring data in the mmCIF tables could be shown no matter how the mmCIF file is loaded -- it would not be limited to fetching from ModBase. Maybe Ben has an opinion about how desirable it is to put the Chimera ModBase fetch capability into ChimeraX, and whether it is more or less desirable than making the new mmCIF tables accessible in ChimeraX, to help figure out priorities. Tom > On Nov 12, 2021, at 3:05 PM, Elaine Meng <meng(a)cgl.ucsf.edu> wrote: > > Chimera had a ModBase Fetch: > > "a SwissProt, TrEMBL, GenPept or PIR accession code will be used to fetch comparative models in PDB format from ModBase (associated information will be shown in a model list)" > > https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/modbase.html <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/modbase.html> > > ...where "model list" is the same dialog as used to show Modeller results. Now that ChimeraX has a Modeller Results dialog for displaying the output from Comparative Modeling and Model Loops, could consider adding analogous Modbase fetch capability. > > I can make a ticket if anybody thinks that's a good idea. > > Elaine > > >> Begin forwarded message: >> >> From: Tom Goddard via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>> >> Subject: Re: [chimerax-users] Any interest in reading ModelArchive metadata from mmCIF files? >> Date: November 12, 2021 at 2:56:49 PM PST >> To: Ben Webb <ben(a)salilab.org <mailto:ben@salilab.org>> >> Cc: ChimeraX Users Help <chimerax-users(a)cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>> >> Reply-To: Tom Goddard <goddard(a)sonic.net <mailto:goddard@sonic.net>> >> >> >> So it looks like only ModBase would currently benefit from ChimeraX reading template sequences and alignments. I do not think it would be too hard to implement it. I've made a ChimeraX feature request for that >> >> https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/5601 <https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/5601>

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Any interest in reading ModelArchive metadata from mmCIF files?
by Ben Webb 12 Nov '21

12 Nov '21

Do you have any plans to extend ChimeraX's mmCIF reader to parse and display metadata on theoretical models, such as quality scores or the alignments to template structures? The folks at PDB have recently done a lot of work to standardize this metadata in the MA mmCIF dictionary: https://mmcif.wwpdb.org/dictionaries/mmcif_ma.dic/Index/ The dictionary has already been adopted by ModelArchive (e.g. AlphaFold2 models) and by ModBase (Modeller models) and I believe that other repositories such as SwissModel are also moving in that direction. See e.g. mmCIF downloads at https://www.modelarchive.org/doi/10.5452/ma-bak-cepc-0250 https://modbase.compbio.ucsf.edu/modbase-cgi/model_search.cgi?databaseID=Q1… (My ulterior motive: we've previously built Chimera web data files to download a ModBase model and the accompanying alignment, and display them in Chimera; now that this data is embedded in the mmCIF file, in principle ChimeraX could do this itself in a less clunky and not ModBase-specific fashion.) Ben -- ben(a)salilab.org https://salilab.org/~ben/ "It is a capital mistake to theorize before one has data." - Sir Arthur Conan Doyle

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Fit in map sequentially with global search?
by Oliver Clarke 12 Nov '21

12 Nov '21

Hi, I frequently use the "global search" option of fitmap in chimera to identify the orientation of proteins or fragments in my map. Fitmap has an option, "sequence", allowing the sequential fitting of multiple structures to a map, after subtracting the density corresponding to the previous fit, but this is not compatible with global search. Would it be possible to add an option to fitmap in ChimeraX such that it considers clashes with designated existing models? This would be useful when one is trying to fit the density of a weakly occupied binding partner in the context of a larger known structure. Presently, when one uses fitmap with global search in such a case, the binding partner frequently gets sucked in to the stronger density for the host protein, even when the density for the binding partner is visually clear. Cheers Oli

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chimera x : how to increase font size of the command line display?
by Rangarajan, Amith 12 Nov '21

12 Nov '21

Dear All, I am wondering if there is a way to increase the font size of the command line display? I found this post with tom's comment https://www.cgl.ucsf.edu/pipermail/chimera-users/2020-April/016776.html [Chimera-users] Make command-line text bigger<https://www.cgl.ucsf.edu/pipermail/chimera-users/2020-April/016776.html> Hi Lothar, I don't know what problem you are encountering using ReadStdin on Windows. It may have something to do with Windows not allowing stdin/stdout for GUI apps. www.cgl.ucsf.edu not sure if things have changed after that. thanks , amith

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saving PDB
by Noriega, Heather 11 Nov '21

11 Nov '21

Hello, I am going to attach my command line. OK, so I created a specific capsid that is not all one monomer. It has 3 different monomers in a specific ratio. I have toggled around with different options below to try to save in PDB, the save option from my understanding should be the selected only because this capsid was created using the matchmaker. I tried display only as well just to try to see if that worked. I also have used the relative model from biological assembly of 1LP3 and tried to save or not save options and have kept all consistent with hybrid 36 (default). All these options say "saved", however when i go to open any of them, they do not at all. My objective is to save the whole capsid so when I open it I can perform the density map to measure the volume inside. The weird part of this is when I open these saved creations in Chimera they will open how I want them to, but not in ChimeraX. I am not too sure why. Please help me and I hope everyone is well, have a good night. UCSF ChimeraX version: 1.3.dev202110160902 (2021-10-16) © 2016-2021 Regents of the University of California. All rights reserved. open "C:\Users\Haten\Documents\AAVgene\AAV 3B VP1 VP2 VP3 118.cxs" format session Log from Mon Nov 1 22:55:58 2021opened ChimeraX session save "C:/Users/Haten/Documents/AAVgene/why wont you open.pdb" models #2-61 displayedOnly true relModel #1 close session open "C:\Users\Haten\Documents\AAVgene\why wont you open.pdb" format pdb UCSF ChimeraX version: 1.3.dev202110160902 (2021-10-16) © 2016-2021 Regents of the University of California. All rights reserved. open "C:\Users\Haten\Documents\AAVgene\AAV 3B VP1 VP2 VP3 118.cxs" format session Log from Mon Nov 1 22:55:58 2021opened ChimeraX session save "C:/Users/Haten/Documents/AAVgene/why wont you open 2.pdb" models #2-61 selectedOnly true close session open "C:\Users\Haten\Documents\AAVgene\why wont you open 2.pdb" format pdb Thank you, Heather Noriega PhD-Pharmaceutical Science student Howard University heather.noriega(a)bison.howard.edu 520-203-1883

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An inquiry
by Victor Ejigah 11 Nov '21

11 Nov '21

Hi Elaine, I am using chimeraX for protein analysis and simulations and recently, we have a question we want to explore by first simulating before going to the wet lab. We want to conjugate a polymer of different molecular weight to an antibody and thereafter determine the impact of the MW of each polymer on the binding affinity of the mAB to its ligand. Therefore, we want to know 1) Can we create polymers of different sizes with chimera? If not, can you recommend alternatives? 2) What tool can we use for conjugation( assuming chimera can be of help)? 3) Can such conjugates be exported to Chimera1.5 for MD ensemble since Chimera X does not have this feature? I will be most glad to hear from you soon. Kind regards, Victor (PhD student @Howard University)

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vop min/max threshold
by Stapleton kevin2017/4/3 10 Nov '21

10 Nov '21

Hello everyone! just trying to get my head around a small problem, but one my brain turns into spaghetti. I am trying to save a density from molmap with a threshold range of given values. for example: open 2gbp molmap #1 10 >From the resulting density (now ID #2) I want to save the map at a very narrow threshold range. for example the current range is 0.0-0.528. But I would like to save the map with a "restricted" level of 0.26-0.27. I have been playing with the vop min/max threshold xxx set 0/1 commands but I keep getting turned around. here is what I did: open 2gbp molmap #1 10 - produces a new map ID #2 vop threshold #2 minimum 0.26 set 0 vop threshold #3 maximum 0.27 set 1 I used the set 0/1 because I want the range 0.26-0.27 to have the density values and anything outside of that to have zero. Like a mask in relion. But for my specific case relion_mask wont work as well. Somewhere I am turning the options around and it has my brain flattened. Any help is appreciated. All the best and thanks for making my science life 1Million times easier with your wonderful program :-) Kako

2 3

Improved VR support in ChimeraX
by tolung.bio＠gmail.com 09 Nov '21

09 Nov '21

Hi, The VR support in ChimeraX and meeting functionality has a great potential especially for teaching and educational purposes. Are you planning to improve that to bring it to the same level as Nanome (or close)? For example, a dedicated VR GUI interface for better VR usability? Cheers, Gökhan

2 1

Labelling w.r.t Secondary structure elements
by Gupta, Arun 09 Nov '21

09 Nov '21

Hello, I was wondering is there a quick fix way around by which we can define in an automated fashion the numbering and further labelling of secondary structural elements labels, alongside the structure, based on “dssp” described symbol notation "for example starting from α1/β1-α10/β14 " for any protein instead of manually labelling later in Power point. Thanks a lot! Arun Arun Gupta PhD, MRSC Research Fellow Challis & Lewandowski Group Chemistry Department University of Warwick Gibbet Hill Road Coventry CV4 7AL United Kingdom

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Removing and Testing Bundles
by Zeng, Jingrou 09 Nov '21

09 Nov '21

Hello, I am working on a selector bundle and need to actively reload it into ChimeraX every time I make changes to the code. I have followed the instructions on the tutorials and successfully loaded my bundle into ChimeraX using 'devel install [path]'. I then tried to reload the bundle after I have made changes to the code with commands 'devel clean [path]' followed by 'devel install [path]'. But ChimeraX didn't receive my update to the bundle. I tried reinstalling ChimeraX, the selector bundle still works without a separate installation and it doesn't register any updates I have made. I am using macOS and have experimented with both daily build and 1.2.5. Is there a way of completely removing the old version of my bundle? What is the best way to do bundle reloading and testing in ChimeraX? I also want to use the print command for debugging, but printing doesn't seem to work with the ChimeraX log, is there a separate log for this situation? Thank you for your help. Regards, Katie

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Re: [chimerax-users] Measuring volume inside virus capsid
by Tom Goddard 05 Nov '21

05 Nov '21

Hi Heather, Your "No symmetry for #1" error when you use command "sym #2 symmetry #1 copies true" is likely because you opened the 1LP3 (#1) PDB file in mmCIF format instead of using the command I suggested "open 1lp3 format pdb" which opens it in PDB format. The ChimeraX sym command currently only uses the "biological assembly" information from PDB format, not mmCIF format as described in the sym command documentation https://www.cgl.ucsf.edu/chimerax/docs/user/commands/sym.html#symmetry <https://www.cgl.ucsf.edu/chimerax/docs/user/commands/sym.html#symmetry> In the future please copy and paste commands and the error message into your email. That gives us enough info to help you and is better than a screenshot. Tom > On Nov 5, 2021, at 6:46 PM, Noriega, Heather <heather.noriega(a)bison.howard.edu> wrote: > > Hi, > > Yes, so I have read your manual about the symmetry and have been trying to do what you suggested, before you suggested it (the symmetry portion). That is why I reverted to the one-by-one. It keeps giving me this error. I have also tried using the chain /A for the symmetry and it does create the complete icosahedral, but once I try to complete the molmap it only does the single monomer. I don't know what to do. > > Thank you, > > Heather Noriega > PhD-Pharmaceutical Science student > Howard University > heather.noriega(a)bison.howard.edu <mailto:heather.noriega@bison.howard.edu> > 520-203-1883 > > > On Fri, Nov 5, 2021 at 6:26 PM Tom Goddard <goddard(a)sonic.net <mailto:goddard@sonic.net>> wrote: > Hi Heather, > > I looked at the ChimeraX session and see you opened 60 copies of your alphafold model, then ran matchmaker 60 times to align those to the 1LP3 virus capsid, then ran molmap 60 times. That is a lot of tedious work and does not get quite what you want. So here are some commands to try go get the enclosed volume. > > open 1lp3 format pdb > open ~/Downloads/ChimeraX/AlphaFold/prediction_23/best_model.pdb > matchmaker #2 to #1 > sym #2 symmetry #1 copies true > molmap #3 12 > volume #4 level 0.07 > # Choose "blob" mouse mode under the "Right Mouse" toolbar tab and right click (option key on Mac) the volume surface to color it. > surface splitbycolor #4.1 > view position #5 sameAs #4 > hide #4,5.1 model > measure volume #5.2 > -> 2.5 million cubic Angstroms > > Here I aligned a single copy of the AlphaFold model (#2) to the 1lp3 capsid monomer (#1) with matchmaker, then applied the symmetry of 1lp3 to the AlphaFold model to produce all 60 copies (#3), then made a density map from those 60 copies (#4), then set a low enough density map threshold so that their are no holes connecting the inside and outside of the capid, then colored the outside surface different from the inside with the blobs mouse mode, then split that two color surface into two pieces (outside #5.1, inside #5.2), then realigned the split surface to the density map (it was a bug that it did not preserve the alignment), then measured the volume of the inside surface. > > If you have questions about any of these commands the ChimeraX user manual has thorough documentation on all of them, so read about them. > > I described a slightly simpler case of finding the interior volume of 1lp3 on the ChimeraX Recipes web page. > > https://rbvi.github.io/chimerax-recipes/virus_volume/virusvol.html <https://rbvi.github.io/chimerax-recipes/virus_volume/virusvol.html> > > Tom > > >> Begin forwarded message: >> >> From: "Noriega, Heather" >> Subject: measuring volume >> Date: November 5, 2021 at 2:25:42 PM PDT >> To: Tom Goddard >> >> Hello Tom, >> >> I hope this email finds you well. I am very grateful for your email a couple days ago with chimeraX and trying to compute the interior volume in a virus capsid shell. I am very new to all this molecular modeling software, but am trying very hard to learn and understand. I have been working on a few different capsids particularly through alpha fold predictions on ChimeraX. I have created this one below through one-by-one aligning the predictions to create T=1 (1LP3 as biological assembly reference). Now, I one-by-one again used the molmap application for each copy and changed to volume level 0.676 and colored dark blue. My issue is when I go to measure volume it says the surface selected is wrong. I am unsure how to fix it or if I can fix it. Also, I do not know if this has anything to do with it, but I am using a Windows computer, I have noticed most of your videos are done through apple. Would this make a huge difference? I await your response and again thank you very much for your help. >> >> Thank you, >> >> Heather Noriega > > > > >> On Nov 3, 2021, at 11:49 AM, Tom Goddard <goddard(a)sonic.net <mailto:goddard@sonic.net>> wrote: >> >> Hi Heather, >> >> Here is a tricky way to compute the interior volume in a virus capsid shell in ChimeraX. >> >> open 1LP3 >> sym #1 assembly 1 copies true >> molmap #2 12 >> volume #3 level 0.676 >> # Choose "blob" mouse mode under the "Right Mouse" toolbar tab and right click (option key on Mac) the volume surface to color it. >> surface splitbycolor #3.1 >> hide #4.1 model >> measure volume #4.2 >> -> 2.6 million cubic Angstroms. >> >> The idea is to make a low resolution (12 Angstrom) density map from the atomic model, low resolution so there are not holes in the capsid, set the map threshold so there are no holes connecting the inside and outside, then color the outside layer with the "pick blob" mouse mode, then split the surface by color (producing inside and outside surfaces), then measure the volume enclosed by the inside surface. >> >> Tom >> >> Here's a cut in half view showing the interior surface produced by the above example >> >> >>> On Nov 3, 2021, at 11:21 AM, Elaine Meng via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>> wrote: >>> >>> I don't know if it would work on your specific case, but there is a "3V" server that makes maps that fill cavities and tunnels that you could try. Namely, I don't know if it works for fully enclosed cavities. >>> >>> <http://3vee.molmovdb.org/ <http://3vee.molmovdb.org/>> >>> >>> If it gave a suitable output (a map blob that fits inside your capsid) then you can use "measure volume" after opening it in ChimeraX and showing its isosurface. >>> >>> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/measure.html#volume <https://rbvi.ucsf.edu/chimerax/docs/user/commands/measure.html#volume>> >>> >>> I'm sure there are other creative ways if you think about it... like trying to make a sphere that fits inside and calculating the volume of the sphere from the standard geometric formula. >>> >>> I was trying to think of a way involving a low-resolution surface (e.g. from using "molmap" on the capsid atoms) and "volume onesmask" but couldn't come up with anything. The problem with just using a molecular surface or low-res surface from molmap is that it is hollow, and the volume calculation will just include the shell with the atoms, not the big empty part inside. >>> >>> As you can see, none of these are like a one-step thing that is already figured out for you. Part of being a PhD student is trying to solve problems that haven't been worked out for your specific situation! >>> >>> Elaine >>> >>>> On Nov 3, 2021, at 10:38 AM, Noriega, Heather via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>> wrote: >>>> >>>> What other ways can you measure the inter space of the icosahedral? >>>> >>>> Thank you, >>>> >>>> Heather Noriega >>>> PhD-Pharmaceutical Science student >>>> College of Pharmacy >>>> Howard University >>>> heather.noriega(a)bison.howard.edu <mailto:heather.noriega@bison.howard.edu> >>>> 520-203-1883 >>>> >>>> On Wed, Nov 3, 2021, 12:09 PM Elaine Meng <meng(a)cgl.ucsf.edu <mailto:meng@cgl.ucsf.edu>> wrote: >>>> Hi Heather, >>>> I guess my first question is "why would you want to do that?" If the goal is to measure the cavity volume, there may be other ways. I'm not aware of any ChimeraX capability to fill it with waters (you may have to write your own code if that's what you really want to do). >>>> >>>> In general you can count the waters (or any other residue type) in some structure using a similar method to what I described recently on the chimera-users list, except that to show the Selection Inspector you click the green magnifying glass on the top bar icons of ChimeraX instead of the lower-right corner of the Chimera window. >>>> <https://plato.cgl.ucsf.edu/pipermail/chimera-users/2021-November/018182.html <https://plato.cgl.ucsf.edu/pipermail/chimera-users/2021-November/018182.html>> >>>> >>>> I hope this helps, >>>> ELaine >>>> ----- >>>> Elaine C. Meng, Ph.D. >>>> UCSF Chimera(X) team >>>> Department of Pharmaceutical Chemistry >>>> University of California, San Francisco >>>> >>>>> On Nov 3, 2021, at 6:20 AM, Noriega, Heather via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>> wrote: >>>>> >>>>> Good morning, >>>>> I am working on trying to find a measurement inside my alphafold prediction icosahedral. My advisor mentioned using the water molecules to fill the inside and then use a counter of some sort. I have no idea how to start this, I have been reading the volume commands but am still having a hard time. Can you direct me to 1) fill only the inside of my icosahedral? and 2) how to count the water molecules inside? >>>>> Thank you, >>>> >>>> _______________________________________________ >>>> 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> >>> >>> >>> _______________________________________________ >>> 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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A couple questions
by Noriega, Heather 05 Nov '21

05 Nov '21

Good morning, I am working on trying to find a measurement inside my alphafold prediction icosahedral. My advisor mentioned using the water molecules to fill the inside and then use a counter of some sort. I have no idea how to start this, I have been reading the volume commands but am still having a hard time. Can you direct me to 1) fill only the inside of my icosahedral? and 2) how to count the water molecules inside? Thank you, Heather Noriega PhD-Pharmaceutical Science student Howard University heather.noriega(a)bison.howard.edu 520-203-1883

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alpha-fold error
by Moustafa, Ibrahim M. 05 Nov '21

05 Nov '21

Dear all, I am trying to use alpha fold in ChimeraX but I get the following error during computing multiple sequence alignmenet step: -------------------------------------------------------- TypeError ________________________________ 2 frames ________________________________ <ipython-input-1-a242dc837c9a><https://localhost:8080/#> in multiple_seq_align(dbs) 247 for i, result in enumerate(db_results): 248 from alphafold.data import parsers --> 249 msa, deletion_matrix, target_names = parsers.parse_stockholm(result['sto']) 250 e_values_dict = parsers.parse_e_values_from_tblout(result['tbl']) 251 e_values = [e_values_dict[t.split('/')[0]] for t in target_names] TypeError: cannot unpack non-iterable Msa object --------------------------------------------------------- I followed the instructions of ChimeraX tutorial. I was able to use it successfully before, but not sure why I keep getting this error. Any idea what could be wrong? I use ChimeraX version 1.3 (09-08-2021) Thanks for help Ibrahim

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Residue priority for Matchmaker alignment?
by Steven Truong 04 Nov '21

04 Nov '21

Dear ChimeraX Admins, I have a question about the Matchmaker (mmaker) command. If I wanted to specify which residues to prioritize in the alignment, how would I specify that in the command line? Is there a way to do this without changing the alignment algorithm/scoring matrix? I have tried tinkering with the matrix but wasn’t able to get it to work. I see that you can specify which chains to align, but I can’t seem to find the equivalent for residue ID numbers. Thank you for your help, Steven Truong Vendruscolo Lab Cambridge University [cid:280F6707-7208-4DBD-9A6C-ED9A0DF8E3BF]

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How to open .py file downloaded from MOLEonline in ChimeraX?
by Kate Kim 01 Nov '21

01 Nov '21

Hello, I've been using Chimera in the past for opening downloaded .py files from MOLEonline to visualize tunnels in my structure. When I try to do the same in ChimeraX, I get the following error: Traceback (most recent call last): File "/Users/katekim/Downloads/mole_channels_6Qzq10eGEqLciv3DpeS8Q_1_chimera.py", line 1, in <module> import chimera, _surface, numpy ModuleNotFoundError: No module named 'chimera' Error opening python file /Users/katekim/Downloads/mole_channels_6Qzq10eGEqLciv3DpeS8Q_1_chimera.py toolshed show Any suggestions on the best approach to visualize MOLE channels using ChimeraX? Thank you, Kate

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Making multiple icosahedral pentamers (assembly 3)
by Noriega, Heather 01 Nov '21

01 Nov '21

Hello, I am trying to make different monomer amounts of the icosahedral for my alphafold prediction. Now, I am able to use 1LP3 as my reference to create a icoshedral pentamer, but that is only 5. I would like to be able to do 10-mer, 15-mer, 20-mer, etc. I however can not seem to connect the pentamers to create the portions of virus capsid. Can you direct me? Thank you, Heather Noriega PhD-Pharmaceutical Science student College of Pharmacy Howard University heather.noriega(a)bison.howard.edu <mailto:heather.noriega@bison.howard.edu> 520-203-1883

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mmcif assemblies for alphafold prediction
by Noriega, Heather 30 Oct '21

30 Oct '21

Hello, I am trying to create an asymmetrical assembly similar to 4 and 6 with an alphafold prediction. There are no mmCIF assemblies connected with this prediction, is there a way to add the assemblies, if so how? Or is there another way to create this figure without the assembly? Thank you, Heather Noriega PhD-Pharmaceutical Science student Howard University heather.noriega(a)bison.howard.edu 520-203-1883

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Distances in the 3D map - visualisation analysis
by Dmitry Semchonok 29 Oct '21

29 Oct '21

Dear colleagues, I would like to measure the distances of within my 3D map - so I want to draw the arrows from the center of the map to the periphery in different directions and probably depth. (I want to have arrows and an length) Do you have any tips how to do that? Thank you Sincerely, Dmitry

2 1

Unit cell box
by Diego Sebastian Ferrero 27 Oct '21

27 Oct '21

Dear all, I am trying to make a figure using ChimeraX to show the contents of the unit cell in one protein structure. I would like to show the cell box with the asymmetric unit (similar to that box obtained in chimera using “Tools>Higher Order Structure>Crystal Contacts” ) but ChimeraX apparently doesn’t recognize the command returning the following message in the log window: unitcell outline Unknown command: unitcell What I’m doing wrong? Is it the right command to show the box? Thanks in advance, Diego

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ChimeraX bug report submission
by Samuel Haysom 27 Oct '21

27 Oct '21

i want to show just the CA atoms of a selection of residues (starting with the rest of the model shown as a cartoon). To do this I am trying to use a command like this: show #3/A:436,464,465,495,498,500,550,697,755,764,795,798,799@CA target a But this doesn't do anything. If I take off the @CA bit I can show all the atoms in the residue. Full .cxc is as follows: open 5ljo open 5d0o hide #1,2 atoms show #1,2/A cartoons color #1,2/A rgb(0.252,0.680,1.000) color #1,2/B rgb(0.000,0.831,0.321) color #1,2/C rgb(1.000,0.861,0.137) color #1,2/D rgb(1.000,0.400,0.100) color #1,2/E rgb(0.780,0.000,0.400) ### Align barrels ### # mmaker #2/A:435-810 to #1/A:435-810 view matrix model #1,1,0,0,0,0,1,0,0,0,0,1,0,#2,-0.82647,-0.51941,0.21716,224.85,-0.53861,0.61724,-0.57351,177.83,0.16385,-0.59096,-0.78989,191.81,#2.1,1,0,0,0,0,1,0,0,0,0,1,0 ### Color EPR regions ### color #1,2/A:424-447 green color #1,2/A:454-518 red color #1,2/A:348-423 dark orange ### Create Morph ### morph #1,2 frames 40 ### Show single mutant CA ### ### New positions ### show #3/A:436,464,465,495,498,500,550,697,755,764,795,798,799@CA target a color #3/A:436,464,465,495,498,500,550,697,755,764,795,798,799 magenta ### Existing Positions ### show #3/A:435,499,501,535,564,751,793 target a color#3/A:435,499,501,535,564,751,793 purple Log: Startup Messages --- note | available bundle cache has not been initialized yet UCSF ChimeraX version: 1.3.dev202110261153 (2021-10-26) © 2016-2021 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open 5ljo Summary of feedback from opening 5ljo fetched from pdb --- warnings | Atom H is not in the residue template for LEU /B:22 Atom H is not in the residue template for CYS /C:25 Atom H is not in the residue template for GLU /D:26 Atom H is not in the residue template for GLU /E:24 Atom H is not in the residue template for PHE /A:24 5ljo title: E. coli BAM complex (BamABCDE) by cryoEM [more info...] Chain information for 5ljo #1 --- Chain | Description | UniProt A | Outer membrane protein assembly factor BamA | BAMA_ECO45 B | Outer membrane protein assembly factor BamB | BAMB_ECOLI C | Outer membrane protein assembly factor BamC | BAMC_ECOLI D | Outer membrane protein assembly factor BamD | BAMD_ECO57 E | Outer membrane protein assembly factor BamE | BAME_ECOL6 > open 5d0o 5d0o title: BamABCDE complex, outer membrane β barrel assembly machinery entire complex [more info...] Chain information for 5d0o #2 --- Chain | Description | UniProt A | Outer membrane protein assembly factor BamA | BAMA_ECOLI B | Outer membrane protein assembly factor BamB | BAMB_ECOLI C | Outer membrane protein assembly factor BamC | BAMC_ECOLI D | Outer membrane protein assembly factor BamD | BAMD_ECOLI E | Outer membrane protein assembly factor BamE | BAME_ECOLI > hide #1,2 atoms > show #1,2/A cartoons > color #1,2/A rgb(0.252,0.680,1.000) > color #1,2/B rgb(0.000,0.831,0.321) > color #1,2/C rgb(1.000,0.861,0.137) > color #1,2/D rgb(1.000,0.400,0.100) > color #1,2/E rgb(0.780,0.000,0.400) > view matrix models > #1,1,0,0,0,0,1,0,0,0,0,1,0,#2,-0.82647,-0.51941,0.21716,224.85,-0.53861,0.61724,-0.57351,177.83,0.16385,-0.59096,-0.78989,191.81,#2.1,1,0,0,0,0,1,0,0,0,0,1,0 > color #1,2/A:424-447 green > color #1,2/A:454-518 red > color #1,2/A:348-423 dark orange > show #3/A:436,464,465,495,498,500,550,697,755,764,795,798,799@CA target a

2 1

clashes after mutagenesis
by tiger wang 26 Oct '21

26 Oct '21

Dear I am quite new to Chimera. I am using ChimeraX to do some mutagenesis in the protein with its 3D structure. After mutagenesis, the clashes were found. I tried to use tool torsion to adjust the atoms' angles and found when one clash was solved the other clashes came up. It seems it is a endless process. The question is how to correct the clashes due to mutagenesis, only manually adjust one by one using tool torsion or there is other ways to do in the same time simutaneously, such as using modeller inbeded in ChimeraX? Thanks very much for your help Sincerely Tiger Wang

2 2

Refine predicted structure by pulling
by Roden Deng Luo 26 Oct '21

26 Oct '21

Dear ChimeraX Users, There is this AlphaFold prediction: https://alphafold.ebi.ac.uk/entry/P02549. And we know this protein should be more or less in a rod-like shape rather than a globular shape: https://en.wikipedia.org/wiki/Spectrin and related literature such as https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3218374/. I wonder is there a way that we can pull the two ends of the predicted structure while maintaining the secondary structures, mostly alpha-helices in this case, inside ChimeraX? I am quite new to ChimeraX. I understand this is more fitted to an MD simulation. But I got to know there are options to fit a PDB to a density map. So I wondered if this can be achieved in ChimeraX. Best, Roden -- This message and its contents, including attachments are intended solely for the original recipient. If you are not the intended recipient or have received this message in error, please notify me immediately and delete this message from your computer system. Any unauthorized use or distribution is prohibited. Please consider the environment before printing this email.

