- Chimera-users - RBVI Mailing Lists

Model placement side by side
by George Tzotzos 07 Jan '22

07 Jan '22

Hi, Having superimposed 4 structures using MatchMaker, is there a way to view the aligned structures in a window grid? Moving them manually after superimposition is not optimal. Thanks in advance for any suggestions and best wishes for 2022

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Introduce a-helices into protein structure ab initio
by Chara Spanou 06 Jan '22

06 Jan '22

Hello chimera-users, I would like to introduce a-helices into my protein structure ab initio. Is it possible to do this with chimera? Another option that I have is to take a-helical pieces of sequence from a different model and introduce these into the desired model. Would that be more feasible? There is a chance I also need to introduce loops and turns ab initio to best localize the introduced a-helices within my protein structure. Can you please indicate how can a chimera user build all this ab initio? Thank you in advance for your time and help, Chara SpanouPhD studentUniversity of Cologne

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report rotate and shift value in MatchMaker
by Yanhe Zhao 06 Jan '22

06 Jan '22

Greeting there, Happy New Year! How can find the rotate and shift value after I done the 'MatchMaker' in Chimera? Thanks and regards, Yanhe

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Question: PDB file creation
by Kenji MATSUI 05 Jan '22

05 Jan '22

Dear Chimera company Thank you for allowing me to use your software. I am Japanese, so I hope you will understand that there are some inappropriate expressions. I would like to ask you one question. I would like to know how to overlay the docked protein (osh4)-ligand (cholesterol) complex (the gray one in the figure) and the complex on the PDB. [image: image.png] Aim I would like to know how well the docked data matches the data in the PDB. Methods I have tried I did it based on the following link from Chimera. https://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/matchalign/matcha… Thank you for your cooperation. --------------------------------------------------------------------------- 松井健治東京農工大学大学院工学府産業技術専攻修士〒184-8588 東京都小金井市中町2-24-16 Mail: s214903z(a)st.go.tuat.ac.jp Kenji Matsui Graduate School of Tokyo University of Agriculture and Technology 2-24-16, Nakamachi, Koganei-shi, Tokyo 184-8588, Japan Mail: s214903z(a)st.go.tuat.ac.jp

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report rotate and shift in MatchMaker
by Yanhe Zhao 04 Jan '22

04 Jan '22

Greeting there, How can find the rotate and shift value after I done the 'MatchMaker' in Chimera? Thanks and regards, Yanhe

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Opening .py files
by Henry Shook 04 Jan '22

04 Jan '22

Chimera User Support, I'm working on dockprepping the sars-2 main protease and whenever I try and save it as a .py file, I can't open it from sources other than the saved session I wrote. Whenever I try and open it from a dropbox or my finder, I get the message: Error while processing /Users/8642165/Desktop/Research/DC AP Research /[7l0d]DOCKPREPPEDFINAL.py: File "[7l0d]DOCKPREPPEDFINAL.py", line 1 @<TRIPOS>MOLECULE ^ SyntaxError: invalid syntax File "/Applications/Chimera.app/Contents/Resources/share/chimera/__init__.py", line 1325, in _openPython loadFunc(sandboxName, fileName, f) See reply log for Python traceback. Is there any way that I can fix this problem? Thanks, Henry Shook

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Helix Display Artefact
by Sebastian Guettler 28 Dec '21

28 Dec '21

Dear Chimera users, I have a problem with what I think is some sort of a helix display artefact is UCSF Chimera (including the latest release, 1.16). I attach an image. In cartoon display, the helix appears turned inside out for the last turn. It is displayed normally in ChimeraX and PyMol, and the display problem is independent of the secondary structure assignment algorithm (dssp, ksdssp, Stride). Any suggestions on how to solve this issue are welcome. Thank you, Sebastian --------------------------------------------- Sebastian Guettler, PhD Team Leader The Institute of Cancer Research (ICR) Divisions of Structural Biology and Cancer Biology London, UK --------------------------------------------- [cid:image001.jpg@01D7FC0A.1ED3ABA0] The Institute of Cancer Research: Royal Cancer Hospital, a charitable Company Limited by Guarantee, Registered in England under Company No. 534147 with its Registered Office at 123 Old Brompton Road, London SW7 3RP. This e-mail message is confidential and for use by the addressee only. If the message is received by anyone other than the addressee, please return the message to the sender by replying to it and then delete the message from your computer and network.

