- Chimera-users - RBVI Mailing Lists

Chimera export morph animation to 3D software
by Rebekah Moore 09 Jan '24

09 Jan '24

Hi, I was wondering if it's possible to export a morph animation to a 3D software like C4D, Maya, or Blender? I don't wish to render a "movie" in Chimera, as I would like to add the protein morph to a 3D scene in C4D with other animated objects and render it using Redshift. Is this possible? I've tried exporting in vrml xmd and glb formats, which in theory can have animation data, but when I import the files into C4D or Blender the protein has no keyframes and is static. Thanks for your help! Best, Rebekah

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Finding interacting residues between receptor and ligand
by Prathvi Singh 04 Jan '24

04 Jan '24

Hi Elaine, I used the HPEPDOCK server (http:// huanglab.phys.hust.edu.cn/hpepdock /) to dock a ligand onto a receptor and downloaded the conformation (pose) of the ligand with lowest energy. Next I opened the receptor and ligand structure in UCSF chimera. The ligand fitted perfectly in the binding site. Now is it possible to know which residues of the ligand are interacting with the receptor and what is the type of non-covalent interaction between them? Thanks in advance, Prathvi

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Need help using AutoDock Vina with Chimera on Mac
by Kush Unadkat 04 Jan '24

04 Jan '24

Greetings I am a student and I just got a new Mac and I am having a difficult time using AutoDock Vina in Chimera on my Mac. When working with two proteins (.mol2) format, I use AutoDock Vina in tools, input the required values and describe the path to “vina” using the browse button but instead of getting a pop up with the docking possibilities, I get an error like this: [Errno 30] Read-only file system: ‘docking.receptor.pdb’ I tried to look into the problem and if I can understand this correctly, I has something to do with Mac not allowing users to Write on the disk but I’m not sure. Can you please tell me what I’m doing wrong or how I can solve this issue? I am currently working on a project and I have a deadline so it is really important that I find a solution soon. Thank you. Your assistance is really valuable to me.

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Unrecognized command: "hide"
by Gourav Das 03 Jan '24

03 Jan '24

Greetings everyone! I am trying to hide the hydrogen atoms of a molecule using the command line in Chimera. But the software does not recognize the "hide" command. In addition, it could not recognize the "undo" command. Please help me regarding this issue. With regards, Gourav Das Research Scholar Department of Chemistry IIT Kharagpur India

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Unrecognized command: "hide"
by Gourav Das 03 Jan '24

03 Jan '24

Greetings everyone! I am trying to hide the hydrogen atoms of a molecule using the command line in Chimera. But the software does not recognize the "hide" command. In addition, it could not recognize the "undo" command. Please help me regarding this issue. With regards, Gourav Das Research Scholar Department of Chemistry IIT Kharagpur India

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Highlighting residues
by Henen, Morkos 18 Dec '23

18 Dec '23

Hello, I'm running into an issue with using Chimera. When I move with the cursor over a protein residue or particular atom, it is used to show the name/number of this residue or atom. Now, for some reason, this option doesn't work. It has to be something I disabled by mistake, but I can't find that. Could you kindly guide me on what I can do to fix that? Thanks a lot Morkos Morkos Henen, Ph.D. Assistant Professor - Research University of Colorado-Anschutz Medical Campus Denver, USA

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Distance between centroids
by Francesco Pietra 17 Dec '23

17 Dec '23

Hello with candidate version 1.15, linux64, X11 I want to measure the distance between the centroids of two aromatic stacking rings. The usual way of measuring distances does not work (clicking as needed has no effect), contrary to what the manual says. And I should have done successfully that measurement in the past. Also between one of the centroids and a regular atom: same issue. Distance between regular atoms works correctly. thanks for advice francesco pietra

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A Software bug
by yongsheng_zhao 12 Dec '23

12 Dec '23

Hello, I installed the latest version of UCSF CHIMERA 1.17.3 on my win11 computer. After the installation, a window of related Settings kept coming up, and the EDGE browser was automatically opened to go to the CHIMERA help website. May I ask why? Now as long as you use this software, it keeps popping up small Windows, and the EDGE browser has been playing websites, like a virus, and it can't be used at all. | | yongsheng_zhao | | yongsheng_zhao2023(a)163.com |