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Re: [chimerax-users] Test files for bug report [ChimeraX] #5467: AmiraMesh
by Tom Goddard 26 Oct '21

26 Oct '21

Hi Roden, These 3 Amira files are vertex/edge/point data, not 3D lattices. The ChimeraX reader only handles 3D lattices Amira files. It does not look like our ChimeraX documentation explains this. I'll try to get this on our docs (3d lattice volume data, float, unsigned 16-bit, uncompressed only). Tom > On Oct 25, 2021, at 12:20 PM, Roden Deng Luo <deng.luo(a)kaust.edu.sa> wrote: > > Dear Tom and Andrea, > > Thanks for the quick responses. Upon the kind approval from Andrea, I attached the .am file I received from Andrea (in the format of 2.0), as well as the other two that are exported from this file (in the format of 3.0, one is in ascii as revealed by the name). > > Best regards, > Roden

2 3

Open AmiraMesh 3.0 in ChimeraX
by Roden Deng Luo 25 Oct '21

25 Oct '21

Dear ChimeraX Users, I have an AmiraMesh .am file exported from Amira 3D 2021.1 (Build date: 2021-06-21 13:21:22, SHA id: 213bd1......13c73e). When I load it into ChimeraX 1.2.5 or ChimeraX 1.3.dev202110231141, ChimeraX tells me the following error. First line of AmiraMesh file must start with "# AmiraMesh BINARY-LITTLE-ENDIAN 2.1", instead got "b'# AmiraMesh BINARY-LITTLE-ENDIAN 3.0\n'" Googling "AmiraMesh site:https://www.rbvi.ucsf.edu/pipermail/chimerax-users" shows no result. Can anyone kindly help here? Many thanks, Roden -- This message and its contents, including attachments are intended solely for the original recipient. If you are not the intended recipient or have received this message in error, please notify me immediately and delete this message from your computer system. Any unauthorized use or distribution is prohibited. Please consider the environment before printing this email.

2 5

problem with displaying secondary structures
by Elżbieta Wątor 24 Oct '21

24 Oct '21

Hi, I am trying to prepare figures for my publications and I have a problem with ss assignment. When I open structure in pymol, everything is assigned correctly. However, when I open the same structure in ChimeraX (1.2.5) I have gaps in helices and also not all of B strands are assigned correctly. I tried "dssp" command, but I probably type something wrong, because everytime I got "expected keyword" reply. Also I tried to do that manually using such commands setattr /B:5-7 res ss_type 1 and for some regions it works and for some not e.g I can change the whole helices with gaps to loop but in other way around it again gives me back helices with gaps. I've just started learning ChimeraX so probably there is some easy explanation, but I would be really grateful for your help. Best regards, Ela Wator

2 1

red-cyan 3D view in chimera X?
by Maya Shmulevitz 22 Oct '21

22 Oct '21

Hi everyone, Does anyone know how to switch to red-cyan for the structures so that my class can see them with 3D red/cyan glasses? I used to do it on the old chimera with the camera feature but cannot find the option in chimera X. Thank you!! -- Maya Shmulevitz Canada Research Chair in Molecular Virology and Oncotherapy Associate Professor University of Alberta Medical Microbiology and Immunology Li Ka Shing Institute for Virology 6-21 HMRC Edmonton, Alberta, T6G 2E1 CANADA

3 3

Running ChimeraX and a REPL
by Tom Mulvaney 21 Oct '21

21 Oct '21

Hi all, I'm wondering if anyone has any experience running ChimeraX with either a standard REPL or IPython REPL? ChimeraX already has a 'shell' tool that allows interacting with ChimeraX through a Python REPL which I've found invaluable for testing out ideas and poking around in ChimeraX in general. It would be really nice though if I could send Python code directly from my IDE to be evaluated. In order to make this work, it would be great if ChimeraX could be run from a terminal and provide a Python (or preferably IPython) REPL. As it stands, I've managed to nearly make this work with the following script: import IPython.terminal.embed IPython.terminal.embed.embed() I then run: ChimeraX --script repl.py After typing, `%gui qt5`, the ChimeraX GUI appears. I can then interact with the REPL directly from the comfort of Emacs and evaluate things - but! - the main 3D view does not end up being displayed. Does anyone know how to get the REPL and 3D stuff to work side-by-side? Kind regards, Tom

3 3

ChimeraX issue
by Amaya Cuesta, Joan 20 Oct '21

20 Oct '21

Dear ChimeraX Team, I'm trying to use ChimeraX on my VM (Ubuntu 20.04.01), but I'm having the error on the screenshot attached below. I tried to update OpenGL to 3.3, and on the terminal it seems that it installed everything but then when I try to open again I'm getting the same issue. I tried to update OpenGL following this: https://www.reddit.com/r/Ubuntu/comments/8tpq05/how_can_update_my_display_d… But always when I do the command: glxinfo | grep "OpenGL version" , it shows: "OpenGL version string: 3.1 Mesa 21.0.3". Not sure why it is not updating to 3.3 while all the other packages are upgraded. Could you please advice? Kind regards Joan Cuesta (BSc) Viral Zoonoses Research Scientist Rabies and Viral Zoonoses Group Animal & Plant Health Agency (APHA) Internal extension: 71528 External: 02087201528 | Email: Joan.Cuesta(a)apha.gov.uk<mailto:Joan.Cuesta@apha.gov.uk> Website: www.gov.uk/apha<http://www.gov.uk/apha> | Twitter: @APHAgovuk<http://www.twitter.com/aphagovuk> | Facebook: aphagov<http://www.facebook.com/aphagov> Address: APHA Weybridge, Woodham Lane, New Haw, Addlestone, Surrey KT15 3NB, UK Working hours - Monday - Friday, 9 - 5:30 pm Department for Environment, Food and Rural Affairs (Defra) This email and any attachments is intended for the named recipient only. If you have received it in error you have no authority to use, disclose, store or copy any of its contents and you should destroy it and inform the sender. Whilst this email and associated attachments will have been checked for known viruses whilst within Defra systems we can accept no responsibility once it has left our systems. Communications on Defra's computer systems may be monitored and/or recorded to secure the effective operation of the system and for other lawful purposes.

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I Have a Problem Installing ChimeraX on Debian Buster
by Stephen P. Molnar 20 Oct '21

20 Oct '21

I am attempting the installation of ChimeraC-1.2.5(chimerax-1.2.5-rc-2021.05.24) on my up to date Debian v-1064 bit platform. I open the tar.gz package without any difficulties, but when I attempt to execute ChmieraX i get the following: comp@AbNormal:~/Apps/chimerax-1.2.5-rc-2021.05.24/bin$ ./ChimeraX qt.qpa.plugin: Could not load the Qt platform plugin "xcb" in "" even though it was found. This application failed to start because no Qt platform plugin could be initialized. Reinstalling the application may fix this problem. Available platform plugins are: eglfs, linuxfb, minimal, minimalegl, offscreen, vnc, wayland-egl, wayland, wayland-xcomposite-egl, wayland-xcomposite-glx, xcb. Fatal Python error: Aborted Current thread 0x00007fcb3dafd740 (most recent call first): File "/home/comp/Apps/chimerax-1.2.5-rc-2021.05.24/lib/python3.8/site-packages/chimerax/ui/gui.py", line 157 in __init__ File "/home/comp/Apps/chimerax-1.2.5-rc-2021.05.24/lib/python3.8/site-packages/ChimeraX_main.py", line 577 in init File "/home/comp/Apps/chimerax-1.2.5-rc-2021.05.24/lib/python3.8/site-packages/ChimeraX_main.py", line 1015 in <module> File "/home/comp/Apps/chimerax-1.2.5-rc-2021.05.24/lib/python3.8/runpy.py", line 87 in _run_code File "/home/comp/Apps/chimerax-1.2.5-rc-2021.05.24/lib/python3.8/runpy.py", line 194 in _run_module_as_main Aborted comp@AbNormal:~/Apps/chimerax-1.2.5-rc-2021.05.24/bin$ xcb is installed, but the Debian v-10 default version of python is 3.7. Is this the problem? Is there a solution? Reinstalling did not fix the problem. Thanks in advance. -- Stephen P. Molnar, Ph.D. www.molecular-modeling.net 614.312.7528 (c) Skype: smolnar1

2 1

Remote Desktop usage
by Dmitry Semchonok 20 Oct '21

20 Oct '21

Dear colleagues, What could be the solution for the remote desktop of Chimera X user? One of the solution can be VNC but is there any other? Thank you Sincerely, Dmitry

2 1

coil thickness
by Lisandro Otero 18 Oct '21

18 Oct '21

Dear Chimera developer; How can I change the coil thickness in a specific loop in ChimeraX? I have tried with the Hierarchical Specifiers but I was unsuccessful? Could you please give me a command line as example? I'm using “cartoon style coil thickness XX” Thanks in advance. Best. Dr. Lisandro H. Otero PhD. Leloir Institute Foundation Av. Patricias Argentinas 435 C1405BWE Buenos Aires, Argentina Phone: +054-11-5238-7500 ext. 2552 Fax: +054-11-5238-7501

2 1

Feature suggestion - Models panel
by William Hofsøy 18 Oct '21

18 Oct '21

Hi, I would like to suggest/request that the "Models" panel should be able to rename models and change their ids from the list of models directly either through double click, like changing file names on windows, or through the right click context menu. Best regards, William

2 1

Re: [chimerax-users] labelling hbond atoms
by Rangarajan, Amith 14 Oct '21

14 Oct '21

Dear Group, I have a possibly rookie level question. When i use name flag with hbonds command to define two groups of hbonds like this hbonds (#1.1 & protein) restrict (#1.2.* ) distslop .2 reveal t rad .2 color gold name HBONDS-1 hbonds(#1.1 & ~protein) restrict(#1.2.*) distslop .2 reveal t rad .2 color magenta name HBONDS-2 then when i try to label the hbond atoms , la hbondatoms residues font "Rockwell Extra Bold" height .6 bg 20,20,20 I am not getting the labels. I am not getting any errors so i figured that it got to do with hbonds being given a name , however i am not able to fix this. welcome to hear your suggestions. thanks again., amith

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ProblemI am attempting he installation of ChmimeraX Installing ChimeraX on Debian mv-10
by Stephen P. Molnar 14 Oct '21

14 Oct '21

I am attempting the installation of ChimeraC-1.2.5(chimerax-1.2.5-rc-2021.05.24) on my up to date Debian v-1064 bit platform. I open the tar.gz package without any difficulties, but when I attempt to execute ChmieraX i get the following: comp@AbNormal:~/Apps/chimerax-1.2.5-rc-2021.05.24/bin$ ./ChimeraX qt.qpa.plugin: Could not load the Qt platform plugin "xcb" in "" even though it was found. This application failed to start because no Qt platform plugin could be initialized. Reinstalling the application may fix this problem. Available platform plugins are: eglfs, linuxfb, minimal, minimalegl, offscreen, vnc, wayland-egl, wayland, wayland-xcomposite-egl, wayland-xcomposite-glx, xcb. Fatal Python error: Aborted Current thread 0x00007fcb3dafd740 (most recent call first): File "/home/comp/Apps/chimerax-1.2.5-rc-2021.05.24/lib/python3.8/site-packages/chimerax/ui/gui.py", line 157 in __init__ File "/home/comp/Apps/chimerax-1.2.5-rc-2021.05.24/lib/python3.8/site-packages/ChimeraX_main.py", line 577 in init File "/home/comp/Apps/chimerax-1.2.5-rc-2021.05.24/lib/python3.8/site-packages/ChimeraX_main.py", line 1015 in <module> File "/home/comp/Apps/chimerax-1.2.5-rc-2021.05.24/lib/python3.8/runpy.py", line 87 in _run_code File "/home/comp/Apps/chimerax-1.2.5-rc-2021.05.24/lib/python3.8/runpy.py", line 194 in _run_module_as_main Aborted comp@AbNormal:~/Apps/chimerax-1.2.5-rc-2021.05.24/bin$ xcb is installed, but the Debian v-10 default version of python is 3.7. Is this the problem? Is there a solution? Reinstalling did not fix the problem. Thanks in advance. -- Stephen P. Molnar, Ph.D. www.molecular-modeling.net 614.312.7528 (c) Skype: smolnar1

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Question about pruned set in rmsd
by Chang Jang 14 Oct '21

14 Oct '21

Hi Chimera Users, I want to understand a result from "match" command. There are two results for 1) pruned set and 2) across all. What exactly is the pruned set in this calculation? Thanks, Chang Woon Jang

2 1

Use values printed from Log inside a script (e.g. RMSD)
by Steven Truong 12 Oct '21

12 Oct '21

Dear ChimeraX Admins, I was hoping to use the “rmsd” command in ChimeraX to measure distances between models within a .py script. Is there a way to use the output of “rmsd” (or generally any other output in Log) within the script? For example, if rmsd > 2 Angstroms, then do X. Ultimately, I am attempting to align chains between models. Because my protein is asymmetric, chain A on Model #1 might actually be chain B on Model #2. I was hoping to use “rmsd” to map one chain to the other. Is it a better idea to do this in another program and re-write chain IDs in the .PDB file? If so, what other program would be better at making RMSD calculations between .PDB chains? Thank you, Steven Truong Cambridge University

4 10

Electrostatic color key problem
by Luca Pellegrini 12 Oct '21

12 Oct '21

Hi, Coloring a surface with ‘electrostatic’ in the ‘Molecule display’ works fine. However, when I try to modify the red-blue boundary values from the default -10, 10 in the color key box, the surface color doesn’t seem to change. Can you please advise? Best wishes, Luca Luca Pellegrini, PhD Department of Biochemistry University of Cambridge Cambridge CB2 1GA UK

2 3

fold
by Ruggero Gabbrielli 11 Oct '21

11 Oct '21

Maybe it’s a little too early for that, but can’t you just add a button for folding a sequence?

2 1

"fly" interrupting "turn"
by Anderson, Jacob 11 Oct '21

11 Oct '21

Dear ChimeraX Users, Making a movie with a CXC script/command file, I find that the "fly" command interrupts the "turn" command. For example if I run these two lines: turn y 0.25 1440 fly Frame_01 400 Frame_02 400 Frame_03 400 Frame_04 400 Frame_05 Before the turn completes, the view goes to Frame_01. Is this the expected behavior? If not, would love any tips on how to complete a turn of the molecular model before flying to Frame_01 (or p1 in the ChimeraX fly user help documentation). Jacob

2 1

Re: [chimerax-users] Measuring Colocalisation using ChimeraX
by Tom Goddard 08 Oct '21

08 Oct '21

Hi Dominic, Ok, here is a way to do what you described that does not need any Python. First you place a marker at the enter of the green blob using ChimeraX Markers toolbar using the Center mode (mark center of connected surface). Once you select that mouse mode, right click on the green blob to place the marker. Then make a sphere centered at that marker with the shape command, e.g. "shape sphere center #3 radius 100". Then mask the red map to get just the part inside that sphere, e.g. "volume mask #1 surface #4". Then measure the volume enclosed in that masked map surface, e.g. "measure volume #5". You might also be interested in exactly how much red blob is inside the green blob and you could mask the red using the surface of the green to do that. Tom > On Oct 8, 2021, at 2:33 AM, BINGHAM Dominic <dominic.BINGHAM(a)univ-amu.fr> wrote: > > The custom python code sounds more applicable to what I am doing. I will give that a try but also would greatly appreciate some tips > > > To give context, I have several maps like shown above, with 2-channels showing the staining of one protein each. Each map is a synapse, and these are taken from 3D-STORM images contains several synapses. I have 3 different conditions, and I would like to compare what I measure and how it changes between these conditions. So for instance, ideally, what I would like to do is to measure from the centre of the large green structure which is colocalised to the large red structure (Circle on image above). I would then like a value to represent the relative amount of the ‘red’ protein within a set volume around the ‘green’ structure. I would then compare this value between each condition. > > So any tips on the code for python would be great here! > > Thanks so much for the help! > > Dominic > >> Le 6 oct. 2021 à 20:08, Tom Goddard <goddard(a)sonic.net <mailto:goddard@sonic.net>> a écrit : >> >> Hi Dominic, >> >> The ChimeraX Distances tools measures distances between atoms in an atomic structure. You have image data, not an atomic structure so that is why it will not report any distances. >> >> One way to proceed would be to place a marker on every connected surface piece in each of the two images, then measure distances between these centroid markers. There is code to place the markers using ChimeraX here >> >> https://rbvi.github.io/chimerax-recipes/mark_blobs/mark_blobs.html <https://rbvi.github.io/chimerax-recipes/mark_blobs/mark_blobs.html> >> >> Markers are treated just like atoms in ChimeraX so the Distance tool would work. But you want all nearby distances so you might try the Contacts tool >> >> https://www.rbvi.ucsf.edu/chimerax/docs/user/tools/clashes.html <https://www.rbvi.ucsf.edu/chimerax/docs/user/tools/clashes.html> >> >> That may not give you what you want. Very likely you would need to write some custom Python code to get exactly what you want. Probably you also want the volume enclosed in each blob. If you need tips on how to write that Python code I can advise if you give specifics of what you want. >> >> Tom >> >> >> >> >> >> >>> On Oct 6, 2021, at 4:11 AM, BINGHAM Dominic via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>> wrote: >>> >>> Hello, >>> >>> I have a problem with which I’m trying to use chimeraX to solve. I have some images of synapses with which I have super-resolved two proteins in 3D (so two images/channels). I want to quantify the colocalisation of a structure of one protein to the blobs of the other protein within a certain distance. Shown below is the non-segmented map of the 2 images of proteins. So for example I would want to quantify the colocalisation of the red blobs within a certain distance of specific larger green blobs. I want to then compare these between different conditions. >>> <Capture d’écran 2021-10-06 à 12.58.42.png> >>> >>> I have segmented the images already using "segmentat map ». I have been trying to start with the « distance » tool to measure how far one blob of protein is from the structure (Image shown below of two selected structures in just the map of one protein to practice). >>> >>> <Capture d’écran 2021-10-06 à 12.57.28.png> >>> >>> However, this doesn’t seem to work functionally as no distance is shown when I try to perform the function. Also, this function may possibly be too basic for what Im trying to do. That said, any help on how to use this function would still be greatly appreciated. >>> >>> >>> Ultimately, I think the best thing for what I would like is to be able to select a specific structure and have a measurement of all the blobs of the other protein within a defined 3D radius of this structure, and then compare this value between different conditions. I have been looking through the user manual and I can’t seem to find anything that will do something like this… I (and my PhD) would be monumentally grateful if you could possibly help me with this problem? Either by pointing me to the correct function, or even a thread that has discussed a similar problem that I may have missed? >>> >>> >>> Thanks and have a wonderful day, >>> >>> Dominic Bingham >>> PhD student at Aix-Marseille University >>> >>> _______________________________________________ >>> 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> >> >

1 0

hbonds display problem
by Maciej Basczok 08 Oct '21

08 Oct '21

Dear Expert, at the beginning would like to thank you for developing such a wonderful tool as ChimeraX is! I have one problem, namely, when hbonds calculation is run on an RNA molecule with an option to display as pseudobonds, there are many hbonds detected, but displayed are only two of them. Do I keep doing something wrong? I would be very grateful for your help. Kind regards, Maciek

2 6

polishing video
by Ruchika Bajaj 07 Oct '21

07 Oct '21

Hi Elaine Hope you're doing well !! I need to polish my videos. I am mainly using the following commands. I am just wondering if you have any more suggestions to improve the quality of the movie. Please let me know. I would appreciate your help in this regard. Thanks !! Regards Ruchika set bgColor white; lighting simple; graphics silhouettes true; lighting soft movie record supersample 3; movie encode quality higher

2 3

Re: [chimerax-users] Error on installing isolde
by benhaijing＠sina.com 07 Oct '21