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Blank screen after MD simulations
by Sri Oruganty 28 Dec '21

28 Dec '21

Hello, I am a senior in high school, and I was interested in learning about proteins and mutations. I download Chimera to run MD simulations on a specific protein, but not all the frames are loading. After the frame number gets to a certain point (i.e. 14) every subsequent frame is completely blank. Why is this happening? Best regards, Srigouri Oruganty Pronouns: She, her, hers sri.oruganty(a)gmail.com (610)-207-6325

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Problem related to the "Near" atom in the "Adjust Torsions" tool of UCSF chimera
by Prathvi Singh 26 Dec '21

26 Dec '21

Hi Elaine, I have one more query. I have a residue (its ID is #0:140.a) in a protein model. I want to change the torsion angle between its backbone N, backbone C-alpha, sidechain C-beta & sidechain C-gamma. In order to do that, I execute the following command: rotation 1 :140.a@CA,140.a@CB The execution activates the torsion & lists it in the "Adjust Torsions" tool. However, I have noticed that the "near" atom in the "Adjust Torsions" tool is sometimes assigned to backbone N & other times is assigned to backbone C. This is messing up my calculations. Is there a way to fix the "near" atom to backbone N so that it does not change to backbone C? Thanks again -- Prathvi Singh, Research Fellow, Department of Biological Sciences & Bioengineering, Indian Institute of Technology, Kanpur-208016

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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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re-sampled map (volume resample #X onGrid #Y) difference with general mrc map
by Dmitry Semchonok 10 Dec '21

10 Dec '21

Dear colleagues, I have an issue with the output map re-sampled from the resampling step protocol. Could you please explain how different the re-sampled map is compared to the general mrc map (without rotation manipulations)? Because it seems that some important information is missing or/changed in the re-sampled.mrc Kind regards, Dmitry

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Questions about IMOD files in Chimera software.
by 박시훈 09 Dec '21

09 Dec '21

Dear chimera-users community, I have questions about opening IMOD files in Chimera software. Can I open the IMOD files (*.mod) in Chimera? Or, Can I make a hand-drawn mask file in Chimera? I could apply several filters and masks in my iso-surface map, however, I don't know how to apply these options in Chimera. Moreover, the reconstructed tomograms were shown to the inverted iso-surface map unlike IMOD.. Can I re-invert the iso-surface map in Chimera? Best regards Si Hoon Park

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Selecting residues from one chain
by Joao M.C. Teixeira 09 Dec '21

09 Dec '21

Hi, I am a bit confused on how to select residues from a chain. This is the command I am trying:

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Chimera error at start-up
by Hernando J Sosa 09 Dec '21

09 Dec '21

Dear Chimera, I cannot open Chimer anymore in a computer (Windos10 64) where it was running until yesterday. I tried with no success reinstalling the program and installing the latestChimera daily release. The error that I get at startup says: [cid:cfb0a3aa-9306-42f0-bfd0-328d433ceb1e] If I start in debug mode I get the following error in a command window: Cannot execute 'gzip': no automatic decompression of .Z files initializing general preferences loading Tix initializing graphics Return code: -1073741819 How can I resolve this issue? Thanks Hernando ___________________________________

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Mismatch between display and saved image
by Visvaldas K. 09 Dec '21

09 Dec '21

Dear all, I get a very odd mismatch between what is displayed and what is saved as a png image. I am attaching two figures, and you can probably guess what I want. Of course I will try this in ChimeraX if I am not able to fix the figure, but the image took quite some work, so I'd hate redoing it... Or I could use screenshot I guess... But certainly this is some sort of bug. I'm using Chimera 1.15 on MacOS 12.0.1. Thank you, Vis

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Chimera on RDS Servers farm
by ROTH Stephane (DNUM) 09 Dec '21

09 Dec '21

Hi, We want to use Chimera on RDS Windows Server (Windows Server 2012). Its possible to use it on this environment ? What is the system recommendation to windows platform ? Best Regards, -- Cordialement, Stephane Roth 03 68 85 11 94 Chef de Projet / Ingénieur Systèmes Direction du Numérique Université de Strasbourg

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aPNG
by Frank Irby 07 Dec '21

07 Dec '21

I produce high quality Animated PNG files and it takes a lot of juggling different computers to accomplish.Is there a way to simply chose APNG from the movie recorder output pulldown menue?Would there be a plug in for that? My animations can be found at:https://www.deviantart.com/mandelscape/gallery/24158715/molecular Thank you Sent from Yahoo Mail on Android

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Re: [Chimera-users] Question about Chimera Fit in Map
by Tom Goddard 06 Dec '21