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[chimera] modeller.SequenceMismatchError
by Yang, Li-Yen 29 Nov '23

29 Nov '23

Hello, I am trying to use the modeler comparative tool in Chimera to model the structure of a protein (in fasta format) by another similar protein’s structure (in pdb format). I first associated this sequence (in fasta) with the corresponding chain in the pdb, and I used the modeller comparative tool to model the structure (I selected the fasta file as the target sequence and selected the corresponding chain in the pdb. ) However, I’m getting this error: _modeller.SequenceMismatchError: read_te_291E> Sequence difference between alignment and pdb : From the log window, I didn’t get any other details beyond the above error. Does anyone know how I can figure out what is going wrong? Thank you! I really appreciate it! Best, Zoey

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Changing threshold value of attributes
by Abril Gijsbers 28 Nov '23

28 Nov '23

Dear community, I want to render my model by attribute and change the thresholds (up and bottom limits). I want to change the 0.3 to 0.1 and the 2.6 to 2.7 (see the figure), this way I can compare the colour intensity with other conditions. [image: image.png] When I do that, I get the following error. My ignorance in command use limits my understanding. Could someone help me out to understand this? I have a colleague that changes the up and bottom limit with no problem. Why? :( ui tool show "Render By Attribute" Traceback (most recent call last): File "/Applications/ ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/widgets/histogram.py", line 759, in _set_value_cb self._redraw_cb() File "/Applications/ ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/widgets/histogram.py", line 646, in _redraw_cb self._bins = left + filled_bins + right ValueError: operands could not be broadcast together with shapes (0,) (157,) ValueError: operands could not be broadcast together with shapes (0,) (157,) File "/Applications/ ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/widgets/histogram.py", line 646, in _redraw_cb self._bins = left + filled_bins + right *See log for complete Python traceback.* Traceback (most recent call last): File "/Applications/ ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/widgets/histogram.py", line 760, in _set_value_cb self._move_cur_marker(v) File "/Applications/ ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/widgets/histogram.py", line 570, in _move_cur_marker self._active_markers._update_plot() File "/Applications/ ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/widgets/histogram.py", line 1222, in _update_plot self._update_marker_coordinates() File "/Applications/ ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/widgets/histogram.py", line 1207, in _update_marker_coordinates x, y = self._scene_xy(m.xy) File "/Applications/ ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/widgets/histogram.py", line 1090, in _scene_xy return self.histogram._scene_xy(abs_xy) File "/Applications/ ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/widgets/histogram.py", line 512, in _scene_xy num_bins = len(self._bins) TypeError: object of type 'function' has no len() TypeError: object of type 'function' has no len() File "/Applications/ ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/widgets/histogram.py", line 512, in _scene_xy num_bins = len(self._bins) *See log for complete Python traceback.*

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saving selected residues
by Dieter Blaas 27 Nov '23

27 Nov '23

Hi, I selected several residues in an icosahedral viral capsid and want to save the corresponding pdb. However, whatever name I try to give this selection I receive the error "You must provide a file name that contains either $name or $number, which will be changed to the model name or model number (respectively) in the final saved file name". Can you please give me an example of a valid name! The viral subunits are 6sk5.pdb1 (#0.1), 6sk5.pdb1 (#0.2), and so on. I have no clue what I should call this selection for it being accepted. Thanks a lot, Dieter ------------------------------------------------------------------------ Dieter Blaas, Max Perutz Laboratories Medical University of Vienna, Inst. Med. Biochem., Vienna Biocenter (VBC), Dr. Bohr Gasse 9/3, A-1030 Vienna, Austria, Tel: 0043 1 4277 61630, Mobile: 0043 699 1942 1659 e-mail: dieter.blaas(a)meduniwien.ac.at ------------------------------------------------------------------------

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recording a movie as series of PNGs with a transparent background
by Eugene Valkov 20 Nov '23

20 Nov '23

Hi folks, Per instructions ( https://www.rbvi.ucsf.edu/chimerax/docs/user/commands/movie.html) I'm trying to make a movie with a series of PNGs with a transparent background to make into a GIF afterward. However, I get an error below. Any help would be appreciated! Thanks, Eugene Eugene Valkov Stadtman Investigator RNA Biology Laboratory National Cancer Institute This works: movie record size 1000,1000 format PNG supersample 4 directory ~/chimera_images; wobble y 120 aspect 2 model #1; wait 50; stop; movie stop This doesn't work: movie record size 1000,1000 format PNG supersample 4 transparentBackground true directory ~/chimera_images; wobble y 120 aspect 2 model #1; wait 50; stop; movie stop and I get this error: "Expected a keyword". Saving individual PNGs with a transparent background works fine. My version is 1.6.1 (2023-05-09).