07 Oct '21

Hi Greg!Thanks very much! After I deleted the two directories: (1) site-packages\ChimeraX_UI-1.2.1.dist-info and (2) site-packages\chimerax\ui in my computer, I have successfully reinstalled chimerax and isolde! It works now!Best regards, Haijing Ben ----- 原始邮件 ----- 发件人：Greg Couch <gregc(a)cgl.ucsf.edu> 收件人：benhaijing(a)sina.com, chimerax-users <chimerax-users(a)cgl.ucsf.edu> 主题：Re: [chimerax-users] Error on installing isolde 日期：2021年09月28日 06点24分 Actually, it worse than I thought. Uninstalling the user-installed version of the UI bundle is not doable from within ChimeraX. And uninstalling ChimeraX and reinstalling it doesn't help, because that only takes care of system files, not any of the user's customization. To get rid of the user installed bundle, the first step is to find where on the filesystem the files are. So start the Shell tool from the Tools / General menu. And then type in it: import chimerax chimerax.app_dirs.user_data_dir That will show where to go. For example, for me on Windows, it prints: 'C:\\Users\\gregc\\AppData\\Local\\UCSF\\ChimeraX\\1.2' So using the Windows file brower, I would navigate to C:\Users\gregc\AppData\Local\UCSF\ChimeraX\1.2. You may need to check "Hidden Items" in the View menu to navigate into AppData directory. macOS and Linux users should have an easier time going to the correct directory. And they would use forward slash, /, instead of backslash, \. The next step is to remove two directories: (1) site-packages\ChimeraX_UI-1.2.1.dist-info, and (2) site-packages\chimerax\ui. And then, when you restart ChimeraX, you'll be back to the version that came with ChimeraX. HTH, Greg On 9/27/2021 2:22 PM, Greg Couch via ChimeraX-users wrote: Hi Haijing, The output you pasted says that ISOLDE is already installed, so you don't need to install it again. It should be reinstallable, so that is a bug. If you use the graphical toolshed interface (click on More Tools... in the Tools menu), you would have seen that the install button for ISOLDE said Installed, meaning it is already installed. In this particular case, it looks you made things worse by deliberately installing an older version of the UI bundle from the toolshed than the version that came with ChimeraX. Using the graphical toolshed interface, you would have seen that it was a downgrade, which means do not install it unless necessary. Or maybe you used the Updates tool to do that? If so, you should have seen that installed version was 1.7.6 and the version on the toolshed is 1.2.1, so much older. Regardless of how you did it, to fix it, give the command: toolshed uninstall ui And that should revert back to version of the UI bundle that came with ChimeraX. The fact that you could install an older, incompatible, version of the UI bundle is a bug that is difficult to fix in the general case. Best regards, Greg On 9/26/2021 5:55 PM, benhaijing--- via ChimeraX-users wrote: Hi all！ I can’t install the plugin isolde using command 'toolshed install isolde'. Looking in indexes: https://pypi.org/simple, https://cxtoolshed.rbvi.ucsf.edu/pypi/ Requirement already satisfied: ChimeraX-ISOLDE==1.2.2 in c:\users\dell\appdata\local\ucsf\chimerax\1.2\site-packages (1.2.2) Requirement already satisfied: ChimeraX-AtomicLibrary~=3.1.0 in c:\program files\chimerax\bin\lib\site-packages (from ChimeraX-ISOLDE==1.2.2) (3.1.3) Requirement already satisfied: ChimeraX-Core~=1.2.0 in c:\program files\chimerax\bin\lib\site-packages (from ChimeraX-ISOLDE==1.2.2) (1.2.5) Requirement already satisfied: ChimeraX-Arrays~=1.0.0 in c:\program files\chimerax\bin\lib\site-packages (from ChimeraX-ISOLDE==1.2.2) (1.0) Requirement already satisfied: ChimeraX-Clipper~=0.16.0 in c:\users\dell\appdata\local\ucsf\chimerax\1.2\site-packages (from ChimeraX-ISOLDE==1.2.2) (0.16.0) Requirement already satisfied: ChimeraX-Atomic~=1.13.0 in c:\program files\chimerax\bin\lib\site-packages (from ChimeraX-ISOLDE==1.2.2) (1.13.2) Requirement already satisfied: ChimeraX-Nucleotides~=2.0 in c:\program files\chimerax\bin\lib\site-packages (from ChimeraX-Atomic~=1.13.0->ChimeraX-ISOLDE==1.2.2) (2.0.1) Requirement already satisfied: ChimeraX-mmCIF~=2.0 in c:\program files\chimerax\bin\lib\site-packages (from ChimeraX-Atomic~=1.13.0->ChimeraX-ISOLDE==1.2.2) (2.3) Requirement already satisfied: ChimeraX-ConnectStructure~=2.0 in c:\program files\chimerax\bin\lib\site-packages (from ChimeraX-Atomic~=1.13.0->ChimeraX-ISOLDE==1.2.2) (2.0) Requirement already satisfied: ChimeraX-Geometry~=1.0 in c:\program files\chimerax\bin\lib\site-packages (from ChimeraX-Atomic~=1.13.0->ChimeraX-ISOLDE==1.2.2) (1.1) Requirement already satisfied: ChimeraX-Graphics~=1.0 in c:\program files\chimerax\bin\lib\site-packages (from ChimeraX-Atomic~=1.13.0->ChimeraX-ISOLDE==1.2.2) (1.0) Requirement already satisfied: ChimeraX-PDB~=2.0 in c:\program files\chimerax\bin\lib\site-packages (from ChimeraX-Atomic~=1.13.0->ChimeraX-ISOLDE==1.2.2) (2.4.1) Requirement already satisfied: ChimeraX-AtomSearchLibrary~=1.0 in c:\program files\chimerax\bin\lib\site-packages (from ChimeraX-ConnectStructure~=2.0->ChimeraX-Atomic~=1.13.0->ChimeraX-ISOLDE==1.2.2) (1.0) Requirement already satisfied: ChimeraX-DataFormats~=1.0 in c:\program files\chimerax\bin\lib\site-packages (from ChimeraX-mmCIF~=2.0->ChimeraX-Atomic~=1.13.0->ChimeraX-ISOLDE==1.2.2) (1.1) Requirement already satisfied: ChimeraX-OpenCommand~=1.0 in c:\program files\chimerax\bin\lib\site-packages (from ChimeraX-mmCIF~=2.0->ChimeraX-Atomic~=1.13.0->ChimeraX-ISOLDE==1.2.2) (1.5) Requirement already satisfied: ChimeraX-PDBLibrary~=1.0 in c:\program files\chimerax\bin\lib\site-packages (from ChimeraX-mmCIF~=2.0->ChimeraX-Atomic~=1.13.0->ChimeraX-ISOLDE==1.2.2) (1.0.1) Requirement already satisfied: ChimeraX-SaveCommand~=1.0 in c:\program files\chimerax\bin\lib\site-packages (from ChimeraX-mmCIF~=2.0->ChimeraX-Atomic~=1.13.0->ChimeraX-ISOLDE==1.2.2) (1.4) Requirement already satisfied: ChimeraX-IO~=1.0 in c:\program files\chimerax\bin\lib\site-packages (from ChimeraX-DataFormats~=1.0->ChimeraX-mmCIF~=2.0->ChimeraX-Atomic~=1.13.0->ChimeraX-ISOLDE==1.2.2) (1.0.1) Requirement already satisfied: ChimeraX-Surface~=1.0 in c:\program files\chimerax\bin\lib\site-packages (from ChimeraX-Nucleotides~=2.0->ChimeraX-Atomic~=1.13.0->ChimeraX-ISOLDE==1.2.2) (1.0) Requirement already satisfied: ChimeraX-UI~=1.0 in c:\users\dell\appdata\local\ucsf\chimerax\1.2\site-packages (from ChimeraX-Nucleotides~=2.0->ChimeraX-Atomic~=1.13.0->ChimeraX-ISOLDE==1.2.2) (1.2.1) INFO: pip is looking at multiple versions of chimerax-pdblibrary to determine which version is compatible with other requirements. This could take a while. INFO: pip is looking at multiple versions of chimerax-pdb to determine which version is compatible with other requirements. This could take a while. INFO: pip is looking at multiple versions of chimerax-opencommand to determine which version is compatible with other requirements. This could take a while. INFO: pip is looking at multiple versions of chimerax-nucleotides to determine which version is compatible with other requirements. This could take a while. INFO: pip is looking at multiple versions of chimerax-io to determine which version is compatible with other requirements. This could take a while. INFO: pip is looking at multiple versions of chimerax-dataformats to determine which version is compatible with other requirements. This could take a while. INFO: pip is looking at multiple versions of chimerax-mmcif to determine which version is compatible with other requirements. This could take a while. INFO: pip is looking at multiple versions of chimerax-graphics to determine which version is compatible with other requirements. This could take a while. INFO: pip is looking at multiple versions of chimerax-geometry to determine which version is compatible with other requirements. This could take a while. INFO: pip is looking at multiple versions of chimerax-core to determine which version is compatible with other requirements. This could take a while. INFO: pip is looking at multiple versions of chimerax-atomsearchlibrary to determine which version is compatible with other requirements. This could take a while. INFO: pip is looking at multiple versions of chimerax-connectstructure to determine which version is compatible with other requirements. This could take a while. INFO: pip is looking at multiple versions of chimerax-clipper to determine which version is compatible with other requirements. This could take a while. INFO: pip is looking at multiple versions of chimerax-atomiclibrary to determine which version is compatible with other requirements. This could take a while. INFO: pip is looking at multiple versions of chimerax-atomic to determine which version is compatible with other requirements. This could take a while. INFO: pip is looking at multiple versions of chimerax-arrays to determine which version is compatible with other requirements. This could take a while. INFO: pip is looking at multiple versions of chimerax-isolde to determine which version is compatible with other requirements. This could take a while. The conflict is caused by: chimerax-nucleotides 2.0.1 depends on ChimeraX-UI~=1.0 chimerax-opencommand 1.5 depends on ChimeraX-UI~=1.0 chimerax-savecommand 1.4 depends on ChimeraX-UI~=1.4 To fix this you could try to: 1. loosen the range of package versions you've specified 2. remove package versions to allow pip attempt to solve the dependency conflict ERROR: Cannot install chimerax-nucleotides==2.0.1, chimerax-opencommand==1.5 and chimerax-savecommand==1.4 because these package versions have conflicting dependencies. ERROR: ResolutionImpossible: for help visit https://pip.pypa.io/en/latest/user_guide/#fixing-conflicting-dependencies WARNING: You are using pip version 21.0.1; however, version 21.2.4 is available. You should consider upgrading via the 'C:\Program Files\ChimeraX\bin\ChimeraX.exe -m pip install --upgrade pip' command. Thanks, Haijing Ben _______________________________________________ ChimeraX-users mailing list ChimeraX-users(a)cgl.ucsf.edu Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimerax-users _______________________________________________ ChimeraX-users mailing list ChimeraX-users(a)cgl.ucsf.edu Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimerax-users

1 0

Mol2 file conversion
by Marcus Agyin 06 Oct '21

06 Oct '21

Hello, I am emailing to get clarification on how I would convert a chimera file into a Mol2 file. If I’m understanding correctly, I would need to click on “File” and in the pop-up menu there would be a “save as Mol2” option, however, all that it is showing the generic “Save” option. Thanks in advance, Marcus Agyin

2 1

Measuring Colocalisation using ChimeraX
by BINGHAM Dominic 06 Oct '21

06 Oct '21

Hello, I have a problem with which I’m trying to use chimeraX to solve. I have some images of synapses with which I have super-resolved two proteins in 3D (so two images/channels). I want to quantify the colocalisation of a structure of one protein to the blobs of the other protein within a certain distance. Shown below is the non-segmented map of the 2 images of proteins. So for example I would want to quantify the colocalisation of the red blobs within a certain distance of specific larger green blobs. I want to then compare these between different conditions. [cid:5E6B5354-093F-44B8-BCD8-9C01AFDEAF72] I have segmented the images already using "segmentat map ». I have been trying to start with the « distance » tool to measure how far one blob of protein is from the structure (Image shown below of two selected structures in just the map of one protein to practice). [cid:ED6171EE-E03F-47C8-A3AE-81A7E5FC9177] However, this doesn’t seem to work functionally as no distance is shown when I try to perform the function. Also, this function may possibly be too basic for what Im trying to do. That said, any help on how to use this function would still be greatly appreciated. Ultimately, I think the best thing for what I would like is to be able to select a specific structure and have a measurement of all the blobs of the other protein within a defined 3D radius of this structure, and then compare this value between different conditions. I have been looking through the user manual and I can’t seem to find anything that will do something like this… I (and my PhD) would be monumentally grateful if you could possibly help me with this problem? Either by pointing me to the correct function, or even a thread that has discussed a similar problem that I may have missed? Thanks and have a wonderful day, Dominic Bingham PhD student at Aix-Marseille University

2 1

Hidden points present in gltf file
by Scott, Brandon L. 06 Oct '21

06 Oct '21

I'm having an issue with gltf exporting with hidden objects. The surface that is exported looks correct; however, when querying the points in the exported file all the hidden ones are there as well which is hindering a downstream analysis. Exported gltf: [cid:18a58daf-6676-4fe8-ab6c-935e631e379d] Rendered points from gltf: [cid:3bd25148-70ad-4079-885b-368e0d2c57af] 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>

2 1

Error messages when executing command file with chimerax --exit
by Guillaume Gaullier 05 Oct '21

05 Oct '21

Hello, When I run the attached command file from within ChimeraX 1.2.5 on macOS 10.15.7 (open 7otq_figure-2-supplement-2.cxc), it completes without any error. However, when I run it from the shell with 'chimerax --exit 7otq_figure-2-supplement-2.cxc', I get the attached errors in the terminal. In both cases, the figures are generated correctly, so as far as I am concerned it seems I can simply ignore these errors. But I thought you (ChimeraX developers) might need to know that this happens. This does not happen with other command files (I have been happily making movies without ever seeing these error messages), which makes me think maybe the problem is specific to this particular one? Cheers, Guillaume När du har kontakt med oss på Uppsala universitet med e-post så innebär det att vi behandlar dina personuppgifter. För att läsa mer om hur vi gör det kan du läsa här: http://www.uu.se/om-uu/dataskydd-personuppgifter/ E-mailing Uppsala University means that we will process your personal data. For more information on how this is performed, please read here: http://www.uu.se/en/about-uu/data-protection-policy

3 3

Structure Prediction on ChimeraX
by Chang Jang 04 Oct '21

04 Oct '21

Hi ChimeraX users, I am trying to find Structure Prediction -> AlphaFold but there seems no such tool. Would you please guide me on how to add the "Structure Prediction" tool on ChimeraX? Thank you. Best regards, Chang Woon Jang

2 1

can isolde work with ChimeraX 1.3 developer versions?
by Sindelar, Charles 04 Oct '21

04 Oct '21

Hi all, any chance I can persuade ChimeraX v1.3 (i.e. nightly downloads) to use the current version of Isolde? I would love to use some of the newest features of ChimX together with Isolde, but the toolshed does not allow this (says only ChimX 1.2 is allowed). Are they really incompatible? Can I perhaps "trick" the toolshed somehow? Thanks for all your work to make these fabulous tools. By the way, Tom, Eric, Elaine and team, I *love* the new tool-switching shortcuts, i.e. shift-esc and control-tab. They make my life so much easier and this is a primary motivation for my request (but other new features in 1.3 also). Cheers! Chuck --------------------- Charles V. Sindelar, Ph.D. Dept. of Molecular Biophysics and Biochemistry Yale University Bass 335 New Haven, CT 06520-8114 Lab (203) 432-3095 Fax (203) 432-5175 http://medicine.yale.edu/mbb/faculty/charles_sindelar.profile

3 2

crossfade command not working from a command file
by Guillaume Gaullier 01 Oct '21

01 Oct '21

Hello, I am using ChimeraX version 1.2.5 (2021-05-24) on macOS 10.15.7. When trying to generate a simple movie with the attached command file, I get the attached wrong result in which the crossfade command seems to fail (instead of a smooth transition, I only get a flashing black screen for a few frames). A similar problem happens with the same version of ChimeraX on Rocky Linux 8.4. Instead of loading the command file from a fresh session (with 'open command-file.cxc'), I tried to prepare my models first, and then sent the commands generating the movie all at once (separated by semi-colons). When I did it this way, I got the correct result (also attached). Is there anything I am doing wrong, or is this a bug? I am pretty sure the command file version worked correctly in a previous version of ChimeraX, because I have done this before. Unfortunately, I don’t remember which version it was (but probably 1.1, since it was just last year). I would appreciate any help with this. Thank you in advance, Guillaume När du har kontakt med oss på Uppsala universitet med e-post så innebär det att vi behandlar dina personuppgifter. För att läsa mer om hur vi gör det kan du läsa här: http://www.uu.se/om-uu/dataskydd-personuppgifter/ E-mailing Uppsala University means that we will process your personal data. For more information on how this is performed, please read here: http://www.uu.se/en/about-uu/data-protection-policy

3 6

Tiling images are stepped
by Pranav Shah 30 Sep '21

30 Sep '21

Hi, I want to create an image of multiple volumes that are tiled horizontally. However, when I run the command "tile columns 6" the volumes get arranged in a step-like manner (attached image). I do not see this happen in chimera so I am wondering if this expected behaviour in ChimeraX? I am on UCSF ChimeraX version: 1.2.5 (2021-05-24) on the M1 MacBookPro, MacOS 11.6. Best, Pranav -- Pranav Shah Postdoctoral Research Fellow. Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK

3 3

Syncing up the movement of "plane" volumes.
by Mayer, Megan 30 Sep '21

30 Sep '21

Hi ChimeraX community. I have a reconstructed tomogram which has 92 ‘Z’ slices, and a segmentation volume that has ‘374’ slices. They are both displayed as “Plane” in the volume viewer (image attached). I would like to record a movie where they are showing the same features simultaneously. I have used the command: “volume #5 planes z,0,92; volume #2 planes z,0,374 ; wait 120 ; “ However, the volumes do not move at the same time: volume 5 completes before volume 2 begins. Is there a way around this, so that I can play both volumes at the same time? Thank you for any tips! Megan

2 2

adding new trajectory format
by Radosław Giziński 30 Sep '21

30 Sep '21

Hi, Is there a way I can add custom, multi-frame trajectory format to ChimeraX so I can view multi frame trajectories? Is there some manual that could guide me through the process like this?: https://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/movie/movie.html (scroll to the bottom) Best regards, Radosław Giziński

3 2

movie encode bug on Rocky Linux 8.4
by Guillaume Gaullier 30 Sep '21

30 Sep '21

Hello, This time I am reporting what looks almost certainly like a bug. Using ChimeraX version 1.2.5 on Rocky Linux 8.4 (installed from the RHEL/CentOS 8 RPM package), I get the following error in the Log when trying to use the movie encode command (I attached a copy of the full error message in the Log): /usr/libexec/UCSF-ChimeraX/bin/ffmpeg: error while loading shared libraries: libbz2.so.1.0: cannot open shared object file: No such file or directory Turns out I definitely have libbz2 on my system, but not under the filename ChimeraX (or ffmpeg bundled with ChimeraX) is looking for: $ ls -l /usr/lib64/ | grep libbz2 lrwxrwxrwx. 1 root root 11 Apr 7 03:44 libbz2.so -> libbz2.so.1 lrwxrwxrwx. 1 root root 15 Apr 7 03:44 libbz2.so.1 -> libbz2.so.1.0.6 -rwxr-xr-x. 1 root root 73008 Apr 7 03:44 libbz2.so.1.0.6 If I create a symlink to libbz2.so.1.0.6 and name it libbz2.so.1.0, my movie encode command finishes fine and produces a movie file. So it was easy to work around this problem, but obviously it would be a lot better if it worked out of the box and the user did not have to mess with system files as root. Thank you in advance, Guillaume N?r du har kontakt med oss p? Uppsala universitet med e-post s? inneb?r det att vi behandlar dina personuppgifter. F?r att l?sa mer om hur vi g?r det kan du l?sa h?r: http://www.uu.se/om-uu/dataskydd-personuppgifter/ E-mailing Uppsala University means that we will process your personal data. For more information on how this is performed, please read here: http://www.uu.se/en/about-uu/data-protection-policy

3 3

Trackpad scaling causes unintended rotation
by Oliver Clarke 29 Sep '21

29 Sep '21

Hi, In recent versions of ChimeraX (I don't think it always did this but can't be 100% sure), when one uses pinch-to-zoom on the trackpad to scale the view, this also changes orientation, causing quite a large and unintended rotation which can be a bit disconcerting. Comparing directly with Chimera using the same model, this does not happen in Chimera. Is there some difference in how the Chimera vs X are interpreting competing trackpad gestures, and could this be adjusted in ChimeraX? Because two fingers can be used both to scale and rotate... Chimera seems to be able to figure out which the user is intending, while ChimeraX presently applies both at the same time. Cheers Oli

3 6

Possible to measure the shortest distance between two models?
by Vorländer,Matthias Kopano 28 Sep '21

28 Sep '21

Dear all, I am interested in measuring the shortest distance between two models (PDBs) without a priori knowledge of which atoms will be the closest ones. I am planning to do this for a large number of model pairs, therefore it would be great if this would be scriptable. Is this possible using ChimeraX? Thanks a lot in advance, Best, Matthias

3 6

Have a map move with its model
by Bullitt, Esther 28 Sep '21

28 Sep '21

Hi, I renamed my map and model to be #9.1 and #9.2, thinking this would make them move together. However, when I used matchmaker to match the model to align it to another model, only the model moved and the map did not. To start with, I used fitmap #9.1 inMap #9.2, but now the model is elsewhere. If I go back and do fitmap again, it moves the wrong thing (I want to put the map where the model is now, not vice versa). Is there something I am missing, or is there a different way to do this? Thanks very much. Sincerely, Esther

2 1

Flat transparency setting absent
by David William Kastner 27 Sep '21

27 Sep '21

ChimeraX community, I noticed that in ChimeraX, the “flat” transparency option that was present in Chimera has been either moved or renamed in ChimeraX. This setting made it so the transparency setting wasn’t overwhelming/distracting when focusing on details. In Chimera, it is accessed with Tools > Viewing controls > Effects > transparency > flat. Does anyone know how to achieve this effect in ChimeraX? I find the default ChimeraX transparency option to be disorienting when visualizing details. Here is a rendering comparing the two rendering styles with and without “flat” option. I look forward to your thoughts! https://www.dropbox.com/s/xrjyjnzegeeltap/transparency_comparison.png?dl=0 David --- David Kastner Ph.D. student | Bioengineering MIT | Kulik Lab kastner.io

2 5

Error on installing isolde
by benhaijing＠sina.com 27 Sep '21

27 Sep '21

Hi all！ I can’t install the plugin isolde using command 'toolshed install isolde'. Looking in indexes: https://pypi.org/simple, https://cxtoolshed.rbvi.ucsf.edu/pypi/ Requirement already satisfied: ChimeraX-ISOLDE==1.2.2 in c:\users\dell\appdata\local\ucsf\chimerax\1.2\site-packages (1.2.2) Requirement already satisfied: ChimeraX-AtomicLibrary~=3.1.0 in c:\program files\chimerax\bin\lib\site-packages (from ChimeraX-ISOLDE==1.2.2) (3.1.3) Requirement already satisfied: ChimeraX-Core~=1.2.0 in c:\program files\chimerax\bin\lib\site-packages (from ChimeraX-ISOLDE==1.2.2) (1.2.5) Requirement already satisfied: ChimeraX-Arrays~=1.0.0 in c:\program files\chimerax\bin\lib\site-packages (from ChimeraX-ISOLDE==1.2.2) (1.0) Requirement already satisfied: ChimeraX-Clipper~=0.16.0 in c:\users\dell\appdata\local\ucsf\chimerax\1.2\site-packages (from ChimeraX-ISOLDE==1.2.2) (0.16.0) Requirement already satisfied: ChimeraX-Atomic~=1.13.0 in c:\program files\chimerax\bin\lib\site-packages (from ChimeraX-ISOLDE==1.2.2) (1.13.2) Requirement already satisfied: ChimeraX-Nucleotides~=2.0 in c:\program files\chimerax\bin\lib\site-packages (from ChimeraX-Atomic~=1.13.0->ChimeraX-ISOLDE==1.2.2) (2.0.1) Requirement already satisfied: ChimeraX-mmCIF~=2.0 in c:\program files\chimerax\bin\lib\site-packages (from ChimeraX-Atomic~=1.13.0->ChimeraX-ISOLDE==1.2.2) (2.3) Requirement already satisfied: ChimeraX-ConnectStructure~=2.0 in c:\program files\chimerax\bin\lib\site-packages (from ChimeraX-Atomic~=1.13.0->ChimeraX-ISOLDE==1.2.2) (2.0) Requirement already satisfied: ChimeraX-Geometry~=1.0 in c:\program files\chimerax\bin\lib\site-packages (from ChimeraX-Atomic~=1.13.0->ChimeraX-ISOLDE==1.2.2) (1.1) Requirement already satisfied: ChimeraX-Graphics~=1.0 in c:\program files\chimerax\bin\lib\site-packages (from ChimeraX-Atomic~=1.13.0->ChimeraX-ISOLDE==1.2.2) (1.0) Requirement already satisfied: ChimeraX-PDB~=2.0 in c:\program files\chimerax\bin\lib\site-packages (from ChimeraX-Atomic~=1.13.0->ChimeraX-ISOLDE==1.2.2) (2.4.1) Requirement already satisfied: ChimeraX-AtomSearchLibrary~=1.0 in c:\program files\chimerax\bin\lib\site-packages (from ChimeraX-ConnectStructure~=2.0->ChimeraX-Atomic~=1.13.0->ChimeraX-ISOLDE==1.2.2) (1.0) Requirement already satisfied: ChimeraX-DataFormats~=1.0 in c:\program files\chimerax\bin\lib\site-packages (from ChimeraX-mmCIF~=2.0->ChimeraX-Atomic~=1.13.0->ChimeraX-ISOLDE==1.2.2) (1.1) Requirement already satisfied: ChimeraX-OpenCommand~=1.0 in c:\program files\chimerax\bin\lib\site-packages (from ChimeraX-mmCIF~=2.0->ChimeraX-Atomic~=1.13.0->ChimeraX-ISOLDE==1.2.2) (1.5) Requirement already satisfied: ChimeraX-PDBLibrary~=1.0 in c:\program files\chimerax\bin\lib\site-packages (from ChimeraX-mmCIF~=2.0->ChimeraX-Atomic~=1.13.0->ChimeraX-ISOLDE==1.2.2) (1.0.1) Requirement already satisfied: ChimeraX-SaveCommand~=1.0 in c:\program files\chimerax\bin\lib\site-packages (from ChimeraX-mmCIF~=2.0->ChimeraX-Atomic~=1.13.0->ChimeraX-ISOLDE==1.2.2) (1.4) Requirement already satisfied: ChimeraX-IO~=1.0 in c:\program files\chimerax\bin\lib\site-packages (from ChimeraX-DataFormats~=1.0->ChimeraX-mmCIF~=2.0->ChimeraX-Atomic~=1.13.0->ChimeraX-ISOLDE==1.2.2) (1.0.1) Requirement already satisfied: ChimeraX-Surface~=1.0 in c:\program files\chimerax\bin\lib\site-packages (from ChimeraX-Nucleotides~=2.0->ChimeraX-Atomic~=1.13.0->ChimeraX-ISOLDE==1.2.2) (1.0) Requirement already satisfied: ChimeraX-UI~=1.0 in c:\users\dell\appdata\local\ucsf\chimerax\1.2\site-packages (from ChimeraX-Nucleotides~=2.0->ChimeraX-Atomic~=1.13.0->ChimeraX-ISOLDE==1.2.2) (1.2.1) INFO: pip is looking at multiple versions of chimerax-pdblibrary to determine which version is compatible with other requirements. This could take a while. INFO: pip is looking at multiple versions of chimerax-pdb to determine which version is compatible with other requirements. This could take a while. INFO: pip is looking at multiple versions of chimerax-opencommand to determine which version is compatible with other requirements. This could take a while. INFO: pip is looking at multiple versions of chimerax-nucleotides to determine which version is compatible with other requirements. This could take a while. INFO: pip is looking at multiple versions of chimerax-io to determine which version is compatible with other requirements. This could take a while. INFO: pip is looking at multiple versions of chimerax-dataformats to determine which version is compatible with other requirements. This could take a while. INFO: pip is looking at multiple versions of chimerax-mmcif to determine which version is compatible with other requirements. This could take a while. INFO: pip is looking at multiple versions of chimerax-graphics to determine which version is compatible with other requirements. This could take a while. INFO: pip is looking at multiple versions of chimerax-geometry to determine which version is compatible with other requirements. This could take a while. INFO: pip is looking at multiple versions of chimerax-core to determine which version is compatible with other requirements. This could take a while. INFO: pip is looking at multiple versions of chimerax-atomsearchlibrary to determine which version is compatible with other requirements. This could take a while. INFO: pip is looking at multiple versions of chimerax-connectstructure to determine which version is compatible with other requirements. This could take a while. INFO: pip is looking at multiple versions of chimerax-clipper to determine which version is compatible with other requirements. This could take a while. INFO: pip is looking at multiple versions of chimerax-atomiclibrary to determine which version is compatible with other requirements. This could take a while. INFO: pip is looking at multiple versions of chimerax-atomic to determine which version is compatible with other requirements. This could take a while. INFO: pip is looking at multiple versions of chimerax-arrays to determine which version is compatible with other requirements. This could take a while. INFO: pip is looking at multiple versions of chimerax-isolde to determine which version is compatible with other requirements. This could take a while. The conflict is caused by: chimerax-nucleotides 2.0.1 depends on ChimeraX-UI~=1.0 chimerax-opencommand 1.5 depends on ChimeraX-UI~=1.0 chimerax-savecommand 1.4 depends on ChimeraX-UI~=1.4 To fix this you could try to: 1. loosen the range of package versions you've specified 2. remove package versions to allow pip attempt to solve the dependency conflict ERROR: Cannot install chimerax-nucleotides==2.0.1, chimerax-opencommand==1.5 and chimerax-savecommand==1.4 because these package versions have conflicting dependencies. ERROR: ResolutionImpossible: for help visit https://pip.pypa.io/en/latest/user_guide/#fixing-conflicting-dependencies WARNING: You are using pip version 21.0.1; however, version 21.2.4 is available. You should consider upgrading via the 'C:\Program Files\ChimeraX\bin\ChimeraX.exe -m pip install --upgrade pip' command. Thanks, Haijing Ben

