- Chimera-users - RBVI Mailing Lists

Move models around independent of each other in Chimera X
by Prathvi Singh 24 Dec '21

24 Dec '21

Hi, First of all, thank a million to the chimera X development team for incorporating the drag & drop feature in chimera X. I really missed it in chimera. However, after opening two models in the same window, I am unable to find a way to move/rotate model-1 in such a way that it does not move/rotate model-2. I could do this in chimera by unchecking the box for model-2 but when I do the same in chimera-X, it doesn't seem to work. Also, I am unable to find a way to disable depth cueing in chimera X. Please help. Thank you -- Prathvi Singh, Research Fellow, Department of Biological Sciences & Bioengineering, Indian Institute of Technology, Kanpur-208016

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Fwd: Chimera bug report submission
by Eric Pettersen 21 Dec '21

21 Dec '21

> Begin forwarded message: > > From: Kenji Matsui <s214903z(a)st.go.tuat.ac.jp> > Subject: Chimera bug report submission > Date: December 19, 2021 at 11:33:41 PM PST > To: chimera-bugs(a)cgl.ucsf.edu > > The following bug report has been submitted: > Platform: windows_x86_64 > Chimera Version: 1.16 > Description > I would like to see the interaction between the ligand and the protein, but I was not able to display it in the way described in the tutorial. How can I do that? > > Method > select →ligand > > Tool Structure analysis Find H-bond Line length 3.0 Å > > check Relax H-bond ~, Only find, Include intera-molecular, Include intra-residue > > apply →OK > File attachment: osh4,OSW-1220.py

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1.16 release
by Eric Pettersen 20 Dec '21

20 Dec '21

Chimera production release 1.16 is now available <https://www.cgl.ucsf.edu/chimera/download.html>. This will be the last release to support Windows 7. See the release notes <https://www.cgl.ucsf.edu/chimera/docs/relnotes/1.16.html> for what's new. --Eric Eric Pettersen UCSF Computer Graphics Lab

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Re: [Chimera-users] .dae export for ChimeraX
by Tom Goddard 18 Dec '21

18 Dec '21

Hi Byrne, Thanks for the info about exporting models for iOS. Glad you found a way to export a virus model from ChimeraX suitable for use in iOS apps made with Xcode. The STL format is just a list of triangles, each with 3 vertex (x,y,z) coordinates, used mostly for 3D printing. It does not have vertex normal vectors which are used to give smoother lighting. In the future maybe ChimeraX will directly export Collada (*.dae) files and you will be able to export a usable model without running it through Blender. As I mentioned before we support GLTF but not Collada currently. Our ChimeraX efforts are mostly to help researchers analyze molecular structures so adding this does not have highest priority. Unfortunately there are hundreds of feature requests we do not have time to implement with our limited funding. Tom > On Dec 18, 2021, at 9:34 AM, Byrne Pedit <bpedit(a)comcast.net> wrote: > > Hello again Tom, > > A follow-up follow-up. After extensive testing I have found a useable workflow from ChimeraX to iOS. Of course iOS apps may utilize PDB viewers, this is for folks who may want to incorporate models, in customized ways, into SceneKit for manipulation. > > ChimeraX ––> STL ––(graphics editor)––> DAE ––Xcode––> SCN > > • In Chimera > – reduce polys as much as possible* > – export individual elements, e.g. chains, if you want individual control (materials, etc) > • In a graphics editor: > – eliminate polygonal faceting of STL files > - Blender, check Auto Smooth in addition to toggling on Smooth Shading > - Cinema 4D, add a phong tag > – recenter if desired, add additional elements > > *You might want to add surfaces to your reducing file-size tutorial. In the model below, the spike's resolution was set to 7, gridSpacing 3. You also need to click Hide for Atoms and Cartoons; otherwise they will severely bloat the file even though not seen. The entire file size of this SARS-CoV-2 model, as used by iOS, is 1.2 Mb (all but one of the spikes are all clones). > > Thanks again for the help, > > Byrne > > > > > > >> On Dec 3, 2021, at 11:00 PM, Tom Goddard <goddard(a)sonic.net <mailto:goddard@sonic.net>> wrote: >> >> Hi Byrne, >> >> Thanks! So Blender can convert GLTF to Collada. The ChimeraX GLTF is binary and Collada is all text, so no surprise that the file size is much larger. If we add Collada support it would be produced directly from the ChimeraX scene, not converting from GLTF. But we have hundreds of new feature requests so I don't think Collada output is likely to be added soon, unless a funded project needs it. >> >> Tom >> >>> On Dec 3, 2021, at 9:48 AM, Byrne Pedit <bpedit(a)comcast.net <mailto:bpedit@comcast.net>> wrote: >>> >>> Hi Tom, >>> >>> A follow-up for future reference. Blender, the one recommendation I found on StackOverflow, is indeed capable of converting GLTF to DAE. But the conversion bloats the files by as much as 10x! In addition, the hierarchy is only partially preserved. I tried an on-line converter with even less satisfactory results. So I think this pathway is a bust. This might serve as a fair warning for ChimeraX developers to avoid an internal conversion from GLTF if introducing a DAE export option. >>> >>> >>> Byrne >>> >>> >>> >>> >>>> On Dec 2, 2021, at 2:22 PM, Tom Goddard <goddard(a)sonic.net <mailto:goddard@sonic.net>> wrote: >>>> >>>> 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 <https://www.rbvi.ucsf.edu/chimerax/data/texture-may2021/export_3d.html> >>>> >>>> Tom >>>> >>>> Model from gltf export from linked ChimeraX example >>>> >>>> <spike.png> >>>> >>>> >>>>> On Dec 2, 2021, at 2:04 PM, Byrne Pedit <bpedit(a)comcast.net <mailto:bpedit@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://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users <https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users> >>>>>>> >>>>>> >>>>> >>>> >>> >> >