06 Dec '21

Hi Rakesh, Chimera Fit in Map and also the measure correlation command by default only compute the cross-correlation within the displayed envelope of the first map. So it should give the masked value you are looking for, although the actual value will depend sensitively on the surface level of the first map that you choose since that will control which grid points near the boundary of your fragment are included. There is no right answer about how tightly to mask and since the correlation value is so sensitive to that it is not too meaningful to try to compare correlation values although people do it anyways. Check out the measure correlation and fit in map docs for more details https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/measure.html#correla… https://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/fitmaps/fitmaps.h… Tom On 12/6/2021 5:09 PM, Rakesh Ramachandran wrote: > Sorry, what I meant was say I am fitting a fragment into a large map, > the cross correlation should be calculated only around the fitted > region of the fragment, that is any voxels outside the fragment > location should not be taken into account in the cross-correlation score. > > I need this because I am fitting fragments of different sizes into a > map and I tend to get quite similar cross correlation scores even > though principally it should. > > On Mon, Dec 6, 2021 at 5:03 PM Tom Goddard <goddard(a)sonic.net > <mailto:goddard@sonic.net>> wrote: > > Hi Rakesh, > > I don't understand what you mean by "length normalized by > masking". Chimera can compute cross-correlation using the Fit in > Map panel. If you are fitting an atomic model to the map it needs > to simulate a map from the atomic model since correlation is > between two maps. You do that using the "Use map simulated from > atoms" option in the Fit in Map panel Options pane. > > Tom > > > On 12/6/2021 4:00 PM, Rakesh Ramachandran wrote: >> Hi Tom, >> I am using Chimera Fit in Map for EM fitting. Though it does >> fit well, I want to calculate a cross correlation score based on >> the model map size, that is the cross correlation should be >> length normalized by masking the rest of the map. >> >> -- >> Regards >> Rakesh Ramachandran > > > > -- > Regards > Rakesh Ramachandran

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Re: [Chimera-users] Question about Chimera Fit in Map
by Tom Goddard 06 Dec '21

06 Dec '21

Hi Rakesh, I don't understand what you mean by "length normalized by masking". Chimera can compute cross-correlation using the Fit in Map panel. If you are fitting an atomic model to the map it needs to simulate a map from the atomic model since correlation is between two maps. You do that using the "Use map simulated from atoms" option in the Fit in Map panel Options pane. Tom On 12/6/2021 4:00 PM, Rakesh Ramachandran wrote: > Hi Tom, > I am using Chimera Fit in Map for EM fitting. Though it does fit > well, I want to calculate a cross correlation score based on the model > map size, that is the cross correlation should be length normalized by > masking the rest of the map. > > -- > Regards > Rakesh Ramachandran

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Error when starting Chimera
by vaishnavy chaurasia 03 Dec '21

03 Dec '21

How I fix it.... Please help... Please it's urgent

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Re: [Chimera-users] mRNA Structure
by Elaine Meng 03 Dec '21

03 Dec '21

> On Dec 3, 2021, at 6:44 AM, SANDOVAL, KENNETH <K.SANDOVAL1(a)nuigalway.ie> wrote: > > Hello, > I have a predicted secondary structure of an mRNA molecule. I am interested in trying to visualize this with UCSF Chimera. But I'm unsure what file format the program accepts for this? Does it need some sort of mRNA equivalent of a .pdb file? > Thank you, > Kenneth Hello Kenneth, The recommended address for Chimera questions is chimera-users(a)cgl.ucsf.edu CC'd here. By secondary structure I'm guessing that you mean the base-pairing pattern, and not actually 3D atomic coordinates. For Chimera you would generally need 3D atomic coordinates, most commonly in PDB format. If that is really what you have (base-pairing information only), then here are two ideas for building a 3D structure in Chimera using that information: (1) The RNArtist plugin to Chimera - quite extensive, has a lot of nice features, needs to be downloaded separately: <https://github.com/fjossinet/RNArtist> <https://www.rbvi.ucsf.edu/chimera/plugins/plugins.html> (2) The "rna" command in Chimera can also build models but much more roughly. See "rna model": <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/rna.html> <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/rna.html#model> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco

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Re: [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://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users <https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users> >>> >> >

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UCSF software cannot be opened normally
by 免孑 02 Dec '21

02 Dec '21

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.dae export for ChimeraX
by Byrne Pedit 02 Dec '21

02 Dec '21

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.)