3 3

Compound Docking in UCSF Chimera
by Ayush Patel 25 Sep '21

25 Sep '21

Sir or Madam; Recently, I was having issues with docking a ligand into a receptor due to surface calculation failures. A quick search told me to use ChimeraX. However, I am not sure how to carry out docking in ChimeraX. Could you please explain how to do this? As a side note, I do currently have AutoDock Vina. Thank you so much, Ayush Patel

2 1

Hi. I have a question about Chimera X program
by dongyoung kim 24 Sep '21

24 Sep '21

Hi. I'm researching protein 3D structure to develop the new drug. In recent, I'm using the Alphafold function in Chimera X daily version. I have 4 questions. First, if I use Alphafold to predict my important project data, is it keep secure privately? I want to keep my data secret. It shouldn't be open to anybody without me. Second, when I using Alphafold in ChimeraX, I faced some error messages that mean 'Not enough disk volume. please remove past data.'. I'm not familiar with google colab...how can I manage the disk to remove past data or expand disk volume? Third, how can I improve the speed of alphafold prediction? ChimeraX shows some resources like ram, disk. fourth, I want to operate simultaneously Alphafold prediction to predict 2 or more structures. Is it possible? If there need some pay to improve the second, third, fourth question, please let me know methods. Many thanks. -from KDY

3 2

Finding Continuous Residue Stretches
by Daniel Wells 23 Sep '21

23 Sep '21

Dear Chimerax Users: I need to find Continuous Residue Stretches between 15-25 amino acids in length on the surface of these two molecules: https://www.rcsb.org/3d-view/4MYV/1 https://www.rcsb.org/structure/3U82 Could anyone here help me perform that function on Chimerax? Thank you for your time. Sincerely, Dan Wells

2 1

Error on save
by Christophe Leterrier 23 Sep '21

23 Sep '21

HI, When I'm saving a session displaying 3D image stacks as surfaces into a csx file, I get this error: TypeError: object of type 'SurfaceUpdaters' has no len() File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/session.py", line 242, in discovery if sm is None and len(value) == 0: However if I switch the displayed stacks as volume, then there is no error on save. This is with the daily build 1.3.dev202109160803 (2021-09-16) on OSX Big Sur (Intel architecture). Thanks, Christophe

3 3

A couple questions about programming in ChimeraX
by William Hofsøy 22 Sep '21

22 Sep '21

Hi, I'm currently working on a plugin that deals with a cmm-file model and have a few questions about how to do certain things. Mainly I would like to be able to modify the model by adding new markers and links to the model. I have managed to figure out how to make new markersets and add them to the session but not how to alter existing ones aka the model that I load from the cmm file. Additionally I am making use of the marker_extra_attributes info since the cmm file im reading has attributes there that I need, but as I read in the documentation these aren't saved in sessions and I wondered if there is a way to do just that. Lastly, I was wondering if it is possible to place any mesh in the scene, for instance a cube. -William

2 3

Re: [chimerax-users] Adding a custom preset question
by Elaine Meng 22 Sep '21

22 Sep '21

Hi Boaz, Just download the file using your standard browser mechanism. When I ctrl-click on the link "kyte-doolittle_hydrophobicity.cxc" in this page: <https://rbvi.ucsf.edu/chimerax/docs/user/preferences.html#startup> ...when viewed in Firefox on Mac, I get a menu that includes "Save link as..." Choosing that brings up a little dialog that I use to save the file (without changing the name, but you can change it if you keep the cxc part) to my desired download location. On other platforms or different browsers it might be slightly different how to get the context menu with the choice to save the file, but should be similar. Or since it is a plain text file, like you said, you can also view contents and then paste them as plain text in a text-editor to create your own cxc file. However it is usually easy just to save the file from the browser as described above. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Sep 21, 2021, at 10:13 PM, Boaz Shaanan via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu> wrote: > > Hi, > You give a nice example of adding the kyte-doolittle_hydrophobicity.cxc to the custom_presets folder that I created, but where can I find this file? Or, should I paste the content of the file which is opened by pressing the link in the user guide into a file by this name ( I doubt it but nevertheless suggest it as a possibility). > Excuse my naive question, please. > Thanks, > Boaz

1 0

color zone colors by atom type
by vincent Chaptal 21 Sep '21

21 Sep '21

Dear ChimeraX users, I just subscribed so apologies if this has been asked before. When is type the command: color zone #2 near #1/A distance 5 sharpEdges false farColor blue I have the volume #2 in blue with chain A colored by atom type: i.e. with carbons in sand, oxygens in red, nitrogens in blue. I tried to follow the tutorial on youtube, downloading the model and emdb like in the tutorial, and it does work like the tutorial, meaning colored by chain. I am wodering what is going on and how to fix it? I've seen this behavior for my protein, on a PDB refined from Phenix, or from a download from the rcsb. I don't see anything special on the PDB, all the atoms are listed normally. Is it possible to assign a specific color per chain using this command? Thank you for your help. best Vincent -- Vincent Chaptal, PhD Director of GdR APPICOM Drug Resistance and Membrane Proteins Lab MMSB -UMR5086 7 passage du Vercors 69007 LYON FRANCE +33 4 37 65 29 01 http://www.appicom.cnrs.fr http://mmsb.cnrs.fr/en/

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Download Speed
by Gulzar Singh 21 Sep '21

21 Sep '21

Dear Chimera Teach team, The download speed of software is less than 200KB/s (mostly 160 KB/s). I tried both Firefox and wget. We have download limit of 11MB/s My location is Pune, India Please have a look at the issue. Regards, Gulzar Singh

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Turning off silhouettes to specific selection
by Abhilash Padvannil 17 Sep '21

17 Sep '21

Hi Is there a way to turn off the silhouettes on specific selections of a model? Thanks Abhilash.

2 1

Remove older ChimeraX Linux
by Nebojsa Bogdanovic 16 Sep '21

16 Sep '21

Hello, I am trying to reinstall the new ChimeraX on the linux system, however my previous incomplete installations are creating problems. I am not sure how to get rid of them and start anew so I would appreciate your help. I can send more context in our next correspondence. Looking forward to hearing from you. Thank you and best regards. Nebojša Bogdanović, Ph.D Department of Physiology and Biophysics, School of Medicine, Case Western Reserve University

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Interface residue selection - command line option?
by Vorländer,Matthias Kopano 15 Sep '21

15 Sep '21

Dear ChimeraX team, I am trying to selected interface residues using the “interface” tool. While doing this through the context menu of the interface plot works, I am analyzing a larger number of PDBs and am therefore looking for a way to achieve this through the command line (the contacting chains are displayed already in the log window. Essentially I wonder if it is possible to expand this to the contacting residues). Thanks a lot in advcance, Matthias

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how to save .pdb file of predicted fusion protein generated by chimerax and alphafold
by Ruby Pelingon 15 Sep '21

15 Sep '21

Hi, I tried using chimeraX and alphafold to predict my fusion protein. The result seems promising and generated a .pdb file. I would like to enquire how to save the .pdb file. I would like to open the .pdb file using pymol. Thank you. Kind Regards, Ruby Pelingon

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Re: [chimerax-users] [ChimeraX] #5218: surface color value on mouseover replaced by chain info in status line
by Elaine Meng 15 Sep '21

15 Sep '21

Hi Boaz, When a bug is reported as fixed, the next successful daily build should contain the fix. Occasionally the fixer might forget to do all the steps to get it in that day, but it is supposed to be in there. Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Sep 15, 2021, at 8:14 AM, Boaz Shaanan via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu> wrote: > > Hi Tom, > Thanks a lot. Is this fix already implemented in the Chimerax daily build? > Cheers, > Boaz > > Boaz Shaanan, Ph.D. > Dept. of Life Sciences > Ben Gurion University > Beer Sheva, Israel > > On 14 Sep 2021 17:26, ChimeraX <ChimeraX-bugs-admin(a)cgl.ucsf.edu> wrote: > #5218: surface color value on mouseover replaced by chain info in status line > ----------------------------------+------------------------- > Reporter: Elaine Meng | Owner: Tom Goddard > Type: defect | Status: closed > Priority: high | Milestone: > Component: UI | Version: > Resolution: fixed | Keywords: > Blocked By: | Blocking: > Notify when closed: | Platform: all > Project: ChimeraX | > ----------------------------------+------------------------- > Changes (by Tom Goddard): > > * status: assigned => closed > * resolution: => fixed > > > Comment: > > Fixed. > > Made surface value status message suppress chain description status > messages on mouse hover. > > -- > Ticket URL: <https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/5218#comment:3> > ChimeraX <https://www.rbvi.ucsf.edu/chimerax/> > ChimeraX Issue Tracker > _______________________________________________ > ChimeraX-users mailing list > ChimeraX-users(a)cgl.ucsf.edu > Manage subscription: > https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users

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Fwd: Display of actual values of APBS electrostatic potential projected on protein surface
by Boaz Shaanan 13 Sep '21

13 Sep '21

Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben Gurion University Beer Sheva, Israel ---------- Forwarded message ---------- From: בעז שאנן <bshaanan(a)bgu.ac.il> Date: 9 Sep 2021 17:39 Subject: Display of actual values of APBS electrostatic potential projected on protein surface To: ChimeraX-users-request(a)cgl.ucsf.edu Cc: Hi, Is there a way in Chimerax to know the actual APBS electrostatic potential values in various points on the surface? Is there such feature already in Chimerax that I missed? Such feature is essential (I think) to monitor subtle changes in surface potential following mutations or other variations (pH, salt concentration etc.). If it's not there yet, could you please add it to the (enormous, I guess) to-do list? In Chimera this is done by moving the cursor to the various points of interest, a feature that I found most useful (and helpful in convincing color blind referees 😉). Cheers, Boaz Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel E-mail: bshaanan(a)bgu.ac.il Phone: 972-8-647-2220 Fax: 972-8-647-2992 or 972-8-646-1710

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Re: [chimerax-users] Problems with Measuring Angles in ChimeraX
by Elaine Meng 10 Sep '21

10 Sep '21

> On Sep 10, 2021, at 11:41 AM, liangb2 <liangb2(a)rpi.edu> wrote: > > Hi Elaine: > I'm new to ChimeraX for Cryo-EM data. Currently, I imported my tomogram (.mrc file) into ChimeraX and acquired a density map of it. I was able to get the x,y,z coordinates of the three points of interest. However, I was not able to find ways to measure the angle among the three points on the tomogram density map. I have looked up tutorials, but all of those I have found are for proteins. > > Can you please provide some help on how I can measure the angle among three points on the density map? I would really appreciate your help. > Thank you for your time! > Best, > Biqing Liang Hi Biqing, Welcome to ChimeraX! We recommend using the chimerax-users(a)cgl.ucsf.edu address for asking questions (CC'd here so you don't need to do anything). Depending on the question, other people might want to see the answer, or give better answers than mine, or I might not know the answer at all. I don't know how you got the X,Y,Z coordinates for those three points. The way I know how to do it: You can put several "markers" (balls, fake atoms) at points on the surface, and/or at peaks in the density values. Then you can select any 3 of the markers (Shift-Ctrl-click on them) and then use the "angle" command: angle sel <https://rbvi.ucsf.edu/chimerax/docs/user/commands/angle.html> The way to put markers on interactively is first to go to the Markers toolbar across the top of the ChimeraX window. The different icons assign different ways of adding markers by mouse click. For example, clicking the third from left icon in the Markers toolbar assigns the right mouse button (= trackpad + Alt on Windows, trackpad + command key on Mac) to adding markers on the surface. See the following for what the different icons mean and explanation of markers: <https://rbvi.ucsf.edu/chimerax/docs/user/tools/markers.html> <https://rbvi.ucsf.edu/chimerax/docs/user/tools/markerplacement.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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Question.
by Yunsik Kang 10 Sep '21

10 Sep '21

Hello, My name is Yunsik Kang, and I am a postdoc in Marc Freeman's lab at the Vollum Institute. I would love to use ChimeraX to predict the structure of my protein of interest. I watched all the YouTube videos and tried to run the program. Unfortunately, my protein is 5005 amino acids in humans and 2958 aa in yeast. I get a message "Please use the full AlphaFold system for long sequences." My question is what is the best way to approach this problem? Should I cut the protein in half and run the program? In one of the videos, it mentions after 700 aa it will have problems. Will it work if I get Colab-Pro? Or would the server crash no matter what. I am not a structural biologist, but I hope the structure can help be predict me with my research. Thank you, Yunsik

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Help with Volume Series
by Ioannis Skalidis 10 Sep '21

10 Sep '21

Greetings to all! I am trying to play a volume series data in ChimeraX (daily build). I open the multiple .mrc frames and they are automatically grouped, but then, when I use the vseries play command, I get an error message that I have not specified a volume series. What am I doing wrong? Should I open the frames differently? I also tried to open them with the open command, a wildcard character for the frame names and vseries true modifier but even then, it only opens the first frame, which I found very strange as well. Could somebody offer some advice? It would be greatly appreciated! Cheers, Yiannis. -- Skalidis Ioannis, MSc Biochemistry & Cryo-EM Scientist PhD Candidate Kastritis Laboratory for Biomolecular Research Cryo-Electron Microscopy & Computational Structural Biology ________________________________________________ Martin-Luther-Universität Halle-Wittenberg Biozentrum, Room A.2.21 IWE ZIK HALOmem NWG III "Kryo-Elektronenmikroskopie an Membranproteinkomplexen" Weinbergweg 22, 06120 Halle tel: +49 345 5524986 web (Lab): https://blogs.urz.uni-halle.de/kastritislab/ web (HALOmem): https://www.halomem.de/en/

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Re: [chimerax-users] [ChimeraX] #5198: Transparent background not transparent when selection outline shown
by Zhao, Bingchun (NIH/VRC) [F] 10 Sep '21

10 Sep '21

Hi, Tom, I received this below email reported that this bug has been fixed. Do I need to download the latest version and re-install the ChimeraX? Thank you very much! Best, Bingchun On 9/9/21, 9:35 PM, "ChimeraX" <ChimeraX-bugs-admin(a)cgl.ucsf.edu> wrote: #5198: Transparent background not transparent when selection outline shown --------------------------------------+------------------------- Reporter: bingchun.zhao@… | Owner: Tom Goddard Type: defect | Status: closed Priority: normal | Milestone: Component: Graphics | Version: Resolution: fixed | Keywords: Blocked By: | Blocking: Notify when closed: | Platform: all Project: ChimeraX | --------------------------------------+------------------------- Changes (by Tom Goddard): * status: assigned => closed * resolution: => fixed Comment: Fixed. Offscreen rendering was making a framebuffer with no alpha channel, even though for image save it already had an offscreen framebuffer with alpha channel. Made offscreen check and not create a new framebuffer if we are already using an offscreen framebuffer. -- Ticket URL: <https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/5198#comment:3> ChimeraX <https://www.rbvi.ucsf.edu/chimerax/> ChimeraX Issue Tracker

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outline the interface region in chimeraX
by Zhao, Bingchun (NIH/VRC) [F] 09 Sep '21

09 Sep '21

Hi, I wonder if there is a way to outline the interface region in ChimeraX like below: [cid:image001.png@01D7A597.5344EDF0] Previously, I did this in photoshop, but can we label the interface regions with those lines in ChimeraX? Thank you very much! Bingchun Bingchun Zhao, PhD Postdoctoral, VF Biodefense Research Section VRC/NIAID/NIH Bldg 40, Room 2607B 40 Convent Drive Bethesda, MD 20892 Tel: 301-761-7649 Email: bingchun.zhao(a)nih.gov<mailto:bingchun.zhao@nih.gov>

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Re: [chimerax-users] getting AlphaFold predictions
by Elaine Meng 09 Sep '21

09 Sep '21

Hi Yk, Forwarding to chimerax-users(a)cgl.ucsf.edu since I don't have a good answer for this currently. (We prefer you use that address for questions unless they include some data that needs to stay private.) Thanks! Elaine > On Sep 9, 2021, at 1:57 PM, Yunsik Kang <kangy(a)ohsu.edu> wrote: > > > Hi Elaine, > > Thank you again! > > I did open it and using ChimeraX I can see the pdb files and see the structure! It is amazing! > > One question. > > Since my protein is massive and this is just parts of my protein, is there a way ChimeraX can stitch it all together? > > Like Tristan says it is 1400 residues each, can I perhaps somehow stitch the whole thing together? > > Yk > > -----Original Message----- > From: Elaine Meng <meng(a)cgl.ucsf.edu> > Sent: Thursday, September 9, 2021 8:12 AM > To: Yunsik Kang <kangy(a)ohsu.edu> > Cc: meng Elaine <meng(a)cgl.ucsf.edu> > Subject: [EXTERNAL] Re: [chimerax-users] getting AlphaFold predictions > > Hi Yunsik, > I do not know the answer to your questions. We are not the developers of AlphaFold or the AlphaFold database. We only added tools in ChimeraX to connect to them. > > Maybe there is information at the AlphaFold database about what's in their download. I have never downloaded these myself. > <https://www.alphafold.ebi.ac.uk/download> > > All I know is that "tar" is a way of putting multiple files together and that you have to "untar" to get them apart. This is a standard computer file thing, not related to any specific kind of files. > > Usually if you doubleclick the tar file your computer will automatically untar it and make some new folder or folders containing the files. You would need to have enough space available on your computer for the large number of files. > > I don't know how they are named but maybe there is a README file that comes with it, or if not, you may need to look at the files with a text editor. Maybe they have the Uniprot IDs of the proteins somewhere in the names or header text of the file. > > Elaine > ----- > Elaine C. Meng, Ph.D. > UCSF Chimera(X) team > Department of Pharmaceutical Chemistry > University of California, San Francisco > > >> On Sep 8, 2021, at 7:36 PM, Yunsik Kang <kangy(a)ohsu.edu> wrote: >> >> Hi Elaine, >> >> Thank you for the fast response. My proteins are not found in the Alphafold search. >> >> I am new to this so bear with me. I downloaded the human TAR file as Tristan has said, but have no idea how to search or even start looking for my protein. >> >> Could you help? Or is this something I need professional help with? >> >> Would it help to tell you the protein I am interested in? >> >> Thank you again. >> Yunsik >> >> From: Elaine Meng <meng(a)cgl.ucsf.edu> >> Sent: Wednesday, September 8, 2021 3:44 PM >> To: Yunsik Kang <kangy(a)ohsu.edu> >> Subject: [EXTERNAL] Fwd: [chimerax-users] getting AlphaFold >> predictions >> >> Forwarding in case you did not get Tristan's reply below: >> >> >> Begin forwarded message: >> >> From: Tristan Croll via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu> >> Subject: Re: [chimerax-users] getting AlphaFold predictions >> Date: September 8, 2021 at 3:17:28 PM PDT >> To: ChimeraX Users Help <ChimeraX-users(a)cgl.ucsf.edu> >> Reply-To: Tristan Croll <tic20(a)cam.ac.uk> >> >> The human protein will be in the EBI-Alphafold2 database, but not accessible to the search tool. For human proteins (and only human, so far) longer than ~2000 residues, the predictions are provided as multiple 1400-residue fragments starting at residue 1, 201, etc.. The only way to get those right now is to download the tarball of the complete set of human protein predictions, and find them in there. >> >> >> On 8 Sep 2021, at 23:08, Elaine Meng via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu> wrote: >> >> Hi Yunsik, >> I don't know where/how you can run a prediction for such a long sequence, maybe others can comment on that. However: >> >> First make sure there is not already a predicted structure for that protein in the AlphaFold Database! E.g. try the Search button on the AlphaFold tool and see if the same UniProt entries as you are interested in are found. The database includes human and other well-studied species (maybe also the yeast you mentioned, depending on the exact species). If the prediction is already in the database, there is no need to run a new calculation. >> >> ChimeraX AlphaFold tool: >> <https://rbvi.ucsf.edu/chimerax/docs/user/tools/alphafold.html> >> >> I hope this helps, >> Elaine >> ----- >> Elaine C. Meng, Ph.D. >> UCSF Chimera(X) team >> Department of Pharmaceutical Chemistry University of California, San >> Francisco >> >> >> On Sep 8, 2021, at 2:45 PM, Yunsik Kang via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu> wrote: >> >> Hello, >> >> My name is Yunsik Kang, and I am a postdoc in Marc Freeman’s lab at the Vollum Institute. >> >> I would love to use ChimeraX to predict the structure of my protein of interest. I watched all the YouTube videos and tried to run the program. >> >> Unfortunately, my protein is 5005 amino acids in humans and 2958 aa in yeast. I get a message “Please use the full AlphaFold system for long sequences.” >> >> My question is what is the best way to approach this problem? Should I cut the protein in half and run the program? In one of the videos, it mentions after 700 aa it will have problems. Will it work if I get Colab-Pro? Or would the server crash no matter what. >> >> I am not a structural biologist, but I hope the structure can help be predict me with my research. >> >> Thank you, >> Yunsik >> >> >> _______________________________________________ >> 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 >> > >

1 0

Save pdb file
by Zhao, Bingchun (NIH/VRC) [F] 09 Sep '21

09 Sep '21

Hi, First, I wanna thank you for all your work to develop ChimeraX, it’s so powerful. I do have a question and would like to have your input. I opened a EM density map (.mrc) and two pdb files in chimerax (version 1.2), then fit all the pdb models into the EM map. Then, I hide the EM map, only show the pdb models after fitting, and then I would like to save these all pdb files in a new pdb file with all position information after fitting. Would you please give me any direction how to do this? I tried saving them, but only partial pdb files saved, also tried combine commend, but it said no such commend. Thank you very much! Best, bingchun Bingchun Zhao, PhD Postdoctoral, VF Biodefense Research Section VRC/NIAID/NIH Bldg 40, Room 2607B 40 Convent Drive Bethesda, MD 20892 Tel: 301-761-7649 Email: bingchun.zhao(a)nih.gov<mailto:bingchun.zhao@nih.gov>

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error saving a surface
by Diego Amaya 08 Sep '21

08 Sep '21

Hi, I'm running a python script in --nogui and --script mode and I'm getting an error when doing rc(session, 'save surface.stl format stl'). The error message is : *QGuiApplication::font(): no QGuiApplication instance and no application font set.Segmentation fault* I'm working with debian 10 and I used the production release 1.2.5-1 Thanks in advance for the help. -- Diego A. Amaya Ramírez -- *Aviso legal:* El contenido de este mensaje y los archivos adjuntos son confidenciales y de uso exclusivo de la Universidad Nacional de Colombia. Se encuentran dirigidos sólo para el uso del destinatario al cual van enviados. La reproducción, lectura y/o copia se encuentran prohibidas a cualquier persona diferente a este y puede ser ilegal. Si usted lo ha recibido por error, infórmenos y elimínelo de su correo. Los Datos Personales serán tratados conforme a la Ley 1581 de 2012 y a nuestra Política de Datos Personales que podrá consultar en la página web www.unal.edu.co <http://www.unal.edu.co/>.* *Las opiniones, informaciones, conclusiones y cualquier otro tipo de dato contenido en este correo electrónico, no relacionados con la actividad de la Universidad Nacional de Colombia, se entenderá como personales y de ninguna manera son avaladas por la Universidad.

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capture reply from run(session, command)
by Sean Connell 08 Sep '21

08 Sep '21

Hello I was wondering if it is possible to capture the output that goes to the log when you run the python command run(session, command). For example if I run: run(session, "mmaker #2/A to #1/A”) Can I store in a variable the reply in the log file that has information about the RSMD? Sean

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distance between centers of mass using python API
by Diego Amaya 08 Sep '21

08 Sep '21

Hello, I'm trying to compute the distance between the centers of mass of two residues using the python API. I tried two different ways : 1. *rc(session, 'define centroid :43 massWeighting true name AA1')rc(session, 'define centroid :35 massWeighting true name AA2')rc(session, 'distance AA1 AA2') * 2. *rc(session, ' measure center :43 mark true name AA1')rc(session, 'measure center :35 mark true name AA2')rc(session, 'distance AA1 AA2')* But I get this error in the third line in both cases : *chimerax.core.errors.UserError: Missing or invalid "objects" argument: invalid objects specifier * What is wrong ? Thanks in advance. -- Diego A. Amaya Ramírez -- *Aviso legal:* El contenido de este mensaje y los archivos adjuntos son confidenciales y de uso exclusivo de la Universidad Nacional de Colombia. Se encuentran dirigidos sólo para el uso del destinatario al cual van enviados. La reproducción, lectura y/o copia se encuentran prohibidas a cualquier persona diferente a este y puede ser ilegal. Si usted lo ha recibido por error, infórmenos y elimínelo de su correo. Los Datos Personales serán tratados conforme a la Ley 1581 de 2012 y a nuestra Política de Datos Personales que podrá consultar en la página web www.unal.edu.co <http://www.unal.edu.co/>.* *Las opiniones, informaciones, conclusiones y cualquier otro tipo de dato contenido en este correo electrónico, no relacionados con la actividad de la Universidad Nacional de Colombia, se entenderá como personales y de ninguna manera son avaladas por la Universidad.