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Selection command for atoms in different models
by Woodbrey Anne 14 Dec '21

14 Dec '21

Hi, Is there a way to select residues from 2 different models using a single line of command? For example, I want to select residues 230 and 260 of Model 0 and residues 232 and 262 of Model 1. I then want to display the side chains, color magenta, then color by heteroatom. This is what my current (annoying) workflow is: select #0:230,260 Actions --> Color --> Magenta Actions --> Color --> By heteroatom select #1:232,262 Actions --> Color --> Magenta Actions --> Color --> By heteroatom I know I can do the following instead: disp #0:230,260 color magenta #0:230,260 color byhet #0:230,260 Repeat for #1:232,262 ...but it doesn't really save any time. I want to select all 4 residues at once without having to ctrl + shift + click on them all. Please tell me there's a way! Thank you, Annie

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calculating radius of gyration
by Elaine Meng 14 Dec '21

14 Dec '21

> On Dec 14, 2021, at 11:10 AM, Simon.Chapman <simon.chapman(a)open.ac.uk> wrote: > > Hello again Elaine. All going very well with Chimera, and I've introduced the software to some more of mt students. > > But, is there a way to plot radius of gyration from the simualtion data? I would have thought somehow the RMSD over time should allow that? > > Best wishes Hi Simon, Thanks for introducing others to Chimera! I'm not the expert on this topic, so I had to consult with others to answer this question. Just as a reminder, it's recommended to send questions to chimera-users(a)cgl.ucsf.edu (CC'd here) unless what you are sending needs to remain private. I don't know everything (surprise!) or I might not understand your question as well as somebody else does. RMSD compares different sets of coordinates, so I don't think that gets you anything like the radius of gyration of a single set of coordinates. There are some scripts to calculate radius of gyration on the Chimera Python Scripts page: <https://plato.cgl.ucsf.edu/trac/chimera/wiki/Scripts> 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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Translate onto the X-axis
by Yasser Almeida 14 Dec '21

14 Dec '21

Hello, I have a complex of two proteins that I want to align to the X-axis. Specifically, I want to define a vector between the COMs of each protein, and then translate the whole system so that the vector is on the X-axis, where the COM of one protein is on the cartesian origin [0, 0, 0] and the other COM is in [+X, 0, 0]. How can I achieve this with Chimera? Thanks in advance, Yasser

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Save multiple fitted maps in Chimera
by Huabin Zhou 13 Dec '21

13 Dec '21

Dear Chimera team and users, I am trying fit hundreds of protein density maps into a tomogram by manually adjusting their positions. After the placement, I found I can't save all the maps together in a single mrc file. Is there anyway to do so? Or is there a way to extract the relative orientations of the individual models? Thank you! Best, Huabin ________________________________ UT Southwestern Medical Center The future of medicine, today.