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Curiosity regarding amino acid category in UCSF chimera
by Prathvi Singh 01 Dec '21

01 Dec '21

Hi, In UCSF chimera, when I go to Select > Residue > Amino Acid Category > Hydrophobic, the LYSINE residues also get selected. However, according to the Kyte-Dolittle scale, LYSINE is a fairly hydrophilic residue. Is there any specific reason why chimera lists them as hydrophobic residues? -- Prathvi Singh, Research Fellow, Department of Biological Sciences & Bioengineering, Indian Institute of Technology, Kanpur-208016

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Minimization on complex
by Francesca Magarotto - francesca.magarotto2＠studio.unibo.it 29 Nov '21

29 Nov '21

Hi, I need an advice regarding minimization of complexes. I've performed a virtual screening and I've selected some molecules of interest. Now, I've looked for the possibile interactions in the binding site and I would like to perform a minimization moving only the hydrogen atoms in the binding site. However, I have to create a new file pdb complex formed by my protein and one molecule from VS results. So, I opened the pdb file of the protein and the mol2 file of the molecule from the VS: now, do I need to save a pdb file of the complex and how to save it? I need the hydrogens to move according to the ligand inside the protein and I don't know if it's possibile with both the type of saving (is it better individual MOLECULE sections or combined MOLECULE section?). Moreover, I don't know if (for this kind of purpose) it's better first to save the complex in pdb file and then to use dockprep and minimization or use dockprep and minimization and only after saving the file of the complex. My main aim is to see if some hydrogens of the residues in the binding site move their places according to the presence of this ligand. Hope someone can help me, thanks.

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Get Minimization Energy
by Leonard Zhao 26 Nov '21

26 Nov '21

Hello, I am running a Python script to perform multiple structure minimizations and I need to extract to final potential energy from each minimization. I see that the potential energy is usually reported in the Reply Log, but when IDLE is open, it is instead redirected to IDLE. Is there any way to redirect it back to the Reply Log so I can more easily extract it in my script, or is there some other method to easily extract the energy value programmatically? Thanks, Leonard Zhao

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question regarding UCSF Chimera FindHBond feature
by Aditi Laddha 25 Nov '21

25 Nov '21

Hello, I have been using the FindHBond feature of Chimera for finding hydrogen bonds between water molecules and the polypeptide chains. I need to use some specific distance and angle criteria to find H-bonds, so I wanted to ask what is the default distance (D....A) and angle criteria (D-H....A) used in the software to find out the H-bonds, -- Regards, Aditi Laddha PhD Scholar Indian Institute of Technology, Kanpur, Uttar Pradesh 208016

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how to rectify error No MMTK name for atom
by Smriti Singh 2018RBT01 24 Nov '21

24 Nov '21

hello administrator, I am trying to minimize the Nucleotide sequence (DNA aptamer) through chimera. While performing energy minimisation steps, Chimera error "No MMTK name for atom 'HO5' in standard residue 'DA' showed. Please let me know how to rectify this issue. With warm regards Smriti Singh Research Scholar Department of Biotechnology MNNIT Allahabad

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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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Chimera compatibility with Window 11
by HK Haris 23 Nov '21

23 Nov '21

Hi, Please confirm can I download the following version of Chimera on my laptop which is operating on Windows 11. Microsoft Windows 64-bit chimera-1.15-win64.exe <https://www.cgl.ucsf.edu/chimera/cgi-bin/secure/chimera-get.py?file=win64/c…> Size: 152310162 bytes MD5: 6a68ab33f35a298059b9ef89f6372cfc Dec 18, 2020 Instructions <https://www.cgl.ucsf.edu/chimera/data/downloads/1.15/win64.html> Documentation <https://www.cgl.ucsf.edu/chimera/data/downloads/1.15/docs/> Runs on Windows 7 or later. *Best Regards,Dr. HIRA KHALID* Associate Professor Chemistry Forman Christian College University (A Chartered University) Lahore, Pakistan.54600 Ph: 042-99231581-88 x: 562 www.fccollege.edu.pk ........................ HEC APPROVED Supervisor Advisor ACS Punjab Associate member RSC Member & Ambassador Chemistry ACS Member AOCS Life-time CSP Member IUPAC Young Fellow

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FAD Topology/Parameter Files
by Zehra GÜNEŞ 22 Nov '21

22 Nov '21

Dear all, I am working on a research protein that contains FAD. I have tried to prepare it for simulation but unfortunately I have neither trajectory nor parameter file of FAD. Would it be possible to share with me these files if you have? Thanks in advance, Zehra Güneş

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chimera, H-bonds
by Rio Aquarius 19 Nov '21

19 Nov '21

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?