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Question about use of ChimeraX
by Jonathan Choong 07 Sep '21

07 Sep '21

Hi there, Hope you are doing well. I just had a question regarding ChimeraX that I was hoping to get some clarity on. I was wondering whether it was possible to use ChimeraX commands (such as open, run, save) in the system command line without actually opening the application interface? Thanks, hope to hear back from you. Kind regards, Jonathan

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Re: [chimerax-users] [Chimera-users] matchmaker for more than one chain
by Elaine Meng 03 Sep '21

03 Sep '21

Hi Mani, There is a different e-mail address for ChimeraX questions: it is chimerax-users(a)cgl.ucsf.edu CC'd here. Responses below... > On Sep 2, 2021, at 2:22 AM, manikandank via Chimera-users <chimera-users(a)cgl.ucsf.edu> wrote: > > Hi ChimeraX-users, > I have used recently the mmaker cmd to align two pdb each have multiple chains as below. > > mmaker #12/L,M,N to #5/S,A,B matrix blosum-62 showAlignment true > > But the sequence view shows only the alignment of chain L and S. > > 1. I would like to have aligned sequences of all chains used in mmaker alignement. Your command above does not use all the chains for fitting, it only chooses the single pair of chains that gives the best sequence-alignment score to superimpose the two models. The other chains might look superimposed but it is only because they moved along with the ones that were actually used for the fit. To use all three pairs of chains, you need to also use the "pairing ss" option: mmaker #12/L,M,N to #5/S,A,B matrix blosum-62 showAlignment true pair ss Then you would get three pairwise sequence-alignment windows: L/S, M/A, and N/B. matchmaker or mmaker command <https://rbvi.ucsf.edu/chimerax/docs/user/commands/matchmaker.html> pairing options <https://rbvi.ucsf.edu/chimerax/docs/user/commands/matchmaker.html#options> > > 2. Is it possible to open the saved RMSD header values in a file later just to color the pdb? Yes, but with several steps so it may not be that convenient. Probably easier just to save and restore the ChimeraX session (which includes the sequence alignment windows). Also remember if you move the structures relative to each other, the RMSD values will change. However, if you really want to save the RMSD values to file after you showed sequence alignments and header, then you could save them as an attribute file (that could be reopened/applied later): <https://rbvi.ucsf.edu/chimerax/docs/user/commands/save.html#attributes> The attribute name is seq_rmsd as explained here: <https://rbvi.ucsf.edu/chimerax/docs/user/tools/sequenceviewer.html#headers> > > 3. Do mmaker align entire pdb based on selected chains and Can calculate RMSD for all residues in the pdb? For the first question, 3A: yes, depending on the "pairing" option as explained above. For the second question, 3B, I'm not sure what you want. Remember that the main purpose of matchmaker is to superimpose the structures well, and then it happens to also give the RMSD over the positions that it chose to use, which are shown in the pinkish boxes on the sequence alignment. By default it uses fit iteration and discards loops that don't superimpose well in space. Matchmaker only gives the RMSD over the positions it uses. You could tell it to use all positions, but that would change the superposition. If you like the default superposition (that does not use all of the positions), you can use a separate command "rmsd" to measure RMSD over any sets of atoms that you want, without moving the structures or changing the superposition. Or, if you really want to use all of the positions in the sequence alignment for the fitting, you would have to use matchmaker option "cutoff none" ... but that usually does not give the best superposition. cutoff option <https://rbvi.ucsf.edu/chimerax/docs/user/commands/matchmaker.html#cutoffDis…> rmsd command (calculate RMSD in current positions, no fitting) <https://rbvi.ucsf.edu/chimerax/docs/user/commands/rmsd.html> Matchmaker only gives alpha-carbon RMSD. The rmsd command can give RMSD for any sets of atoms that you want, alpha-carbons only, or backbone only, or all atoms, as long as you give equal numbers of atoms from the two structures. However, it can be tricky to specify the correct sets of atoms if the residue numbering or residue types are different between the two structures. So you might want to first use "mmaker" with whichever options give you the best superposition, and then to measure RMSD over all positions in the alignment (which might not be used in the matchmaker fit), use the "rmsd" command afterward. > > 4. I also would like to change the displayed text for the sequence name. Presently it puts the filename as sequence name. > > [similar to 'Edit sequence name' in the sequence viewer in chimera] Sorry, there is no way yet to change the displayed sequence name in ChimeraX. > > Please let me know how this can be done. > thank you very much > with kind regards > Mani. 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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bundle dependency not installed
by Lagerwaard, I.M. (Ilse) 02 Sep '21

02 Sep '21

Hello, I'm currently developing a bundle with a dependency on pandas. Even though I included this dependency in my bundle_info.xml file, I get "ModuleNotFoundError: No module named 'pandas'". For now, I have installed pandas on the ChimeraX console via the command prompt. For future distribution, however, it would be nice if it were immediately installed together with the bundle. I would greatly appreciate your help with this issue. Thanks in advance, Ilse

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Re: [chimerax-users] output mmCIF file
by Elaine Meng 02 Sep '21

02 Sep '21

> On Aug 31, 2021, at 1:50 PM, Liu, Xiangan <Xiangan.Liu(a)uth.tmc.edu> wrote: > > Hi, > I have issue to output the models I build in pdb formation to mmCIF formation. I did not provide the sequences in orginal pdb files. Could please let me know what is the problem and how to fix it? > Thanks, > Xiangan > ---------- > File "/usr/lib/ucsf-chimerax/lib/python3.8/site-packages/chimerax/mmcif/__init__.py", line 89, in save > mmcif_write.write_mmcif(session, path, **kw) > File "src/mmcif_write.pyx", line 145, in chimerax.mmcif.mmcif_write.write_mmcif > File "src/mmcif_write.pyx", line 149, in chimerax.mmcif.mmcif_write.write_mmcif > File "src/mmcif_write.pyx", line 542, in chimerax.mmcif.mmcif_write.save_structure > KeyError: ('a1', 'RPGMMDSQEFS') > > KeyError: ('a1', 'RPGMMDSQEFS') > > File "src/mmcif_write.pyx", line 542, in chimerax.mmcif.mmcif_write.save_structure Hi Xiangan, We recommend using the chimerax-users(a)cgl.ucsf.edu address for questions (CC'd on this message, so you don't need to do anything this time). The address you used is just for commercial licensing. Actually, if you get a traceback like this, you can usually use ChimeraX menu: Help... Report a Bug instead of sending e-mail. You may need to attach your session file so that we can reproduce the problem. I don't know the answer, so I'm using this address to share your question with the others. Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco

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ChineraX saves huge session files
by Dror Noy 31 Aug '21

31 Aug '21

Hi Recently, ChimeraX on my Mac (macOS Catalina) started saving very large session file. Regardless of the size of the pdb file I load - the session file is 124 MB even for small 2-3 MB pdb files. I’d appreciate any help. Thanks Dror

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Region-wise specific sub-coloring of SS elements
by Gupta, Arun 30 Aug '21

30 Aug '21

Dear ChimeraX team, Is there an easier way around by which we can do region-wise specific sub-coloring of secondary structural elements within a large protein instead of using the tedious way of identifying the secondary structural elements and then describing the residue wise specific selection of set of residues related to secondary structure elements? I am aware that we can do coloring of specific secondary structure elements in ChimeraX by following commands for e.g “color helix “darkcyan” targ c”. But, I am looking forward to do coloring, let’ say “all the helices within a protein from residues 1-300 as dark cyan and residues 300-500 as blue” Thanks!!! Arun Arun Gupta PhD, MRSC Research Fellow Challis & Lewandowski Group Chemistry Department University of Warwick Gibbet Hill Road Coventry CV4 7AL United Kingdom

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Adding labels in chimera X?
by rob.gruninger＠gmail.com 27 Aug '21

27 Aug '21

I am trying to figure out how to add labels to a figure in chimeraX. It was easy in the older Chimera using 2d labels but I can’t find a similar function in chimeraX and the website seems to be down so I can’t access documentation. Any direction for how I can do this? I’m wanting to add residue labels to some specific residue (catalytic and substrate binding site residues) I want to point out in a paper Thanks Sent from my iPhone

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ChimeraX site down?
by Jonathan Sheehan 27 Aug '21

27 Aug '21

It might be pointless to send this query to the list (if it runs on the same server), but are you aware of any problems with your webserver right now? I'm trying to get the files for the latest density-fitting tutorial here: www.cgl.ucsf.edu According to this site, I'm not the only one having trouble reaching it: https://www.isitdownrightnow.com/cgl.ucsf.edu.html It claims it's "Down for everyone" and "for more than a week." Thanks! -Jonathan

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Save cropped map visible coordinates
by Isabelle Phan 26 Aug '21

26 Aug '21

Hello, I have 2 maps that I want to combine into a single one. I cropped each map by reducing the box size. I now want to save the map that is displayed. Impossible?! “Save” fails to keep the relative orientation of the display. I get 2 cropped maps that are no longer correctly oriented with respect to each other. "volume add” also fails to preserve the relative orientation. The volume resample sounds like it could be helpful, but I don’t understand how to get the grid values that match the displayed box. I’ve now tried multiple options for over 5 hours solid and am at my wits’ end. Any hints greatly appreciated. Isabelle

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ChimeraX Bundle
by Mirko Plößer 26 Aug '21

26 Aug '21

Dear ChimeraX Team, my name is Mirko Ploesser, I am a Phd student in the Frankgakis group at the BMLS (Buchmann Institue for Molecular Life Sciences) in Frankfurt (Germany) and currently working on a ChimeraX bundle. Thanks to your detailed tutorial on how to develop bundles, I have already made a good progeress in doing so. Currently, however, I am stuck with a problem that I hanve't found a solution to yet. I would be very thankful if you could give me advice on how to progress. The problem is described as follows: I click a set of markers in a volume (tomogram as an EM file) and save the corresponding positions. At those positions I want to load different and smaller volumes (also EM Files). The information about those smaller volumes - position and rotation - I have saved in a different file (a motivelist in also an EM format). Now I am stuck with the problem on how to update the rotation angles when I use the tool "Rotate model" using the right mouse. I know that the corresponding rotation matrix is printed in the log. Is there any way that I can use the information given to the log in my bundle code? Also, since we already have a working version of the bundle in Chimera, I found the module "openModel" very useful. Unfortunately I haven't been able to find an equivalent module in ChimeraX. So I guess there is a different approach to this used in ChimeraX. I would be very happy if you could also help me out in this regard. Thank you very much in advance for your time and effort. I am looking forward to hearing from you soon. Best, Mirko Ploesser

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How to make nucleotides same color?
by Visvaldas K. 25 Aug '21

25 Aug '21

I couldn't find how to change the default coloring of the nucleotides in ChimeraX. I'd like the color of all nucleotides to be blue like in the "old" Chimera: multiple colors distract from the details I am trying to convey. Is it possible? Best regards, Visvaldas

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ChimeraX File Error :: .vdb File Not Recognized
by Olivia Leland 24 Aug '21

24 Aug '21

Hello, I’m trying to upload a .vdb file from the Virus Particle Explorer databank. To my understanding, I should be able to upload a .vdb file for visualization. Every time I try to open said file, however, it returns the error: Is there a setting I haven’t activated in order to upload this file properly? Additionally, I’m unable to connect the software to the internet so I can’t use File>Fetch By ID... (it won’t show up for me) Do you have any suggestions on how to fix this? Best, Olivia Leland (she/her) Doctoral Student || Fraden Lab Martin A. Fisher School of Physics Brandeis University Waltham, MA 02453

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identifying surface residues
by Elaine Meng 23 Aug '21

23 Aug '21

On Aug 23, 2021, at 2:54 PM, Brian Yang <by2289(a)columbia.edu> wrote: > > Dear Dr. Meng, > I hope you are doing well. My name is Brian. I am a senior at Columbia University. I am currently doing research at the Columbia University Medical Center. I am contacting you because I have a few questions about using Chimera X. > > I am trying to use Chimera X to identify surface residues on a protein. [...] > > I have been looking through the Chimera API, and I found this method that I think could work: > https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/surfnorm.html > > However, I'm not able to figure out how to do the Attribute Calculator in Chimera X, nor am I able to get the SES area. > > I saw your response in this email chain: > https://www.rbvi.ucsf.edu/pipermail/chimerax-users/2020-September/001484.ht… > > and I have tried it, but this is only for SAS area. > > So my questions are: > Do you think the surfnorm method is appropriate? If so, how would I achieve the Attribute Calculator functionality in Chimera X? If not, could you give me a better approach to remove these surface residues? > > Thank you for your time! > > Kind regards, > Brian Yang > Hi Brian! For asking questions about ChimeraX, we recommend using the address chimerax-users(a)cgl.ucsf.edu (CC'd here so you don't need to do anything this time) unless you are including something that needs to remain private. I edited out some details about your project above just in case. ChimeraX does not calculate solvent-excluded surface area (SESA) nor does it have an Attribute Calculator tool. However, if all you want to do is to identify which residues are on the surface, you could: (1) calculate solvent-accessible surface area (SASA) per residue. Command "measure sasa protein setAttribute true" or something like that. The "protein" part is that so waters, ligands, etc. are not enclosed in the calculated surface. The "setAttribute true" part assigns values to a residue attribute named "area" so that you can do the next step, although it could be omitted since it is already true by default. There are various other options too. <https://rbvi.ucsf.edu/chimerax/docs/user/commands/measure.html#sasa> (2) delete all residues with SASA greater than some value. You wouldn't be normalizing to a percentage exposed since we don't have the values to use for the denominator, but just the raw amount of solvent-accessible area. So you may want to tinker around with what value of the cutoff gives you reasonable results. <https://rbvi.ucsf.edu/chimerax/docs/user/commands/select.html> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/atomspec.html#attributes> Example: open 4hvp measure sasa protein setAttribute true show hide ~protein hide ribbons sel ::area>20 color sel red color ~sel white ~sel ... see what you think, or try some other value... sel ::area>15 color sel red color ~sel white ~sel When you figure out what value you want to use, you could delete those residues, e.g. delete ::area>15 ...or if you're not sure what to use as a single cutoff and may want to process several times at different cutoffs, you can just write out all of the residues and their area values to an "attribute file"... see <https://rbvi.ucsf.edu/chimerax/docs/user/commands/save.html#attributes> However, if you really need a % exposure value normalized to account for different residue sizes, you would need to stick with Chimera, at least for now. 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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Labelling w.r.t Residue description
by Gupta, Arun 23 Aug '21

23 Aug '21

Dear ChimeraX team, How can we label the PDB structure in ChimeraX based on the selection as well as "description or residue type". I tried the specific "residues selection" for a PDB structure first and then typed the following command "label @ca residues attr residuename". I could get the residue numbering for the selected residues. But, I failed to get the residue description for the specific selected residues such as "residue 59 should be labelled as His59". Also, I noticed the "size " of the residue numbers "label " is bit small. How can we increase the " font size" ? Please find attached pic. Thanks!!! Arun Arun Gupta PhD, MRSC Research Fellow Challis & Lewandowski Group Chemistry Department University of Warwick Gibbet Hill Road Coventry CV4 7AL United Kingdom

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ChimeraX for Windows 10 Not Starting
by Mason Long 20 Aug '21

20 Aug '21

Hi, We're having problems getting ChimeraX to run on Windows 10 21H1. Each time we try running it, the cursor spins for a second or so and then nothing happens. I checked the Event Viewer and see every time we try running it an error event shows up in the Windows Application Error Event Log. Here's the output that shows up in the log for each of those versions: ---------------------------------------- Faulting application name: ChimeraX.exe, version: 1.2.5.0, time stamp: 0x60ab2a1d Faulting module name: Qt5WebEngineCore.dll, version: 5.15.2.0, time stamp: 0x5fad38ab Exception code: 0x80000003 Fault offset: 0x000000000014baff Faulting process id: 0x2b14 Faulting application start time: 0x01d795f43b7d3176 Faulting application path: C:\Program Files\ChimeraX 1.2.5\bin\ChimeraX.exe Faulting module path: C:\Program Files\ChimeraX 1.2.5\bin\lib\site-packages\PyQt5\Qt\bin\Qt5WebEngineCore.dll Report Id: db7d3af7-6986-47ed-ba27-3ce5e6bfcbae Faulting package full name: Faulting package-relative application ID: ---------------------------------------- Faulting application name: ChimeraX.exe, version: 1.1.0.0, time stamp: 0x5f5afaf7 Faulting module name: Qt5WebEngineCore.dll, version: 5.12.9.0, time stamp: 0x5ee3364a Exception code: 0x80000003 Fault offset: 0x0000000001989fb3 Faulting process id: 0x25d4 Faulting application start time: 0x01d795f5be3a354e Faulting application path: C:\Program Files\ChimeraX 1.1\bin\ChimeraX.exe Faulting module path: C:\Program Files\ChimeraX 1.1\bin\lib\site-packages\PyQt5\Qt\bin\Qt5WebEngineCore.dll Report Id: 5284e8f0-d191-4d3d-a49f-a93dc84117b0 Faulting package full name: Faulting package-relative application ID: ---------------------------------------- Faulting application name: ChimeraX.exe, version: 1.3.0.0, time stamp: 0x611f7fb2 Faulting module name: Qt5WebEngineCore.dll, version: 5.15.2.0, time stamp: 0x5fad38ab Exception code: 0x80000003 Fault offset: 0x000000000014baff Faulting process id: 0x2940 Faulting application start time: 0x01d795f6781afa93 Faulting application path: C:\Program Files\ChimeraX 1.3.dev202108200941\bin\ChimeraX.exe Faulting module path: C:\Program Files\ChimeraX 1.3.dev202108200941\bin\lib\site-packages\PyQt5\Qt\bin\Qt5WebEngineCore.dll Report Id: c07bfcd1-8b63-4e87-9217-a1a77cc449f8 Faulting package full name: Faulting package-relative application ID: ---------------------------------------- As you can see, this happens on both of the most recent production versions of ChimeraX (1.2.5 and 1.1.0.0) as well as on the latest daily build (1.3.dev202108200941) as of 8/20/2021. Please let me know if there's any more information you need from us. Thanks, Mason -- Mason Long Information Technology Consultant ITS Client Technology Natural Resources Building 211C Humboldt State University 1 Harpst St. Arcata, CA 95521 (707) 826-5636 (email only for now) Create a new request for help at http://www.humboldt.edu/ithelp

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Re: [chimerax-users] Automated Fitting of models into maps and saving fits with a correlation score > X
by Tom Goddard 18 Aug '21

18 Aug '21

Hi Matthias, When opening a script with the forEachFile option you can use $file in the script which will be replaced by the file basename. So in your script use fitsearch #2 in #1 resolution 20 search 1000 cutoff 0.9 save Tomo_fitted_$file_%d.pdb This is described in the forEachFile documentation https://www.rbvi.ucsf.edu/chimerax/docs/user/commands/open.html#forEachFile <https://www.rbvi.ucsf.edu/chimerax/docs/user/commands/open.html#forEachFile> Tom > On Aug 18, 2021, at 7:57 AM, Vorländer,Matthias Kopano <matthias.vorlaender(a)imp.ac.at> wrote: > > Dear Tom, > > Thank you again for the code for saving PDBs above a certain correlation score sing the fitmap command! I am now trying do use this on a large number of input volumes, and it’s working well except that I have a problem with naming the saved PDBs. So, my approach is the following: > > Open ChimeraX_Daily in no-gui mode > Type “open FitPDBinVolume.cxc foreach *.mrc” > The script FitPDBinVolume.cxc is very simple and looks like this: > > open 7apk > open /Volumes/matthias.vorlaender/Scripts/Chimera/fit_search.py > fitsearch #2 in #1 resolution 20 search 1000 cutoff 0.9 save /Volumes/plaschka/shared/data/em/Krios/20210616_endoTHO_tomo/Visualisation/mapping_back_using_imod/test/Tomo_fitted_%d.pdb > > What I would like to achieve is that the fitted PDBs are saved with a base name that matches that of the opened .mrc. Is there an easy way to do that? > > Thanks a lot in advance, > Best, > Matthias > > > From: ChimeraX-users <chimerax-users-bounces(a)cgl.ucsf.edu <mailto:chimerax-users-bounces@cgl.ucsf.edu>> on behalf of "Vorländer,Matthias Kopano via ChimeraX-users" <chimerax-users(a)cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>> > Reply to: "Vorländer,Matthias Kopano" <matthias.vorlaender(a)imp.ac.at <mailto:matthias.vorlaender@imp.ac.at>> > Date: Tuesday, 27. July 2021 at 07:40 > To: Tom Goddard <goddard(a)sonic.net <mailto:goddard@sonic.net>> > Cc: "chimerax-users(a)cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>" <chimerax-users(a)cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>> > Subject: Re: [chimerax-users] Automated Fitting of models into maps and saving fits with a correlation score > X > > Hi Tom, > > Thanks so much, that's amazing! > > To be clear, I am not searching tomograms, I am searching artificial tomograms that contain perfect "molmaps" of my protein of interest, so they are free of noise. Trying this in Chimera gave very good fits when asking for for enough initial placement. > > Thanks a lot for your help, > Best, > Matthias > > Holen Sie sich Outlook für Android <https://aka.ms/AAb9ysg> > > From: Tom Goddard <goddard(a)sonic.net <mailto:goddard@sonic.net>> > Sent: Tuesday, July 27, 2021 12:15:13 AM > To: Vorländer,Matthias Kopano <matthias.vorlaender(a)imp.ac.at <mailto:matthias.vorlaender@imp.ac.at>> > Cc: chimerax-users(a)cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu> <chimerax-users(a)cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>> > Subject: Re: [chimerax-users] Automated Fitting of models into maps and saving fits with a correlation score > X > > Hi Matthias, > > You can run ChimeraX command scripts or Python scripts without a GUI, just start it at the shell with the "--nogui" option, for example > > chimerax --nogui mycommands.cxc > > I made some example Python code that runs fitmap search and saves PDB files for each unique fit with correlation over 0.9. > > https://rbvi.github.io/chimerax-recipes/fit_search/fit_search.html <https://rbvi.github.io/chimerax-recipes/fit_search/fit_search.html> > > I don't expect this to be a good way to search tomograms. It will be very inefficient. Template matching code designed for that problem is likely to work much better. Such code usually uses Fourier space methods to search all translations at once, so it can be much faster and more thorough. Even with that optimization it takes a long time to do the rotational search. > > Tom > > Example search of monomers in 14-mer GroEL. > > > > > > On Jul 25, 2021, at 9:05 AM, Vorländer,Matthias Kopano via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>> wrote: > > Dear all, > > I have a set of 100 “artificial” tomograms, each containing approx 100 copies of a simulated density map of my protein of interest. I would like to fit each tomogram with the PDB of my POI, and save copies for all fits with a correlation score > 90%. Using the fitmap command in Chimera and then manually selecting the fits that meet the criterium works, but takes quiet a long time for a larger amount of data. I wonder if this could be automated, and if somehow would be able me to put together a script (is it possible to execute such tasks in a non-gui way, by submitting it to a cluster so that it could be parallelized?). > > Thanks a lot in advance, > Best, > Matthias > _______________________________________________ > 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] How to adjust chimeraX's loop display style?
by Elaine Meng 17 Aug '21

17 Aug '21

Hi Xiangan, Sorry no, there is no way to smooth the loops (coil) parts of a ribbon or cartoon. Currently only strands can be smoothed. By "smoothed" I mean that the path of the ribbon may not follow the CA atoms exactly, which can cause problems when the sidechains are displayed. In Chimera when the sidechains were displayed with ribbon, you could get unrealistically long or short CA-CB bonds. So in ChimeraX we decided it was more important to have an accurate CA-CB bond length when sidechains are displayed. In the helix and coil (loop) there is no smoothing option so the ribbon is exactly on the CA positions. Strands have a smoothing option turned on by default, because people expect them to be drawn as mostly straight, and if strands are not smoothed, they are very ripply. In ChimeraX when the strands are smoothed but sidechains are shown, the CA atoms that fall off the ribbon are shown with a connecting "tether" instead of stretching or shrinking the CA-CB bond artificially. This is discussed in the "cartoon" help, see the "smooth" for how to adjust strand smoothing and "cartoon tether": <https://rbvi.ucsf.edu/chimerax/docs/user/commands/cartoon.html> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/cartoon.html#tether> I investigated whether I could make a smoother representation with the "shape tube" command, but was unsuccessful. Sorry for the inconvenience -- I'm hoping that explaining the reasons might make it less annoying. :-) Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Aug 17, 2021, at 1:12 PM, Liu, Xiangan <Xiangan.Liu(a)uth.tmc.edu> wrote: > > Hi, > ChimeraX's default loop style shows very cursive. I like the way loop shows in chimera. > Is there any way to make chimeraX's loop display straighter? > Thanks, > Xiangan > > <image.png>

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Chimerax for Ubuntu 21.04
by jobiph 17 Aug '21

17 Aug '21

Dear all, thank you for your fast and thorough answers. I reinstalled lifbffi7 and libllvm6.0 and now Chimerax works. Thanks a lot! Kind regards Jonas

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Re: [chimerax-users] Chimerax for Ubuntu 21.04
by Gabriel Goetten 16 Aug '21

16 Aug '21

Hi, I was able to run chimeraX on ubuntu 21.04 by installing the following package https://answers.launchpad.net/ubuntu/hirsute/amd64/libllvm10/1:10.0.1-6 Then you just need to download chimerax of the following version Ubuntu 20.04 (Linux) 64-bit from their website (deb package). Gabriel

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Chimerax for Ubuntu 21.04
by jobiph 16 Aug '21

16 Aug '21

Dear all, is the current version of Chimera for Ubuntu (20.04) compatible with the 21.04 Ubuntu release? If i try to install the 20.04 version a weird dependency error pops up and I can't install the missing library because on the canonical website it states that this library is deprecated. Thank you for your help and kind regards Jonas

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All-numeric residue names
by Tristan Croll 16 Aug '21

16 Aug '21

Was just looking at 2rg6, which happens to have a ligand with an all-numeric 3-character ID (287)... clearly not much thinking went into allowing that. Anyway, does the residue selection syntax have a way to disambiguate residue *number* 287 from residue *name* 287?