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Help please: extracting distances from each frame of a short MD
by Anne-Frances Miller 11 Dec '21

11 Dec '21

Dear Chimera support, I want to extract a set of distances and one angle from each snapshot of an MD trajectory (there are 11 of them). My plan was to have all my distances appear in one of the MD-movie analysis>plot distances windows and use ‘Dump Values’ to get my numbers out in a way I could use for other plots. I realize angles cannot appear in the same plot, but hope I can measure an angle in the same script. I have a ‘per-frame’ script that runs fine on the first frame, however it returns ‘Problem in per-frame script: Distance monitor already exists’ when I step forward to a second frame. Nothing appears in a 'MD plots' window (such a window does not open on its own either). Reply Log shows the correct distances for the first frame but then only repeats the error after that. Problem in per-frame script: Distance monitor already exists My work-flow: Open MD/movie, load my trajectory open analysis, Per-Frame copy my script into the window (chimera commands) click ‘apply' in the script window, click ‘play’ or step forward one frame in the MD GUI (looping disabled) My script: ~disp ~ribbon disp :718,720,721,722,730,740,741,1058 distance :1058@O2 :741@ND1 distance :730@OH :741@NE2 distance :721@OG1 :1058@N5 distance :718@O :1058@N3 distance :721@N :1058@O4 distance :722@N :1058@O4 distance :720@N :1058@O4 distance :740@O :720@N angle :1058@C2 :1058@O2 :741@HD1 :741@ND1 Reply Log output: Distance between FDM 1058 O2 and HID 741 ND1: 2.8 Distance between TYR 730 OH and HID 741 NE2: 2.8 Distance between THR 721 OG1 and FDM 1058 N5: 3.4 Distance between ILE 718 O and FDM 1058 N3: 3.2 Distance between THR 721 N and FDM 1058 O4: 2.9 Distance between GLY 722 N and FDM 1058 O4: 3.2 Distance between GLN 720 N and FDM 1058 O4: 3.2 Distance between GLN 740 O and GLN 720 N: 3.0 Dihedral #0:1058@C2 #0:1058@O2 #0:741@HD1 #0:741@ND1: -51.0515 Problem in per-frame script: Distance monitor already exists Thank you for any assistance, Anne-Frances - • - • - • - • - • - • - • - • - A.-F. Miller, Ph. D. (she/elle/sie) University Research Professor Professor of Chemistry University of Kentucky https://www.uky.edu/~afm/ Visiting Fellow, Einstein Foundation of Berlin

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Questions about Matchmaker and GDT
by Ralph Loring 10 Dec '21

10 Dec '21

Hi, I don't know if there's a special user group for Matchmaker but this also involves other aspects of Chimera. 1) I'm looking at AlphaFold structures of RIC-3, a chaperone for nicotinic receptors that is also an intrinsically disordered protein. There are pdbs for six species in the AlphaFold database: Human, mouse rat, fish, fly and worm. These differ tremendously in terms of sequence, size and predicted secondary structures but they all have a putative signal sequence and a transmembrane domain. I used Matchmaker to align the human pdb to each of the others. The results of combining all 6 looks like a bowl of spaghetti until the parts before the putative signal sequence and the C-terminal tails are deleted. Then I can see that the putative signal sequences and the transmembrane domains are in the same plane as if they are in a membrane. I just want to confirm that this is merely a lucky coincidence and that Matchmaker has no preference for aligning hydrophobic alpha helices into a planar space corresponding to a membrane. The coincidence, if it is one, is striking and I just want to make sure. Note that I have a similar question for AlphaFold, the source of the pdbs. 2) Does Chimera do Global Distance Testing (GDT)? For that matter, does ChimeraX (I've been thinking about switching and if it does, this may be what it takes to get over the activation energy barrier)? I can't find GDT in any of the directions. When Matchmaker runs, for instance comparing human and fly RIC-3, the sequence alignment score is only 270 but the RMSD is 1.6 angstroms (but only for 7 pruned atom pairs and when all 233 atom pairs are considered, the RMSD is 55 angstroms, so clearly not much overlap). I've heard that GDT corrects somewhat better than RMSD for not having precise superimposition. However, I don't know that it would make a lot of difference in this case but I'd like to find out. The mystery is that drosophila RIC-3 works almost as well as human RIC-3 in helping assemble human pentameric nicotinic receptors even though the structures are so different. Thanks for your help, Ralph Loring

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