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How to smooth trajectory?
by Saikat Pal 15 Nov '21

15 Nov '21

Dear all, I want to make a movie using chimera. So, what are the steps to smooth the trajectory? Thanks and Regards, Saikat Pal

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Chimera Launch Error
by Cassidy Terrell 12 Nov '21

12 Nov '21

Hello, A student in my course (cced here) is trying to open Chimera 1.15 and this is the error message that appears: "chimera exited abnormally; the exit code was -1073741819. Use the --debug command line option for the full error message." We cannot open the program, which mean we cannot get to the command line. Thoughts about how to proceed? We have already removed/uninstalled previous version and re-downloaded new one. The same messages appears each time. Best Cassidy -- Cassidy R. Terrell, Ph.D. (she/her/hers) Assistant Professor, Biochemistry Center for Learning Innovation | University of Minnesota | Rochester 300 University Square | Rochester, MN 55904 *Always believe something wonderful is about to happen*

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Regarding publication using Chimera.
by Kavya Pandya 11 Nov '21

11 Nov '21

Dear Sir/Ma'am, I am a PhD scholar at the Institute of Advanced Research, India. I have been using the free version of Chimera for the last few days. I wanted to ask if I could publish the images created in Chimera using that free version by citing it appropriately using the citation provided on the website or do I need to buy the license to publish? Would you please guide me for the same. Thank You Kavya PhD Scholar -- Disclaimer : This e-mail and any files transmitted with it are for the sole use of the intended recipient(s) /addressee and may contain confidential and privileged information. If you are not the intended recipient/addressee, please contact the sender by reply e-mail and destroy all copies and the original message. Any unauthorized review, use, disclosure, dissemination, forwarding, printing or copying of this email or any action taken in reliance on this email is strictly prohibited and may be unlawful. The recipient /addressee acknowledges that Institute of Advanced Research (IAR) are unable to exercise control or ensure or guarantee the integrity of/over the contents of the information contained in e-mail transmissions and further acknowledges that any views expressed in this message are those of the individual sender and no binding nature of the message shall be implied or assumed unless the sender does so expressly with due authority of Institute of Advanced Research (IAR). Internet communications cannot be guaranteed to be timely, secure, error or virus-free, thus the sender does not accept liability for any errors or omissions. Before opening any attachments please check them for viruses and defects.

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Solvation question
by Noriega, Heather 09 Nov '21

09 Nov '21

Hello, I have a quick question. I am running the solvate command before the minimization, equilibrium, and production run in Chimera. I click the start solvate tool and put my water box size and apply. This gives me my box and in the command line it says created...with however many water molecules. I then go run parameters, set up everything. Once I hit run, the water box dissappears. I just want to make sure that the solvation did occur even though the water box dissappears from the screen. Everything else ran smoothly to show simulation. I just want to be certain and have confirmation that the solvation does occur as long as I use apply and do not close out of the window. Thanks in advance for your help. Thank you, Heather Noriega PhD-Pharmaceutical Science student College of Pharmacy Howard University heather.noriega(a)bison.howard.edu 520-203-1883

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Writing data to a text file
by Prathvi Singh 08 Nov '21

08 Nov '21

Hi, Suppose I want to find the distance between all atoms of residue-A and residue-B & write the distances to a file. Is it possible to do so in a meaningful way? -- Prathvi Singh, Research Fellow, Department of Biological Sciences & Bioengineering, Indian Institute of Technology, Kanpur-208016

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the version of Ambertools that are used in the command "Write prmtop"?
by Victor Nazarychev 08 Nov '21

08 Nov '21

Dear Chimera's users, I built amber's .inpcrd and prmtop files using command write prmtop from Tools/Amber/Write Prmtop. I used Chimera 1.15 (build 42334), but how could I figure out what version of AmberTools is incorporated in this Chimera release? Best regards, Victor

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Chimera Laucher Error
by Paulo Roberto da Silva Santos 08 Nov '21

08 Nov '21

Hi, I was intalated Chimera 1.5 64bit under Windows 10 64 bit, I was intalated Chimera 1.5 64bit under Windows 10 64 bit, and all was fine until I started executed, Chimera crashed and now it gives me an error at launch and quits, so I cannot run it anymore. After launch, the error window shows: -------------------------------------------------------------------------------- Chimera exited abnormally; the exit code was: -1073741819. Use the --debug command line option for the full error message. -------------------------------------------------------------------------------- Paulo Roberto da Silva Santos Bacharel em Química - UFPB Mestrando em Química - UFPB LCCQS - Laboratório de Compostos de Coordenação e Química de Superfície (83) 99915-5963

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error while running chimera
by Saniya Kate 03 Nov '21

03 Nov '21

Good evening, i am Student and Installed chimera for WINDOWS (chimera-1.15-win64.exe <https://www.cgl.ucsf.edu/chimera/cgi-bin/secure/chimera-get.py?file=win64/c…>) from your website but I am unable to run it on my system since it is a 64 bit release and my system is 32 bit. I urgently need chimera for my project work but I'm not able to use it since the 32 bit release of chimera isn't available. please let me know what can be done

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