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Coulombic color combined surface
by W. C. 13 Aug '21

13 Aug '21

ChimeraX has no way to color ONE continous surface formed by combining multiple chains with coulombic or hydrophobic. It always color each chain surface separatly . Even though I generated a surface of combined chains by "surface enclose" command, ChimeraX still colors each chian seperately. In Chimera (not ChimearX), I could use surfcat to combine chains, generate one surface for combind chains, and color the surface as one continous. However, that could color large set of molecules. So please make ChimeraX can do the same.

3 3

(no subject)
by Haaris Ahsan Safdari 12 Aug '21

12 Aug '21

Rrg together with the university international realty of

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Morphing with ligands
by Volodymyr Dvornyk 10 Aug '21

10 Aug '21

Dear Colleagues, Tried to do morphing of the following structures: 6rdc, 6rep, and 6rd9. All three have the same ligands: ADP, ATP, Mg, and Zn. However, the resulting model lacks all of them. Any thoughts and/or suggestions? Thank you. Volodymyr ________________________________ DISCLAIMER: This electronic mail transmission contains confidential information intended only for the person(s) named. Any use, distribution, copying or disclosure by any other person is strictly prohibited. If you received this transmission in error, please notify the sender by reply e-mail and then destroy the message. Opinions, conclusions, and other information in this message that do not relate to the official business of Alfaisal University shall understand to be neither given nor endorsed by Alfaisal University. The contents of any attachment to this e-mail may contain software viruses, which could damage your own computer system. While "Alfaisal University" has taken every reasonable precaution to minimize this risk, we cannot accept liability for any damage which you sustain as a result of software viruses. You should carry out your own virus checks before opening the attachment.

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Trying to open .py files on Windows gives cPickle error
by Carnes, Jason 09 Aug '21

09 Aug '21

Hello, I am collaborating with someone using ChimeraX on a Mac. Their only option to save modified files results in a .py file extension. When I try to open .py files on my Windows install of ChimeraX I get an error: "ModuleNotFoundError: No module named 'cPickle'" Is there a way to manually install cPickle on my Windows computer that will allow me to open the .py files, or are Mac & PC not compatible? Thanks, Jason Jason Carnes, PhD Research Scientist IV | Center for Global Infectious Disease Research Seattle Children's Research Institute 206-884-3137 OFFICE CONFIDENTIALITY NOTICE: This e-mail, including any attachments, is for the sole use of the intended recipient(s) and may contain confidential and privileged information protected by law. Any unauthorized review, use, disclosure or distribution is prohibited. If you are not the intended recipient, please contact the sender by reply e-mail and destroy all copies of the original message.

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Difficulties Visualizing Isosurfaces from Cube File - Nathan Wood
by Nathan Wood 09 Aug '21

09 Aug '21

Dear ChimeraX I was having difficulty attempting to visualize computationally generated electrostatic potential isosurfaces originating from a Gaussian *.cube file. I tried to open the cube file from the shell only for it to incompletely visualize. I can provide an image if necessary. I found the following correspondence concerning cube files and isosurfaces, but unfortunately I am unable to resolve the issues of the cube file visualizing. https://www.rbvi.ucsf.edu/pipermail/chimerax-users/2021-April/002126.html <https://www.rbvi.ucsf.edu/pipermail/chimerax-users/2021-April/002126.html> https://www.rbvi.ucsf.edu/pipermail/chimerax-users/2020-May/001110.html <https://www.rbvi.ucsf.edu/pipermail/chimerax-users/2020-May/001110.html> I was curious if anyone has had experience with cubefiles. Any assistance would be greatly appreciated, Very Respectfully, Nathan Wood

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Superimpose
by Wisoot Chanit 08 Aug '21

08 Aug '21

Dear ChimeraX team, I am having a quesition. I am going to superimpose 2 monomers of P domain of norovirus GII.3 into a template PDB 6if5, but the template showed that information of its chains are missing. What should I do to make a dimer into 6if5. This is different from PDB 3mfg, which was a templete I used for my previous paper. Thank you. Jay

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Re: [chimerax-users] Saving 300dpi high resolution images with ChimeraX
by Elaine Meng 04 Aug '21

04 Aug '21

Hi Nada, ChimeraX questions should be sent to chimerax-users(a)cgl.ucsf.edu (CC'd here so you don't need to do anything this time). ChimeraX does not set the dpi. You just figure out the number of pixels you need and then save in pixels. I.e. if you want 3 inches wide at 600 dpi then you know you need 1800 pixel width, e.g. save myfile.png width 1800 If you open the resulting image file in just about any general image application like Photoshop, Gimp, or Mac Preview (etc.) then you can set the "resolution" or "dpi", but it's really the number of pixels you save in the first place that matters. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Aug 4, 2021, at 10:04 AM, Bejar, Nada <nbejar(a)houstonmethodist.org> wrote: > > Hello, > I am Nada, a postdoctoral fellow at Houston Methodist. > > I saw your name in this thread. https://www.rbvi.ucsf.edu/pipermail/chimerax-users/2020-January/000816.html > I tried your suggestion, but any number I put on width would still give me a 96dpi. > > I switched to the old Chimera and I can change the unit to print unit and that resolves the issues, but I have all my work done on ChimeraX. > > I do need to make figures today and help would be much much appreciated. > > Nada Bejar, Ph. D. > Postdoctoral Fellow > Kiss RNA Lab > Houston Methodist Research Institute > 6670 Bertner Avenue > Houston, TX 77030 USA

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Re: [chimerax-users] Error in ChimeraX application installation linux ubuntu
by Elaine Meng 04 Aug '21

04 Aug '21

Hi Vanessa, Please send ChimeraX questions to chimerax-users(a)cgl.ucsf.edu (CC'd here, so no need to do anything this time). Since I don't know the answer, I kept waiting for somebody else to answer your question... and didn't notice until now that you had sent it to only me. Thanks, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Aug 1, 2021, at 1:51 AM, Vanessa Roy <vanessaroy(a)mail.tau.ac.il> wrote: > > Dear ChimeraX development team, > > We encountered issues while installing ChimeraX on our server and wanted to ask whether you could help us understand what the problem is? We haven't yet found a solution to our problem. > Here is the output after installation: > > # /home/apps/chimerax-1.2.5-rc-2021.05.24/bin/ChimeraX > X11 connection rejected because of wrong authentication. > qt.qpa.xcb: could not connect to display localhost:10.0 > qt.qpa.plugin: Could not load the Qt platform plugin "xcb" in "" even though it was found. > This application failed to start because no Qt platform plugin could be initialized. Reinstalling the application may fix this problem. > > Available platform plugins are: eglfs, linuxfb, minimal, minimalegl, offscreen, vnc, wayland-egl, wayland, wayland-xcomposite-egl, wayland-xcomposite-glx, xcb. > > Fatal Python error: Aborted > > Current thread 0x00007f479c05d740 (most recent call first): > File "/home/apps/chimerax-1.1/lib/python3.7/site-packages/chimerax/ui/gui.py", line 119 in __init__ > File "/home/apps/chimerax-1.1/lib/python3.7/site-packages/ChimeraX_main.py", line 500 in init > File "/home/apps/chimerax-1.1/lib/python3.7/site-packages/ChimeraX_main.py", line 919 in <module> > File "/home/apps/chimerax-1.1/lib/python3.7/runpy.py", line 85 in _run_code > File "/home/apps/chimerax-1.1/lib/python3.7/runpy.py", line 193 in _run_module_as_main > Aborted (core dumped) > > We would greatly appreciate your advice on how to solve this issue. > > Many thanks for your help! > > Best, > Vanessa > -- > Vanessa Roy > Gil Ast Lab > Department of Human Molecular Genetics and Biochemistry > Sackler Faculty of Medicine | Tel Aviv University

4 3

Maps comparison
by Dmitry Semchonok 04 Aug '21

04 Aug '21

Dear colleagues, I have 2 cryo-em maps of different resolutions. What will be the correct strategy to compare them and what are the tools and steps? Thank you Sincerely, Dmitry

2 1

C-alphas rendered as dots
by Pranav Shah 03 Aug '21

03 Aug '21

Hi Team, I am working with a huge model (and a correspondingly huge map), which makes the handling on my GPU accelerated desktop an agonisingly frustrating experience. In order to speed up simple (rigid-body) fitting of the map and model, I decided to use the -C-alpha trace of the pdb. However, the pdb gets rendered as a bunch of disconnected dots whereas the same pdb in Chimera is rendered correctly with all things. Is this a normal behaviour for ChimeraX? I could use Chimera, but I prefer the way ChiemraX handles large maps as compared to Chimera. In the absence of a quick fix, would there be a way to increase the size of the atoms? Best, Pranav -- Pranav Shah Postdoctoral Research Fellow. Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK

4 8

Showing C-alphas
by Casey 30 Jul '21

30 Jul '21

I am trying to show a single sphere at c-alpha carbons for some point mutants that i designed. When I use the command: show /a:473,476,477 atoms I can see all the atoms in chain A for residues 473, 476, 477. Using: show /a:473,476,477@cb atoms I can show "two spheres" for the c-alpha and c-beta carbon. When I use: show /a:473,476,477@ca atoms nothing happens and i don't see any spheres. If I show the full atom and then do: hide /a:473,476,477@ca* atoms Just the c-alpha sphere gets hidden. Why is it that i can't just show the c-alpha spheres? Unfortunately for my figure i make silhouettes of my model and so i can't just hide the other atoms by making them fully transparent

2 1

Re: [chimerax-users] Automating Map segment
by Tom Goddard 30 Jul '21

30 Jul '21

To group by connectivity looks like you need to add d._group_con.value = True To figure out this stuff you would need to look at the Segger user interface code, it is in the ChimeraX distribution (under site-packages/chimerax/segger/segment_dialog.py) or on GitHub https://github.com/tomgoddard/segger/blob/master/Segger/src/segment_dialog.… <https://github.com/tomgoddard/segger/blob/master/Segger/src/segment_dialog.…> Tom > On Jul 30, 2021, at 10:42 AM, Sam W Marchant <smarchant(a)UCSD.EDU> wrote: > > Thanks so much im trying to group by connectivity and I am having trouble finding the right line of code to add that ability. Any thoughts? > >> On Jul 29, 2021, at 3:56 PM, Tom Goddard <goddard(a)sonic.net <mailto:goddard@sonic.net>> wrote: >> >> Hi Sam, >> >> I did an initial port of Segger from Chimera to ChimeraX (also called Segment Map) but that code was written by Greg Pintilie and he has not worked the ChimeraX version so there is no new command to run it in a script. It would probably not be too hard to write some Python to run it. The Chimera script mentioned in the mailing list is attached to my message about it. >> >> https://plato.cgl.ucsf.edu/pipermail/chimera-users/2017-October/013979.html <https://urldefense.proofpoint.com/v2/url?u=https-3A__plato.cgl.ucsf.edu_pip…> >> >> That won't work in ChimeraX, but here I attach the equivalent for ChimeraX. >> >> Segger was developed to segment molecules in EM maps, so I have doubts that it will do much good for your light microscopy. But you can decide that by running it by hand on some time steps and see if you like the result. >> >> Here is a different approach we used to quantify protrusions of crawling neutrophils in light sheet microscopy by placing markers that might be of interest. >> >> https://www.cgl.ucsf.edu/chimera/data/protrusion-sep2015/protrusions.html <https://urldefense.proofpoint.com/v2/url?u=https-3A__www.cgl.ucsf.edu_chime…> >> >> Tom >> >> >> >>> On Jul 29, 2021, at 3:24 PM, Sam W Marchant via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>> wrote: >>> >>> Hi, >>> I am looking to apply the Map Segmenting to multiple time series of light sheet imaging and so I was wondering if there is either a command or a python function to automate the process. It looks here <https://urldefense.proofpoint.com/v2/url?u=http-3A__plato.cgl.ucsf.edu_pipe…> that you said it was going to be added to ChimeraX but I cannot find any info on how to do it. If not you mentioned a script in this answer, could you potentially send that to me? >>> Thanks, >>> Sam Marchant. >>> _______________________________________________ >>> 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…> >> >> <segscript.py> >

1 0

How to Align Chromosome Models with Different Number of Atoms?
by Cardiff Jiang 30 Jul '21

30 Jul '21

Dear ChimeraX User List, How can I compare two chromosome 3D models (PDB files) that have different numbers of "atoms"? Matchmaker tool reports, "Reference and/or match model contains no nucleic or amino acid chains. Use the command-line 'align' command to superimpose small molecules/ligands." align #1 toAtoms #2 reports, "Unequal number of atoms to pair, 49 and 63." align #1 toAtoms #2 matchNumbering true reports, "Pairing dropped 49 atoms and 63 reference atoms. No atoms paired for alignment." align #1:1-40 to #2:1-40 reports, "No atoms paired for alignment." How should I compare two chromosome 3D models below? Thank you. [image: image.png] Best regards, Zichen "Cardiff" Jiang

4 9

Automating Map segment
by Sam W Marchant 29 Jul '21

29 Jul '21

Hi, I am looking to apply the Map Segmenting to multiple time series of light sheet imaging and so I was wondering if there is either a command or a python function to automate the process. It looks here<http://plato.cgl.ucsf.edu/pipermail/chimera-users/2017-October/013980.html> that you said it was going to be added to ChimeraX but I cannot find any info on how to do it. If not you mentioned a script in this answer, could you potentially send that to me? Thanks, Sam Marchant.

2 1

Re: [chimerax-users] command line way for inverting selection
by Rangarajan, Amith 29 Jul '21

29 Jul '21

Hi, I am looking for a way to invert selection without reaching for the tool bar. I would like to know if there is a way to invert selection via the select command ( or some other command) thanks a lot, Amith

3 3

ATOM has no alt loc B
by James Loy 28 Jul '21

28 Jul '21

Hi folks- I'm trying to add hydrogens to an mmCIF file (5byl) using the addh command. However, every time I try, I encounter the following error: Traceback (most recent call last): File "/usr/lib/ucsf-chimerax/lib/python3.8/site-packages/ChimeraX_main.py", line 712, in init run(sess, cmd) File "/usr/lib/ucsf-chimerax/lib/python3.8/site-packages/chimerax/core/commands/run.py", line 36, in run results = command.run(text, log=log, return_json=return_json) File "/usr/lib/ucsf-chimerax/lib/python3.8/site-packages/chimerax/core/commands/cli.py", line 2852, in run result = ci.function(session, **kw_args) File "/usr/lib/ucsf-chimerax/lib/python3.8/site-packages/chimerax/addh/cmd.py", line 63, in cmd_addh add_h_func(session, structures, template=template, in_isolation=in_isolation, **prot_schemes) File "/usr/lib/ucsf-chimerax/lib/python3.8/site-packages/chimerax/addh/cmd.py", line 170, in hbond_add_hydrogens add_hydrogens(session, atoms, type_info_for_atom, naming_schemas, hydrogen_totals, File "/usr/lib/ucsf-chimerax/lib/python3.8/site-packages/chimerax/addh/hbond.py", line 214, in add_hydrogens _attach_hydrogens(atom, altloc_hpos_info, bonding_info) File "/usr/lib/ucsf-chimerax/lib/python3.8/site-packages/chimerax/addh/hbond.py", line 895, in _attach_hydrogens add_altloc_hyds(atom, altloc_hpos_info, invert, bonding_info, total_hydrogens, naming_schema) File "/usr/lib/ucsf-chimerax/lib/python3.8/site-packages/chimerax/addh/cmd.py", line 862, in add_altloc_hyds h = new_hydrogen(atom, i+1, total_hydrogens, naming_schema, File "/usr/lib/ucsf-chimerax/lib/python3.8/site-packages/chimerax/addh/cmd.py", line 882, in new_hydrogen metal_pos = metal.get_alt_loc_coord(alt_loc) File "atomic_cpp/cymol.pyx", line 587, in chimerax.atomic.cymol.CyAtom.get_alt_loc_coord ValueError: Atom /A MG 702 MG has no alt loc B I'm using ucsf-chimerax_1.2.5-1_amd64.deb installed on Ubuntu 20.04. I've done some digging, and I cannot figure out what is going on. Any help would be appreciated. Thanks in advance! -James -- James Loy, Ph. D. 614.915.9792 LinkedIn <https://www.linkedin.com/in/james-m-loy-ph-d-ba2256a/>

3 4

The PDB code for the demo picture on the website
by BAOCHENG LIU 28 Jul '21

28 Jul '21

Hi chimerax group, I am a postdoc in UCLA using chimerax. Thanks for providing all scientists this powerful software that makes life easier. I have a question here when I was learning the cartoon/ribbon style command line. So, I saw the 4 demo pictures on the website https://www.rbvi.ucsf.edu/chimerax/docs/user/commands/cartoon.html#style and just realized the structure just looks similar to one of my structures. Could you please tell me the PDB code for that structure so I can compare it with mine in detail? Hope it is released. Thank you. Best regards, Baocheng

2 1

resfit command for nuclei acid
by Wen-Jin Winston Wu 27 Jul '21

27 Jul '21

Hi Tom, I have just tried to use the "resfit" command ChimeraX Does the nice command of "resfit" in ChimeraX support inspection on nuclei acid? It seems that it only support protein residues as with the command " resfit #1/D:DT map #3", it returned with the message that "None of the 9 specified residues have backbone atoms N, CA and C". I have not checked out the daily build version yet, but thought that I can ask first. Thanks, Best wishes, Winston

2 2

Custom colour for atoms with bfactor==0
by Lorena Zuzic 27 Jul '21

27 Jul '21

Hi, I wanted to know if there is a way of colouring my structure by bfactor, but with an additional condition where all bfactor==0 atoms are coloured in grey. Currently, I am using a white to red gradient for my B-factors: color bfactor range -2.2, 2.2 In this case, bfactor==0 values are coloured white. However, I would like them to be grey and outside the gradient (as they represent an unmapped portion of the protein). Thanks! Lorena

2 2

create mask from "shapes"
by Roberto Marabini 27 Jul '21

27 Jul '21

Hi, It is possible to create a mask from a shape?. For example from the result of "*shape icosahedron".* If the command does not exist I guess I may create it as follows * the input would be the 3D map to be masked and the shape to be used as mask * request all the (varray, tarray) from the shape. * from varray,tarray build the triangles that define the surface of the shape * for each triangle create the normal vector * multiply each normal vector by the position of each voxel (dot product) * keep those voxels that have negative dot products for all the triangles. thanks for the help

2 2

Automated Fitting of models into maps and saving fits with a correlation score > X
by Vorländer,Matthias Kopano 26 Jul '21

26 Jul '21

Dear all, I have a set of 100 “artificial” tomograms, each containing approx 100 copies of a simulated density map of my protein of interest. I would like to fit each tomogram with the PDB of my POI, and save copies for all fits with a correlation score > 90%. Using the fitmap command in Chimera and then manually selecting the fits that meet the criterium works, but takes quiet a long time for a larger amount of data. I wonder if this could be automated, and if somehow would be able me to put together a script (is it possible to execute such tasks in a non-gui way, by submitting it to a cluster so that it could be parallelized?). Thanks a lot in advance, Best, Matthias

2 2

unexpected behavior of build start
by Alexis Rohou 26 Jul '21

26 Jul '21

Hi ChimeraX team, I'm running into unexpected behavior when using the build tool. Here's what I'm doing: - open map --> model #1 - open PDB --> model #2 - fit #2 in #1 (the PDB moves by ~20 Å at this step) - cofr centerOfView showPivot true - move the view around so that the pivot axes intersect where I want to place a new atom - build start atom #2 expected result: a new H atom is created exactly at the center of view (where the pivot axes intersect) actual result: the new H atom is created some distance away; I think the vector from where the new H atom is built to the cofr is the same vector as the PDB model was displaced by the fitting into the map (my second step, above), but I haven't checked that carefully. Is this what is expected? It confused me :) Is there a command I can use to move the atom to the correct location after it's been created? Interestingly, if I add a H atom into a new model, then it appears where I expect it, at the cofr: - build start atom "custom built" This is with 1.2.5 (2021-05-24) Cheers, Alexis

2 2

question
by 王镐锋 26 Jul '21

26 Jul '21

Dear guys, Sorry to disturb you guys. When I use the UCSF ChimeraX, I try to define the second structure for part of model. I type the command like "dssp (#1 & sel) energy cutoff 0.5 minheliexlen 3", it works for the whole model instead of what I choose specially. Could you please help me? Thanks so much! Best, Haofeng Wang Ph.D student Tianjin University, China

2 3

measure volume in ChimeraX
by Andrew Blyth 24 Jul '21

24 Jul '21

Hi, I am having trouble getting the ‘measure volume’ and ‘measure area’ command to work in chimera. I have been trying the command: measure volume #3/A:457 for the structure that I have been using, however, nothing happens when I execute this command. Could you please provide me with an example command that will work for measuring the volume or area of a residue? Thanks, Andrew Blyth PhD Candidate Medical Biochemistry - Flinders University Room 6E109 Flinders Medical Centre | South Australia 5001, Australia Phone: +61 8 8204 5098 | E: andrew.blyth(a)flinders.edu.au<mailto:andrew.blyth@flinders.edu.au>

2 1

Model missing residues in Chimera X
by He, Amy 23 Jul '21

23 Jul '21

Dear Chimera X community, I’m a new user of Chimera X and I have a question about the built-in Modeller function in Chimera X Previously in Chimera 2, we use the “Model/Refine Loop” function to model missing residues in the experimental structure, before any further calculation or simulations. The “Model/Refine Loop” function uses Modeller and the function provides modeled, complete structures in which the non-missing residues do not move. In Chimera X, a similar function is “Modeller Comparative” but it works differently. The “Modeller Comparative” performs a modeling for the full structure with the given sequence. Is possible in Chimera X to model the missing residues, without moving the existent residues? Thank you for your kind advice in advance! Thanks, Amy -- Amy He Chemistry Graduate Teaching Assistant Hadad Research Group Ohio State University he.1768(a)osu.edu<mailto:he.1768@osu.edu>

2 2

How to access ChimeraX remotely from macbook (OS mojave)?
by Rayees Mattoo 22 Jul '21

22 Jul '21

Hi, I am trying to access ChimeraX remotley using my mac book pro. The ChimeraX is installed on linux machine. Upon launching, the chimeraX GUI appears and suddenly disappears with the following error message: "ChimeraX requires OpenGL graphics version 3.3. Your computer graphics driver provided version 1.4, Try updating your graphics driver". My mac currently has macOS mojave version 10.14.6 and it seems it does not have OpenGL graphics version 3.3 required to display chimeraX remotely. Is there any way out to fix the problem? Not sure if updating my macbook to Catalina or BigSur is going to help! Best Rayees

3 2

Re: [chimerax-users] How to access ChimeraX remotely from macbook (OS mojave)?
by Tom Goddard 22 Jul '21

22 Jul '21

Hi Rayees, Mac Air graphics is pretty slow for running ISOLDE. But Tristan Croll who develops ISOLDE added a nice option "Sim Fidelity" to the ISOLDE panel in the middle -- by default it is set to "High" and setting it to "Quick" will make the simulations run much faster. Here is what Tristan told me about what it does: "The latest ISOLDE release has new “sim fidelity” radio buttons on the “Sim settings” tab. The “quick” mode (no implicit solvent, nonbonded cutoff tightened to 9 Å) runs about 4x faster on my MacBook Air and still gives reasonable results in good density. Still not *fast*, but I think definitely usable." This is in ISOLDE 1.2.2. If you need to update ISOLDE use ChimeraX menu Tools / More Tools.... If this is still too slow, I'm afraid it is a limitation. You have to use faster hardware. The realtime dynamics simulations used by ISOLDE need fast graphics - the molecular dynamics is done with OpenMM using OpenCL or CUDA GPU accelerated computation. CUDA is fastest and needs Nvidia graphics and the CUDA driver installed -- Macs don't support Nvidia gpus. The macOS OpenCL implementation is very slow, almost as slow as just running on the CPU. Tristan has ISOLDE benchmarks on different hardware here https://isolde.cimr.cam.ac.uk/performance-benchmarks/ Tom > On Jul 22, 2021, at 6:03 PM, Rayees Mattoo <rmattoo(a)stanford.edu> wrote: > > Hi Tom, > Thanks for responding. Actually, I wanted to run ISOLDE from chimeraX and already tried it running on Mac with my 500KDa protein complex. It was very slow, wanted to try on linux machine and ran into the OpenGL problem. Do you have any suggestions how to run ISOLDE faster on mac? > > Best > Rayees > From: Tom Goddard <goddard(a)sonic.net> > Sent: Thursday, July 22, 2021 5:32 PM > To: Rayees Mattoo <rmattoo(a)stanford.edu> > Cc: chimerax-users(a)cgl.ucsf.edu <chimerax-users(a)cgl.ucsf.edu>; chimerax-bugs(a)cgl.ucsf.edu <chimerax-bugs(a)cgl.ucsf.edu> > Subject: Re: [chimerax-users] How to access ChimeraX remotely from macbook (OS mojave)? > > Hi Rayees, > > I guess you have X Windows (XQuartz) running on your Mac and are hoping that X remote display from Linux to the Mac will work with ChimeraX. Unfortunately X Windows remote display of 3D OpenGL graphics has not worked reliably since the days Silicon Graphics computers in the 1990s. It is possible to get it to work between two Linux machines with identical OpenGL drivers. But it would be a near miracle if the XQuartz implementation of X Windows on Mac could handle the OpenGL from a Linux machine. > > The sensible approach is to run ChimeraX directly on your MacBook Pro. We don't recommend remote display even when it works because rendering speed is likely to be poor. > > Tom > > >> On Jul 22, 2021, at 1:31 PM, Rayees Mattoo via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>> wrote: >> >> Hi, >> I am trying to access ChimeraX remotley using my mac book pro. The ChimeraX is installed on linux machine. Upon launching, the chimeraX GUI appears and suddenly disappears with the following error message: "ChimeraX requires OpenGL graphics version 3.3. Your computer graphics driver provided version 1.4, Try updating your graphics driver". >> My mac currently has macOS mojave version 10.14.6 and it seems it does not have OpenGL graphics version 3.3 required to display chimeraX remotely. Is there any way out to fix the problem? Not sure if updating my macbook to Catalina or BigSur is going to help! >> >> Best >> Rayees >> >> >> _______________________________________________ >> 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>

1 0

Re: [chimerax-users] python loop with ChimeraX
by Rangarajan, Amith 21 Jul '21

21 Jul '21

Hi, I am new to chimeraX , i want to loop through a set of biological assemblies measuring SASA of selecting residues and write them to a file. I need some help with starting on this .How to include this into the .cxc script? is there a example somewhere? please share your tips and suggestions, thanks everyone ! warm regards, Amith

4 8

Hide dust tool & threshold of the map
by Dmitry Semchonok 20 Jul '21

20 Jul '21

Dear colleagues, I would like to ask you for the common practice in showing the threshold of the 3D map and usage of the "hide dust tool”. Am I allowed to use the “hide dust tool” when making the figures for the paper? And if yes, if/how shall I specify that in the description to the figure? Thank you Sincerely, Dmitry

2 1

Moving labels
by Maciej Basczok 15 Jul '21

15 Jul '21

Dear ChimeraX staff, I have a problem with moving 3D labels. I would like to move them in the z-axis, but I cannot find how to do it. My version is 1.2.5. In some earlier release it could be done with the right mouse button + ctrl, but it seems to be changed. I have also tried to find a solution in archive messages, but the hint to click favourites and preferences also appears to be no longer an issue. Under favourites, there are no preferences or mouse settings. I would be extremely grateful for any suggestions. Kind regards, Maciej

2 3

scale_bar
by Dmitry A. Semchonok 09 Jul '21

09 Jul '21

4 7

Making movie with crop function
by SHIQING LIAO 07 Jul '21

07 Jul '21

Hi there! I am trying to make movies with different cropped views in order to see the inside of my 3D model. I tried view name command and it cannot store the cropped information. The command seems to only work with rotation and translation. Any help would be appreciated! Best, Shiqing

2 1

fit map and bring other maps or models with it
by Alpay Burak Seven 07 Jul '21

07 Jul '21

Hi ChimeraX developers, I would like to fit one map to another and move some other maps with it using ChimeraX. This was possible with matrixcopy in Chimera. In ChimeraX, this type of translation/rotation is possible with matchmaker using "match #2 to #1 bring #3" I believe bring option is not available to "fitmap" command. Please let me know if there is a way. Would it be possible to implement the bring option to fitmap command or implement the matrixcopy command to ChimeraX? Kind regards, -- Alpay B. Seven Stanford University

2 2

Question about libLLVM
by Zhe Wang 07 Jul '21

07 Jul '21

Hi, We were trying to install ChimerX 1.2 on our Centos 8 system. It seems like ChimeraX 1.2 asks for libLLVM with version 10 which is not a default package that built in the rpm. The default one for CentOS 8 is version 9. Centos 7 does not provide and not available in EPEL either. Could ChimeraX provide the corresponding library for centos 8 and 7? Another question that I have is if the following is correct for ChimeraX 1.1: ChimeraX 1.1 is using the default libLLVM3.9-mesa.so for centos 8. And for centos 7, you have ChimeraX 1,1 using the libOSMesa.so.8.0.0 which ChimeraX provided, as I see ChimeraX 1.1 works fine one both, but not 1.2. Best, Zhe

3 6

Using ChimeraX as a Python Library
by James Loy 06 Jul '21

06 Jul '21

Hello! Thank you for creating such an amazing piece of software! I'm trying to use portions of ChimeraX for part of a CIF file processing pipeline. In order to automate the process, I'm building a docker image that has ChimeraX installed. Ideally, we would like to use the pieces of ChimeraX we need by importing the relevant python modules. Is this possible? If so, must I build ChimeraX from source? Additionally, I have tried several times to build v1.1.1 from source and I have not been able to. I am always prompted for a password when trying to rsync the dependencies: /bin/sh -c 'rsync -a $1 .' -- plato.cgl.ucsf.edu: /usr/local/projects/chimerax/www/data/prereqs/python/Python-3.7.8.tar.xz user(a)plato.cgl.ucsf.edu's password: In order to build from source, do I need to register somewhere to get credentials? Just to be clear, this CIF file processing pipeline is for academic (UT Austin) use, not commercial. Thanks in advance! James -- James Loy, Ph. D. 614.915.9792 LinkedIn <https://www.linkedin.com/in/james-m-loy-ph-d-ba2256a/>

4 8

Toolshed server maintenance
by Yu Low 06 Jul '21

06 Jul '21

Hi ChimeraX, I encountered a problem accessing the toolshed in ChimeraX. I have attached a picture of the error message below. Is the server currently down? When would it be back up again? Regards, Yu Shang [cid:image001.png@01D7719E.469E4D30]

2 1

ChimeraX VR Feedback
by Gökhan Tolun 06 Jul '21

06 Jul '21

Hi, Thanks for all your hard work in getting ChimeraX going in VR and also for implementing a Meeting component. Here is some feedback after trying a VR meeting for the first time today: * Is it possible to have the same functionality of mouse-hover showing the labels, in VR? * Is it possible to add a button to the toolbar to turn labels for all residues on/off? * The VR cones do not show the correct controller layout while using a WMR controller (they still show the Vive controller layout). Is it possible to show the correct controller layout? * While using WMR controllers, the grip button is very easy to press by mistake, resetting the view. Can this be changed to a hold for X seconds behavior instead of being instantaneous? * While adding labels in VR, especially since the hover does not show the label (indicating youre at the correct place to add a label), a misplaced click removes all labels. May the removal all labels upon clicking to an empty area also changed to hold for X seconds or asking for a confirmation? Thanks, Gökhan

2 1

"Render by attribute" tool in ChimeraX
by Francesco Musiani 06 Jul '21

06 Jul '21

Dear ChimeraX developers, I would like to use one feature from the old "render by attribute" tool present in Chimera. My aim is to adapt the atomic radius of a series of atoms according to the value written in the B-factor column of the PDB file. Then I would like to calculate the molecular surface of the resulting molecule in order to calculate the surface volume. Chimera can do the first part by using "render by attribute" tool, but unfortunately it fails in the creation of the surface of the resulting molecule. How can I achieve the same result by using ChimeraX? Thanks in advance. Francesco

2 1

Python/Pip Inquiry - ChimeraX - Nathan Wood
by Nathan Wood 05 Jul '21

05 Jul '21

Dear ChimeraX With regards to the python and pip utilities organic to ChimeraX, is it possible to use the conda installed modules within the same script executed by ChimeraX? When running the script through ChimeraX I return an error that the module is not found. The module was installed using "pip install -e . " while in the conda environment. When I attempted this using the pip provided in ChimeraX Daily Release (22/06/2021, Generic X64 Linux) I return the error: /"/tmp/chx-develop.eKjBho/ChimeraX.app/bin/python3.8: bad interpreter: No such file or directory"/ This error can be resolved if I modify the /"#!"/ at the beginning of the pip in a text editor to the python3.8 found within ChimeraX, with pip installing correctly, but ChimeraX still returning that the module is not found. Furthermore I believe this method is not sound. Any assistance would be appreciated Very Respectfully, Nathan Wood

2 2

Is the toolshed server down?
by tolung.bio＠gmail.com 05 Jul '21

05 Jul '21

Hi, From https://cxtoolshed.rbvi.ucsf.edu/ I am getting Service Unavailable The server is temporarily unable to service your request due to maintenance downtime or capacity problems. Please try again later. _____ Apache/2.4.6 (CentOS) Server at cxtoolshed.rbvi.ucsf.edu Port 443 Is this something on my side, or a known issue that is being resolved? Is there an alternative way for installing the tools, when this happens? Best, Gökhan

2 1

how to change the radius of loop
by Wen-Jin Winston Wu 02 Jul '21

02 Jul '21

Hello, Does anyone know how to modify the radius of loops? I am trying to show structural difference between the three aligned proteins with the cartoon helices shown as tubes. However, when I reduced the helix radius from 2 to 1 ( "cartoon style modeh tube rad 1 sides 24"), the radius of a helix is only about twice that of a loop/coil. Also, what does the number "24" do in the "sides 24"?. I could not find the description on this on ChimeraX Any help will be appreciated. Thanks, Best wishes, Winston

2 3

Re: [chimerax-users] Generating surfaces from a specific selection
by Eric Pettersen 01 Jul '21

01 Jul '21

Hi Diego, If there are interior voids within the structure your main surface is enclosing, there will be "bubbles" like what you're seeing, where solvent (or possibly larger things) could theoretically be contained. If you want to only create the outermost surface and not any of the interior void surfaces then add "visiblePatches 1" to your surface command, and only the single largest surface will be created. --Eric > On Jun 30, 2021, at 8:32 AM, Diego Amaya <diaamayaram(a)unal.edu.co> wrote: > > Hi Eric, > > Thanks for your fast reply. The script works but I identify a "weird behavior" in some surfaces. In some cases, you can find "isolated spheres" and if you superimpose them with the corresponding entire surface, these spheres are buried in the structure. All the pdb files have the same atom order and there are no waters, ions or other molecules. The structure is composed of two protein chains. I tried several probeRadius and gridSpacing values but the problem stays. Any suggestions ? > > Best regards, > > > > > El mar, 29 jun 2021 a las 22:58, Eric Pettersen (<pett(a)cgl.ucsf.edu <mailto:pett@cgl.ucsf.edu>>) escribió: > Hi Diego, > It's impossible to be 100% certain without knowing exactly which line it crashed in, but my strong suspicion is that the long atom spec you generate overran some limit in the atom spec or command parser and resulted in a crash. I will be investigating in more detail later, but working off that assumption I would change your script to directly select the atoms in Python rather than via a command. I'm going to assume the atoms in your PDB files are always in the same order, and that the structure is the only model open. If so, change these lines in the 'if' block: > > cur_sel = selected_atoms(session).unique_structures[0].atoms.serial_numbers > for a in cur_sel: > list_atoms.append('@@serial_number='+str(a)) > sel_atoms = ' | '.join(list_atoms) > > to: > > selected = session.models[0].atoms.selecteds > > and these lines in the 'else' block: > > rc(session, 'sel {}'.format(sel_atoms)) > rc(session, 'surface {} enclose #1'.format(sel_atoms)) > to: > > session.models[0].atoms.selecteds = selected > rc(session, 'surface sel enclose #1') > --Eric > > Eric Pettersen > UCSF Computer Graphics Lab > > >> On Jun 29, 2021, at 10:00 AM, Diego Amaya via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>> wrote: >> >> Hello, >> >> I have a pdb trajectory of 50 frames (in separated pdb files). I want to generate only the solvent accessible surface around amino acid 31 within a radius of 15 A. I want to use the same set of atoms when generating each surface with respect to the first frame of the trajectory. I'm using the python script here below but it doesn't work, I get a segmentation error in the else block. It works if I use "rc(session, 'surface zone #1.1 nearAtoms :{} distance {}'.format(resid, radius))" in the else block but in that way I don't use exactly the same atoms each time. Any suggestions? >> >> Thanks in advance. >> >> Here the code : >> >> ########################################################### >> from chimerax.core.commands import run as rc >> >> def get_surfaces(resid, radius): >> from chimerax.core.commands import run as rc >> from chimerax.atomic import selected_atoms >> >> with open('list_pdbs.txt', 'r') as list_pdbs: >> flag = 0 >> for pdb_file in list_pdbs: >> if flag == 0: >> list_atoms = [] >> rc(session, 'open ' + pdb_file.strip()) >> rc(session, 'sel :{} @<{}'.format(resid, radius)) >> cur_sel = selected_atoms(session).unique_structures[0].atoms.serial_numbers >> for a in cur_sel: >> list_atoms.append('@@serial_number='+str(a)) >> sel_atoms = ' | '.join(list_atoms) >> rc(session, 'surface #1 enclose #1') >> rc(session, 'surface zone #1.1 nearAtoms :{} distance {}'.format(resid, radius)) >> rc(session, '~ribbon') >> rc(session, '~disp') >> rc(session, "save {}_resid_{}_radius_{}.stl format stl".format(pdb_file.strip()[:-4], resid, radius)) >> rc(session, 'surface close') >> rc(session, '~sel') >> rc(session, "close all") >> flag = 1 >> else: >> rc(session, 'open ' + pdb_file.strip()) >> rc(session, 'sel {}'.format(sel_atoms)) >> rc(session, 'surface {} enclose #1'.format(sel_atoms)) >> rc(session, '~ribbon') >> rc(session, '~disp') >> rc(session, "save {}_resid_{}_radius_{}.stl format stl".format(pdb_file.strip()[:-4], resid, radius)) >> rc(session, '~sel') >> rc(session, 'surface close') >> rc(session, "close all") >> >> resid = 31 >> radius = 15 >> >> get_surfaces(resid, radius) >> rc(session, "quit") >> ############################################################# >> >> >> -- >> Diego A. Amaya Ramírez >> >> Aviso legal: El contenido de este mensaje y los archivos adjuntos son confidenciales y de uso exclusivo de la Universidad Nacional de Colombia. Se encuentran dirigidos sólo para el uso del destinatario al cual van enviados. La reproducción, lectura y/o copia se encuentran prohibidas a cualquier persona diferente a este y puede ser ilegal. Si usted lo ha recibido por error, infórmenos y elimínelo de su correo. Los Datos Personales serán tratados conforme a la Ley 1581 de 2012 y a nuestra Política de Datos Personales que podrá consultar en la página web www.unal.edu.co <http://www.unal.edu.co/>. Las opiniones, informaciones, conclusiones y cualquier otro tipo de dato contenido en este correo electrónico, no relacionados con la actividad de la Universidad Nacional de Colombia, se entenderá como personales y de ninguna manera son avaladas por la Universidad. >> _______________________________________________ >> 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> > > > > -- > Diego A. Amaya Ramírez > > Aviso legal: El contenido de este mensaje y los archivos adjuntos son confidenciales y de uso exclusivo de la Universidad Nacional de Colombia. Se encuentran dirigidos sólo para el uso del destinatario al cual van enviados. La reproducción, lectura y/o copia se encuentran prohibidas a cualquier persona diferente a este y puede ser ilegal. Si usted lo ha recibido por error, infórmenos y elimínelo de su correo. Los Datos Personales serán tratados conforme a la Ley 1581 de 2012 y a nuestra Política de Datos Personales que podrá consultar en la página web www.unal.edu.co <http://www.unal.edu.co/>. Las opiniones, informaciones, conclusiones y cualquier otro tipo de dato contenido en este correo electrónico, no relacionados con la actividad de la Universidad Nacional de Colombia, se entenderá como personales y de ninguna manera son avaladas por la Universidad.

2 1

Having multiple marker files
by SHIQING LIAO 30 Jun '21

30 Jun '21

Hi! I’m trying to have multiple marker files because I would like them to have different radius and coloring distance. I figured out that I can create new marker files by “marker #5 1,1,1 radius 100”, for example. However, if I add new markers, the new marker always goes to the first marker file, instead of the selected marker file that I want. Any help is really appreciated! Best, Shiqing

3 9

Python API Inquiry
by Nathan Wood 29 Jun '21

29 Jun '21

To Whom it May Concern, My name is Nathan Wood and I am currently a Google Summer of Code Intern with the OpenChemistry Group. Currently I am currently in the process of replacing Visualizing Molecular Dynamics (VMD) with ChimeraX as a means to visualizing computationally generated electrostatic potential diagrams. To accomplish this I am having to use the Python API in a script. However, I am having difficulties enabling the Python API. When I execute a Tutorials example found in the online developer's documentation, I receive the error: /ImportError: No module named chimerax.core.commands// / which suggests that the python modules were never installed properly. I also recieve similar errors when attempting to import the toolshed. Otherwise, the ChimeraX GUI and its shell work properly and I am unsure how to resolve the API error. I am currently using the Generic Linux 64 Bit Daily Release and can provide more information if necessary. Any assistance would be greatly appreciated ------------------------------------------------------ Very Respectfully, Nathan Wood Undergraduate Year 3, GSOC Intern University of Florida

3 2

Fit crystal structure into mrc
by SHIQING LIAO 29 Jun '21

29 Jun '21

Hi, I am trying to build an illustration using marker/color zone. I successfully colored my mrc file. Now, I want to fit a crystal structure I downloaded from pdb into the mrc. But they apparently have different sizes. I tried voxelSize to scale up my mrc, but then all my markers don’t fit with the enlarged mrc. However, voxelSize doesn’t seem to work with the crystal structure (.pdb1) as I got an error message “no volumes specified” when I indeed wrote “volume #5 voxelSize 2”. I am wondering is there any function like voxelSize to scale down the crystal structure? Thank you!

3 3

Generating surfaces from a specific selection
by Diego Amaya 29 Jun '21

29 Jun '21

Hello, I have a pdb trajectory of 50 frames (in separated pdb files). I want to generate only the solvent accessible surface around amino acid 31 within a radius of 15 A. I want to use the same set of atoms when generating each surface with respect to the first frame of the trajectory. I'm using the python script here below but it doesn't work, I get a segmentation error in the else block. It works if I use "*rc(session, 'surface zone #1.1 nearAtoms :{} distance {}'.format(resid, radius))*" in the else block but in that way I don't use exactly the same atoms each time. Any suggestions? Thanks in advance. Here the code : ########################################################### *from chimerax.core.commands import run as rcdef get_surfaces(resid, radius): from chimerax.core.commands import run as rc from chimerax.atomic import selected_atoms with open('list_pdbs.txt', 'r') as list_pdbs: flag = 0 for pdb_file in list_pdbs: if flag == 0: list_atoms = [] rc(session, 'open ' + pdb_file.strip()) rc(session, 'sel :{} @<{}'.format(resid, radius)) cur_sel = selected_atoms(session).unique_structures[0].atoms.serial_numbers for a in cur_sel: list_atoms.append('@@serial_number='+str(a)) sel_atoms = ' | '.join(list_atoms) rc(session, 'surface #1 enclose #1') rc(session, 'surface zone #1.1 nearAtoms :{} distance {}'.format(resid, radius)) rc(session, '~ribbon') rc(session, '~disp') rc(session, "save {}_resid_{}_radius_{}.stl format stl".format(pdb_file.strip()[:-4], resid, radius)) rc(session, 'surface close') rc(session, '~sel') rc(session, "close all") flag = 1 else: rc(session, 'open ' + pdb_file.strip()) rc(session, 'sel {}'.format(sel_atoms)) rc(session, 'surface {} enclose #1'.format(sel_atoms)) rc(session, '~ribbon') rc(session, '~disp') rc(session, "save {}_resid_{}_radius_{}.stl format stl".format(pdb_file.strip()[:-4], resid, radius)) rc(session, '~sel') rc(session, 'surface close') rc(session, "close all") resid = 31radius = 15get_surfaces(resid, radius)rc(session, "quit")* ############################################################# -- Diego A. Amaya Ramírez -- *Aviso legal:* El contenido de este mensaje y los archivos adjuntos son confidenciales y de uso exclusivo de la Universidad Nacional de Colombia. Se encuentran dirigidos sólo para el uso del destinatario al cual van enviados. La reproducción, lectura y/o copia se encuentran prohibidas a cualquier persona diferente a este y puede ser ilegal. Si usted lo ha recibido por error, infórmenos y elimínelo de su correo. Los Datos Personales serán tratados conforme a la Ley 1581 de 2012 y a nuestra Política de Datos Personales que podrá consultar en la página web www.unal.edu.co <http://www.unal.edu.co/>.* *Las opiniones, informaciones, conclusiones y cualquier otro tipo de dato contenido en este correo electrónico, no relacionados con la actividad de la Universidad Nacional de Colombia, se entenderá como personales y de ninguna manera son avaladas por la Universidad.

2 1

Accessing Chain IDs
by Diana Lee 29 Jun '21

29 Jun '21

Hi team! I have what I hope is an easy question. I'm accessing ChimeraX commands via python script, and I need a list of the Chain IDs. I'm currently getting the number of chains using the num_chains property. I've done quite a bit of digging through documentation and can only find ways to rename, or view interfaces, but I can't seem to find any specific command to list them. I feel as though it must be so basic, no one has needed to ask. :) Thanks for your help, Diana Lee Graduate Student Luque Lab, SDSU VII

3 2

Global Fit List and Model Seperation
by Christian Tüting 28 Jun '21

28 Jun '21

Dear ChimeraX-Team & MailingListUsers, My question is actually two different questions: I would like to perform a global fitting in ChimeraX and seperate all fitting solutions into independent models. I loaded the map (#1) and a dimeric model (#2) into ChimeraX and perform the global fitting by: fit #2 inMap #1 search 50 My map represents a homo-oligomeric model with 40+ monomers (20+ dimers), so multiple fitting solutions are probably correct solutions. This is the log of the fitting: "Found 41 fits. List window not yet implemented." which matches with my assumption. I would like to now (a) inspect all fittings, but the list window is not implemented yet. Can I access the fitting solutions via console commands? And (b) I would like to save each fitted solution as an indepent object, reconstruction the entire model in the map for furhter refinement. Again, could this be done via commands like: "fit #2 inMap #2 search 50 saveFit fittings.pdb", which results in a multi-state pdb? The "Save PDB" button is probably only available in the List windows, which is not implemented yet. Thanks in advance Best Christian

2 2

Fwd: Problem with preset original command in Chimerax 1.2.5
by Tom Goddard 28 Jun '21

28 Jun '21

Saverio reports his problem where ChimeraX "preset original" hung was solved by updating his graphics driver. Tom > Begin forwarded message: > > From: svle(a)tiscali.it > Subject: Re: [chimerax-users] Problem with preset original command in Chimerax 1.2.5 > Date: June 26, 2021 at 1:21:04 AM PDT > To: Tom Goddard > > I have upgraded the graphics driver by a program from AMD website and now it seems that all is working fine and the graphics operations are more responsive and faster. > The picture is very nice. > I have used the Report a Bug before and after the driver upgrading to give driver version information. > > Many thanks. > Saverio > Il 25.06.2021 21:05 Tom Goddard ha scritto: > >> These commands work fine for me in ChimeraX 1.2.5 on Windows 10. It is likely a bug in your graphics driver. Updating your graphics driver might fix it. You can use ChimeraX menu entry Help / Report a Bug and then we will see what graphics card and driver you are using which may give us further ideas. >> By the way maybe you will like preset cylinders/stubs shown below. >> Tom >> >> >>> On Jun 25, 2021, at 12:34 AM, svle--- via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>> wrote: >>> >>> Hi, >>> I have a problem with Chimerax 1.2.5 on windows 10. >>> In the command line I use the following: >>> >>> open 5u1c ( ok ) >>> preset riboon (ok) >>> preset original >>> >>> After the last command the application freezes and I must to kill it. >>> >>> What I can do? >>> >>> Thanks >>> >>> Saverio >>> >>> >>> >>> >>> Con Tiscali Mobile Smart 70 hai 70 GB in 4G, minuti illimitati e 100 SMS a soli 7,99€ al mese http://tisca.li/Smart70 <http://tisca.li/Smart70> >>> >>> _______________________________________________ >>> 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 > > > > Con Tiscali Mobile Smart 70 hai 70 GB in 4G, minuti illimitati e 100 SMS a soli 7,99€ al mese http://tisca.li/Smart70 <http://tisca.li/Smart70> >

1 0

saving coordinates with respect to map in ChimeraX
by khaja faisal tarique 28 Jun '21

28 Jun '21

Hello everyone While doing rigid body fit we know that after placing the coordinate to its correct position we can save it with respect to the map. Does anyone know if a similar feature exists in ChimeraX ? Is there a way where the coordinates .pdb/cif file can be saved with respect to its map in ChimeraX ? Thank you -- Faisal Tarique Khaja

2 1

Problem with preset original command in Chimerax 1.2.5
by svle＠tiscali.it 25 Jun '21

25 Jun '21

Hi, I have a problem with Chimerax 1.2.5 on windows 10. In the command line I use the following: open 5u1c ( ok ) preset riboon (ok) preset original After the last command the application freezes and I must to kill it. What I can do? Thanks Saverio Con Tiscali Mobile Smart 70 hai 70 GB in 4G, minuti illimitati e 100 SMS a soli 7,99€ al mese http://tisca.li/Smart70

2 1

access to current selection
by Diego Amaya 25 Jun '21

25 Jun '21

Hello everyone, I would like to find the equivalent to chimera expression "chimera.selection.currentAtoms()" in ChimeraX. Any idea ? Thanks in advance. Best regards -- Diego A. Amaya Ramírez -- *Aviso legal:* El contenido de este mensaje y los archivos adjuntos son confidenciales y de uso exclusivo de la Universidad Nacional de Colombia. Se encuentran dirigidos sólo para el uso del destinatario al cual van enviados. La reproducción, lectura y/o copia se encuentran prohibidas a cualquier persona diferente a este y puede ser ilegal. Si usted lo ha recibido por error, infórmenos y elimínelo de su correo. Los Datos Personales serán tratados conforme a la Ley 1581 de 2012 y a nuestra Política de Datos Personales que podrá consultar en la página web www.unal.edu.co <http://www.unal.edu.co/>.* *Las opiniones, informaciones, conclusiones y cualquier otro tipo de dato contenido en este correo electrónico, no relacionados con la actividad de la Universidad Nacional de Colombia, se entenderá como personales y de ninguna manera son avaladas por la Universidad.

2 1

Chimerax 1.2.5/CentOS-7 Rizen cpu: WARNING: RDRND generated: 0xffffffff 0xffffffff 0xffffffff 0xffffffff
by Tru Huynh 25 Jun '21

25 Jun '21

Hi I have just installed the centos7 rpm (and rpm2cpio into our NFS shared software installation tree). tru@sillage ~]$ chimerax WARNING: CPU random generator seem to be failing, disabling hardware random number generation WARNING: RDRND generated: 0xffffffff 0xffffffff 0xffffffff 0xffffffff is diplayed upon startup on my desktop: /proc/cpuinfo: model name : AMD Ryzen 9 3900X 12-Core Processor stepping : 0 microcode : 0x8701012 .. fpu : yes fpu_exception : yes cpuid level : 16 wp : yes flags : fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush mmx fxsr sse sse2 ht syscall nx mmxext fxsr_opt pdpe1gb rdtscp lm constant_tsc art rep_good nopl nonstop_tsc extd _apicid aperfmperf eagerfpu pni pclmulqdq monitor ssse3 fma cx16 sse4_1 sse4_2 movbe popcnt aes xsave avx f16c rdrand lahf_lm cmp_legacy svm extapic cr8_legacy abm sse4a misalignsse 3dnowprefetch osvw ibs skinit wdt tce topoext perfctr_core perfctr_nb bpext perfctr_l2 cpb cat_l3 cdp_l3 hw_pstate sme retpoline_amd ssbd ibpb stibp vmmcall fsgsbase bmi1 avx2 smep bmi2 cqm rdt_a rdseed adx smap clflushopt clwb sha_ni xsave opt xsavec xgetbv1 cqm_llc cqm_occup_llc cqm_mbm_total cqm_mbm_local clzero irperf xsaveerptr arat npt lbrv svm_lock nrip_save tsc_scale vmcb_clean flushbyasid decodeassists pausefilter pfthreshold avic v_vmsave _vmload vgif umip overflow_recov succor smca ... No error is shown on other machines equipped with: Intel(R) Xeon(R) Silver 4114 CPU @ 2.20GHz Cheers Tru -- Tru Huynh (PhD) | mailto:tru@pasteur.fr | tel +33 1 45 68 87 37 https://research.pasteur.fr/en/team/structural-bioinformatics/ Institut Pasteur, 25-28 rue du Docteur Roux, 75724 Paris CEDEX 15 France

2 1

Your site is not working
by Moradkhan, Tiglath A 24 Jun '21

24 Jun '21

Hi, I'm trying to download a daily build of ChimeraX but when I try to access the UCSF ChimeraX website it seems to be down. Also when I try to access user guides, I'm also not able to access them. Are you experiencing some system-wide issue today? Thanks Tiglath

2 1

Open a PDB-formatted file and a MTZ file
by Wen-Jin Winston Wu 22 Jun '21

22 Jun '21

Hi, I am trying to inspect electron density of X-ray data. I have the PDB-formatted coordinate file a.pdb (not been submitted to PDB yet) and a mtz file (a.mtz). I have downloaded Clipper to Chimera X (1.2.5) running on Window 10. I have opened my a.pdb, and I then tried to open my a.mtz file from the File-Open and I specified the file type with "*.mtz", and opened the a.mtz file, but I then got the error message: "Must specify a structure model to associate with crystallographic data". I know that I was not doing it correctly (e.g. not typing proper commands with correct syntax.). I looked into the description in the URL below. However, I just could not get it work. Any help will be appreciated. Thanks! http://rbvi.ucsf.edu/chimerax/docs/user/commands/open.html#clipper Best wishes, Winston

4 7

Chimerax 1.2.5 Ubuntu 16.04 failed to start
by Zhou, Bing-Rui (NIH/NCI) [E] 22 Jun '21

22 Jun '21

Hello ChimeraX developer, I am trying to update ChimeraX from v1.1 to v1.2.5 on a Ubuntu 16.04 Linux machine, but Chimerax v1.2.5 failed to start with the following error message: > sudo apt-get install ~/Downloads/ucsf-chimerax_1.2.5_amd64.deb >chimerax qt.qpa.plugin: Could not load the Qt platform plugin "xcb" in "" even though it was found. This application failed to start because no Qt platform plugin could be initialized. Reinstalling the application may fix this problem. Available platform plugins are: eglfs, linuxfb, minimal, minimalegl, offscreen, vnc, wayland-egl, wayland, wayland-xcomposite-egl, wayland-xcomposite-glx, xcb. Fatal Python error: Aborted Current thread 0x00007f5866636700 (most recent call first): File "/usr/lib/ucsf-chimerax/lib/python3.8/site-packages/chimerax/ui/gui.py", line 157 in __init__ File "/usr/lib/ucsf-chimerax/lib/python3.8/site-packages/ChimeraX_main.py", line 577 in init File "/usr/lib/ucsf-chimerax/lib/python3.8/site-packages/ChimeraX_main.py", line 1015 in <module> File "/usr/lib/ucsf-chimerax/lib/python3.8/runpy.py", line 87 in _run_code File "/usr/lib/ucsf-chimerax/lib/python3.8/runpy.py", line 194 in _run_module_as_main Aborted (core dumped) I could downgrade to ChimeraX v1.1 and it works fine, just wondering what has changed in v1.2.5 and if there is a fix for this issue. Thanks, Bing-Rui

2 2

Ball-and-stick model modification
by Volodymyr Dvornyk 21 Jun '21

21 Jun '21

Hello, I wonder whether it is possible to modify the ball-and-stick model shape, i.e., change color, ball diameter, stick length, etc. Right now, the only available presentation style is like one in the attachment. Maybe there is some way to modify it but I was unable to find. Thank you, Volodymyr ________________________________ DISCLAIMER: This electronic mail transmission contains confidential information intended only for the person(s) named. Any use, distribution, copying or disclosure by any other person is strictly prohibited. If you received this transmission in error, please notify the sender by reply e-mail and then destroy the message. Opinions, conclusions, and other information in this message that do not relate to the official business of Alfaisal University shall understand to be neither given nor endorsed by Alfaisal University. The contents of any attachment to this e-mail may contain software viruses, which could damage your own computer system. While "Alfaisal University" has taken every reasonable precaution to minimize this risk, we cannot accept liability for any damage which you sustain as a result of software viruses. You should carry out your own virus checks before opening the attachment.

4 7

Fwd: Troubles when saving a map
by Tom Goddard 18 Jun '21

18 Jun '21

Stephane's problem with the MRC map written by ChimeraX looking like noise in Coot was because the map origin was not correct. Tom > Begin forwarded message: > > From: Stéphane ROCHE > Subject: RE: [chimerax-users] Troubles when saving a map > Date: June 18, 2021 at 5:37:12 AM PDT > To: "Vadim Kotov" , "Tom Goddard" > > Thanks to both of you for your help ! > > I have finally understood what was happening, the origin of my map was changed and it was a very long way from its old position given that the box was quite large. So basically, when if I was looking around for densities, I was only scrolling inside the solvent. > > Thanks again, > Stephane Roche > > > On 17.06.21 10:07, Stéphane ROCHE via ChimeraX-users wrote: >> Dear Mr/Mrs, >> >> I am new to ChimeraX (v 0.7) and I have a trouble when saving a map. >> >> I am working with a .ccp4 map from an electron microscopy project. I would like to slightly change the pixel size that was inaccurately estimated during data processing and chimeraX seems to be the program for doing that. >> - Opening the map is fine. >> - Then I change the pixel voxelsize which is also fine. >> - I then save the modified map (I use the .mrc format here given that I do not find a .ccp4 format). >> - However if I then use the map with my usual softwares (phenix, coot) it looks like pure noise. But the map looks normal with some other softwares (e.g. pymol). I also have no problem usually with my .mrc maps with any software so I would assume the problem is with the .mrc map I created >> >> Do you know what I could do to solve this problem ? >> >> Thanks, >> Stephane Roche >> Institut de Biologie Intégrative de la Cellule >> 91198 Gif sur Yvette >> France >>

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Assistance
by Priyanka Abeyrathne 18 Jun '21

18 Jun '21

Hi, Could someone assist me to sort out the following? In Chimera, we can save PDB relative to the electron microscopy density map. Can we save the electron microscopy density map relative to the PDB? Any suggestion? Thank you. Priyanka

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Troubles when saving a map
by Stéphane ROCHE 17 Jun '21

17 Jun '21

Dear Mr/Mrs, I am new to ChimeraX (v 0.7) and I have a trouble when saving a map. I am working with a .ccp4 map from an electron microscopy project. I would like to slightly change the pixel size that was inaccurately estimated during data processing and chimeraX seems to be the program for doing that. - Opening the map is fine. - Then I change the pixel voxelsize which is also fine. - I then save the modified map (I use the .mrc format here given that I do not find a .ccp4 format). - However if I then use the map with my usual softwares (phenix, coot) it looks like pure noise. But the map looks normal with some other softwares (e.g. pymol). I also have no problem usually with my .mrc maps with any software so I would assume the problem is with the .mrc map I created Do you know what I could do to solve this problem ? Thanks, Stephane Roche Institut de Biologie Intégrative de la Cellule 91198 Gif sur Yvette France

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listing all-by-all atom distances
by Elaine Meng 15 Jun '21

15 Jun '21

> On Jun 15, 2021, at 9:33 AM, Juliana Glavina <jglavina(a)gmail.com> wrote: > > Hi Elaine, > I am trying to calculate the distance between one residue and a set of residues (within a name selection). I couldn't do this in Chimera either and I couldn't find the answer online. > Thanks! > Juliana Hi Juliana, (We recommend using the chimerax-users address CC'd here for questions, so that the Q & A will be archived and searchable.) One way to do it in ChimeraX is with the "contacts" command or Contacts tool. In this case you aren't necessarily using it to find contacts, but instead to measure and list atom-atom distances. You say "residues" but really all the distances are measured from atom to atom. You will get all by all distances between two sets of atoms, where the first set is your first residue and the second set is all the residues in your named selection. In ChimeraX, you can name the current selection or some other specification with the "name" command. To name the current selection "blah" it would be command: name frozen blah sel See "name" help: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/name.html> Then if you want to measure all atom-atom distances between (1) atoms in residue 55 of chain A of model 1 and (2) your named selection "blah" and show them in the Log, you could use a command something like contacts #1/A:55 restrict blah overlap -1000 log true The large negative overlap value is used to force measuring all the distances even if the atoms are 1000 Angstroms apart, instead of the usual behavior of finding only the contacts. The Log will have lines like the following, where the last column is the distance between atomic centers: 1728 contacts atom1 atom2 overlap distance /A BGC 310 C6 /A TYR 10 CE2 0.018 3.622 /A BGC 310 O6 /A HIS 152 NE2 -0.134 2.834 /A BGC 310 O4 /A TRP 183 CG -0.202 3.272 /A BGC 310 C3 /A TRP 183 CE3 -0.253 3.893 /A BGC 310 C2 /A PHE 16 CD1 -0.323 3.963 /A BGC 310 C5 /A HIS 152 NE2 -0.360 3.880 /A BGC 310 C6 /A HIS 152 NE2 -0.366 3.886 /A BGC 310 O4 /A TRP 183 CD2 -0.424 3.494 /A BGC 310 C5 /A TRP 183 CE2 -0.429 3.919 /A BGC 310 O6 /A HIS 152 CD2 -0.490 3.710 /A BGC 310 C3 /A TRP 183 CZ3 -0.495 4.135 /A BGC 310 O4 /A TRP 183 CD1 -0.499 3.719 /A BGC 310 O6 /A HIS 152 CE1 -0.556 3.776 /A BGC 310 C5 /A TRP 183 NE1 -0.596 4.116 [...] The lines are in order of largest VDW overlap which is similar to shortest distance but not exactly the same. If you save to text file you can then sort by column, for example, by the second residue number to group those together, or by the distance. The "contacts" command has a lot of options including saving results to text file, as detailed here: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/clashes.html> You can do the same thing in Chimera, name selection and use "findclash" but the exact commands and their syntax are slightly different. 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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Adjusting coil width
by Edgar A Hodge 15 Jun '21

15 Jun '21

Hello, I'm struggling to adjust the coil width. This seems easy to do using the "cartoon style" command, but I can't seem to figure it out with coils. Thanks! Eddie

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align peptide to model sequence
by Lagerwaard, I.M. (Ilse) 15 Jun '21

15 Jun '21

Hi everyone, I want to write a script that can align the sequences of peptides to a model sequence and return the identical residues. Because I am new to programming, I could really use some help to get started. Could I use the search() method of the Sequence class for this? And if so, how could I go about this? Kind regards Ilse Lagerwaard

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Mesh resolution/smoothness
by Saren Tasciyan 15 Jun '21

15 Jun '21

Hi, I am trying to generate STL files out of protein models. Often the problem is that the mesh doesn't as smooth as the models (see pics below). I wonder if this is an artifact of rendering in ChimeraX or the mesh is actually hard coded to have certain resolution, which makes it look like this? I tried to find out why and ended up in custom_x3d function but didn't notice anything. Post-export smoothing is an option but I wonder, if that's the optimal approach? Perhaps, smoothing can create collisions between 2 STL models, where a higher resolution export may avoid this. Best, Saren -- Saren Tasciyan /PhD Student / Sixt Group/ Institute of Science and Technology Austria Am Campus 1 3400 Klosterneuburg, Austria

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dual conformation
by Wen-Jin Winston Wu 14 Jun '21

14 Jun '21

Hi, I am trying to use Chimera X to display an amino acid with dual side chain conformations (PDB code: 7a5v) together with its cryoEM density map (EMDataResource: <https://www.emdataresource.org/EMD-11657> EMD-11657). For example, Tyr 66 have two side chain conformations, however using the command below, it only showed one conformation. resfit /a:66 map #1 (a very nice command, by the way) I then used Chimera 1.15 to view the PDB coordinate, and it showed two side chain conformations for Tyr66 (as I saw in PyMol); on the other hand, Chimera X only shows a single conformation. Is there any way to display the two alternative conformations using Chimera X? Thanks a lot for your time, and possible help! Best wishes, Winston ************************* ATOM 495 N ATYR A 66 124.799 162.717 112.222 0.50 11.67 N ATOM 496 N BTYR A 66 125.017 162.760 112.080 0.50 12.99 N ATOM 497 CA ATYR A 66 124.008 162.914 110.998 0.50 12.05 C ATOM 498 CA BTYR A 66 124.035 162.916 111.002 0.50 14.20 C ATOM 499 C ATYR A 66 124.638 164.062 110.190 0.50 11.84 C ATOM 500 C BTYR A 66 124.433 164.115 110.140 0.50 13.40 C ATOM 501 O ATYR A 66 125.008 165.077 110.788 0.50 11.86 O ATOM 502 O BTYR A 66 124.411 165.246 110.660 0.50 14.99 O ATOM 503 CB ATYR A 66 122.562 163.249 111.355 0.50 13.02 C ATOM 504 CB BTYR A 66 122.666 163.125 111.624 0.50 17.22 C ATOM 505 CG ATYR A 66 121.759 162.139 111.997 0.50 14.56 C ATOM 506 CG BTYR A 66 121.542 163.315 110.654 0.50 21.09 C ATOM 507 CD1ATYR A 66 121.860 161.839 113.348 0.50 16.21 C ATOM 508 CD1BTYR A 66 120.718 162.258 110.325 0.50 25.90 C ATOM 509 CD2ATYR A 66 120.832 161.436 111.248 0.50 17.74 C ATOM 510 CD2BTYR A 66 121.189 164.579 110.209 0.50 29.25 C ATOM 511 CE1ATYR A 66 120.974 160.942 113.960 0.50 18.53 C ATOM 512 CE1BTYR A 66 119.590 162.443 109.543 0.50 32.51 C ATOM 513 CE2ATYR A 66 119.990 160.494 111.824 0.50 18.57 C ATOM 514 CE2BTYR A 66 120.067 164.784 109.421 0.50 27.89 C ATOM 515 CZ ATYR A 66 120.076 160.228 113.177 0.50 20.29 C ATOM 516 CZ BTYR A 66 119.252 163.714 109.107 0.50 30.80 C ATOM 517 OH ATYR A 66 119.241 159.287 113.722 0.50 24.21 O ATOM 518 OH BTYR A 66 118.168 163.886 108.291 0.50 39.05

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using pandas
by Lagerwaard, I.M. (Ilse) 11 Jun '21

11 Jun '21

Hello everyone, Is it possible to use the pandas package in ChimeraX? I tried opening a Python script containing the line 'import pandas', but I get the error: 'ModuleNotFoundError: No module named 'pandas''. Kind regards, Ilse

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Independent centres of rotation
by Shahid, Taha (Dr.) 10 Jun '21

10 Jun '21

Hi, Is there a method, even if an indirect one via a long command or a series of commands, to set independent rotation centres for a series of (cryo-EM) maps that would then turn together. This could be easily achieved by 'set independent' in the original Chimera, and is much missed by our group of structural biologists. Kudos otherwise on a wonderful upgrade to the program. Many thanks, Taha

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Re: [chimerax-users] saving multiple .obj files from a morph
by Elaine Meng 09 Jun '21

09 Jun '21

On Jun 9, 2021, at 3:38 AM, Brett Murrah <murrahx5(a)att.net> wrote: > I’m trying my best to use the perframe command to save each frame / model out from a morph and slider animation after morphing some pdbs. It is exporting something.. but only 1k files. I’m not sure what I’m doing wrong. Any help? My command is this: > > perframe "save D:/Projects/OBJs/model$1.obj model #3.$1" frames 10 > > PS, I put model #3 because the ID’s for 1 and 2 are the models I used for the morphs. The final morph is #3. If I export each slider frame by hand.. that seems to work. Trying to automate it best I can. > > Thanks you for any help! > Brett Hi Brett, I'm guessing you meant to send this to chimerax-users(a)cgl.ucsf.edu (CC'd here, the recommended address for questions). The morph #3 is a trajectory model. It does not have the frames as submodels #3.1, 3.2, ... so your save command doesn't make sense. I don't know what you mean by "1k files" either... do you mean it makes 10 files but they are too small? You would use "perframe" in combination with "coordset" to replay the existing morph trajectory. E.g. put something like this into a command file (plain text named something.cxc) and then open it in ChimeraX: perframe "save D:/Projects/OBJs/model$1.obj models #3" coordset #3 1,10; wait 10 ~perframe <https://rbvi.ucsf.edu/chimerax/docs/user/commands/coordset.html> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/perframe.html> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/save.html> The reason I say to put it in a command file is to make the commands execute instantly one afer the other. I expected it to work when I entered them all as one long line in the command line (with semicolon separators) but then I got a parsing error, possibly due to a bug. E.g. I tried entering this as one long line (the mail tool may choose to break it up): perframe "save D:/Projects/OBJs/model$1.obj models #3"; coordset #3 1,10; wait 10; ~perframe ... but that gave an "incomplete quoted text" error which I will report as a bug. 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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Change default volume display settings?
by Oliver Clarke 08 Jun '21

08 Jun '21

Hi, Is there any way in ChimeraX to change default volume display settings? For example, I would like to set all volumes to "step 1" by default - in Chimera I can set these defaults in the Volume Viewer menu but I can't see an equivalent in ChimeraX. Sort of related - I wonder if it would be possible to have the option to set default display preferences for molecules or maps? Or more generally, have a script that executes when a file of a particular type is loaded - similar to how the startup commands are executed when ChimeraX is started, but triggered by the opening of a particular filetype and applied to that particular model? Cheers Oli

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Surface Coloring
by Juliana Glavina 07 Jun '21

07 Jun '21

Dear All, I am moving from Chimera to ChimeraX and I am trying to reproduce some of things that I used to do in Chimera. I managed to colour the surface by the kdHydrophobicity scale. However, the coloring is discrete with sharp edges between the residues. I was wondering if it was possible to smooth the edge between two different colors on the surface - similar to mlp but with customized attributes. Thank you very much in advance UCSF ChimeraX version: 1.2.3 (2021-05-13) Ubuntu 20.04 Juliana

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Re: [chimerax-users] Unit cell orientations
by Elaine Meng 04 Jun '21

04 Jun '21

> On Jun 4, 2021, at 10:39 AM, Silva, Chinthaka Mahesh <silva228(a)llnl.gov> wrote: > > Hi Elaine, > Is it possible to orient a unit cell along different axes in ChimeraX? I tried using ‘Unit cell’ option, but not sure if this is the correct place to do it. > Thanks! > -chinthaka Hi Chinthaka, (CC to chimerax-users(a)cgl.ucsf.edu ... please use that address for ChimeraX questions) Sorry, I don't understand the question. You can build the unit cell or a block of multiple unit cells with the Unit Cell tool: <https://rbvi.ucsf.edu/chimerax/docs/user/tools/unitcell.html> The axes of the unit cell are defined in the data... it is not something that you control. Of course, you can rotate it after you build it. Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco

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Consultation about developing plug-ins in ChimeraX
by Chen, Xiang 28 May '21

28 May '21

Dear Sir or Madam, I am a graduate student in the Department of Computer Science at the Memorial University of Newfoundland. I am currently engaged in developing and researching VR applications to visualize biological microstructures. I learned that Chimerax is a relatively mature piece of software, containing many excellent functions and features. So I'd like to know: 1. Is ChimeraX completely open-source and free? I will only use it for research and non-profit purposes. 2. If ChimeraX is open source, is there a description or summary of the structure/principles of the source code? (In order to learn what features are implemented by each code file.) 3. May I develop new plug-ins/bundles/modules based on ChimeraX's VR mode to implement one or more new features/functions? Could you please briefly describe the feasibility of developing it? Best regards, Xiang Chen --- Xiang Chen, M.Sc. # 201992538 Department of Computer Science Memorial University of Newfoundland St. John's, NL, Canada T (709) 219-2960 / E xiangc(a)mun.ca

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Structure move
by Silva, Chinthaka Mahesh 28 May '21

28 May '21

Hello, If I have more than one structure opened in ChimeraX and want to move them apart, can I do that? I see that I can move a structure model using 'right mouse' option, but not the structures. Chimera had the option to do this by deactivating a structure. Thanks! -chinthaka

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Pair-fitting in ChimeraX
by Rachael Coleman 28 May '21

28 May '21

Hello again, You guys were so helpful last time I figured I'd just ask for help again! I'm trying to do something that I know is a feature in PyMol but I'm not sure if it is a feature in ChimeraX (yet). In PyMol, there is a function to pair fit over specific atoms between two different structures. I have tried using the Matchmaker tool in ChimeraX to do this, but I think the dilemma is I'm trying to align the protein relative to the position of specific atoms in a heme cofactor across two different structures and that isn't something in the primary sequence of the protein. I also could just be doing something wrong in the matchmaker process. Do you know if there is an easy way to accomplish this in ChimeraX? Best regards, Rachael Coleman -- *Rachael E. Coleman* PhD Candidate, Lancaster Group Department of Chemistry and Chemical Biology Cornell University Ithaca, NY 14853 Pronouns: She, her, hers

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ChimeraX version 1.2 released!
by Elaine Meng 28 May '21

28 May '21

UCSF ChimeraX version 1.2 has been released! Major changes since v1.1 (Aug 2020) include: - Surface Color tool - Unit Cell tool - Color Key tool and command - Crystal Contacts tool and command - volume tools: Hide Dust, Color Zone, Surface Zone - Meeting panel for multiperson VR - "fly" command for smooth motion along multiple saved views - "rmsd" command for calculating RMSD in current positions (w/o fitting) - nucleic-acid building - bond deletion/addition - UniProt fetch includes sequence feature annotations (domains, mutations, modification sites, etc.) - support for Amber netCDF trajectories - smaller session files - faster saving of sessions with maps - mouse mode for moving a clicked model without having to select it For more details, see the ChimeraX change log: https://www.rbvi.ucsf.edu/trac/ChimeraX/wiki/ChangeLog Downloads: https://www.rbvi.ucsf.edu/chimerax/download.html

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Downloading Daily builds
by Moradkhan, Tiglath A 27 May '21

27 May '21

Hi, I don't know why the Fetch Additional Scores button is not returning these scores. I get the message that scores have been initiated but then nothing happens. It's annoying that I keep have to download newly released daily builds on my computer, so I can use it. Thank you Tiglath

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Web services down
by Eric Pettersen 25 May '21

25 May '21

Hi all, Due to computing cluster maintenance starting this evening (5/25) through tomorrow evening (5/26), the web services in Chimera and ChimeraX that use our cluster will be down. The frequently used web services are BLAST and Modeller for both programs, and for Chimera only: sequence realignment via Clustal Omega or MUSCLE; SAXS2; and 2D ligand depiction. --Eric Eric Pettersen UCSF Computer Graphics Lab

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Fwd: Wireframe option
by Eric Pettersen 24 May '21

24 May '21

> Begin forwarded message: > > From: "Silva, Chinthaka Mahesh" <silva228(a)llnl.gov> > Subject: Wireframe option > Date: May 24, 2021 at 12:38:13 PM PDT > To: "chimerax-bugs(a)cgl.ucsf.edu" <chimerax-bugs(a)cgl.ucsf.edu> > > Hello, > > Can you tell me how to draw pdb models using the ‘wireframe’ mode? > > Thanks! > -chinthaka

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