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Announcement: Release of DOCK 6.11
by Scott Brozell 16 Nov '23

16 Nov '23

We are pleased to announce the release of DOCK 6.11. DOCK is a suite of programs for molecular docking. The source code for DOCK 6.11 is available for download and free for academic users at http://dock.compbio.ucsf.edu/DOCK_6/index.htm This is a release of the new descriptor-driven de novo design method DOCK_D3N which takes advantage of the integration of the open source toolkit RDKit into DOCK6. DOCK_D3N tailors ligand growth towards desirable regions of chemical space by calculating cheminformatic descriptors at each stage of ligand construction. For full information on what is new in DOCK 6.11, please visit: http://dock.compbio.ucsf.edu/DOCK_6/new_in_6.11.txt Sincerely, The DOCK Team Please visit us at the DOCK Web site. http://dock.compbio.ucsf.edu

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Unable run Modeller: [Errno 13] Permission denied
by naghmehn85＠gmail.com 27 Oct '23

27 Oct '23

Hello, I was trying to use the Modeller (run it locally) on Chimera UCSF but I encountered this error: Unable run Modeller: [Errno 13] Permission denied. I, as well, received this error when I wanted to load PDB files from my local MacOs. Would you mind please telling me what the issue is? Thank you so much.

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Chimera(X) website and web services down Oct 30-31
by Elaine Meng 26 Oct '23

26 Oct '23

Dear users, Due to system upgrades, the Chimera and ChimeraX websites, associated web services hosted by the UCSF RBVI (Modeller, Blast Protein, etc.), and the ChimeraX Toolshed will be unavailable -- the estimated downtime is from Monday, Oct 30 8:00 am PDT through Tuesday, Oct 31 11:59 pm PDT. Please pardon the inconvenience, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco

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Error on Chimera
by Giovanni Stelitano 23 Oct '23

23 Oct '23

Dear developers, first of all thank you for your work, the program is quite useful and interesting. I'm using it to perform molecular dynamics for small organic molecules but I have quite a few troubles. I was able to perform a MD in void, but I got this error when I try to analyze the energies, for both kinetic and potential. File "C:\Program Files\Chimera 1.17.3\share\md\mdMovie.py", line 22, in <lambda> name, lambda i, values=values: values[i-1]) Moreover, when I try to run a MD in water (I followed a tutorial on youtube to set up the system and balancing), it stops at the first step of minimization (after 2 days of running it didn't go further according to the log file). I used the Amber preparation (since Gestgeiger seems to not work for my molecules) integrated with AmberFF18SB or 99 that are the one that mostly worked out. I don't think the problem is the calculation power of my machine since I've an Intel i5 processor with a GeForce MX230 and in the options I set up 4 processors. Probably the troubles are just related to the fact that I'm working with small organic molecules instead of proteins? Hoping to find some help/hint in your kind reply, whish a good day and good work, Giovanni. -- *Giovanni Stelitano, PhD in Biomedical Science - Biochemistry* *Department of Biology and Biotechnology "L. Spallanzani"* *University of Pavia* *via Ferrata 9, Pavia, Italy*

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How to obtain transformation matrix between protein structures
by 夏前程 22 Oct '23

22 Oct '23

Hi, I want to use chimera to obtain the transformation matrix between two protein structures. I know that matchmaker can superimpose them together, but I still want to obtain the transformation matrix. I've noticed that matchmaker in chimerax (https://www.rbvi.ucsf.edu/chimerax/docs/user/commands/matchmaker.html) offer a keyword "reportMatrix" to do that. But when I use that keyword in chimerax, "Expected a keyword" will be returned without match or a matrix. With Regards, Qiancheng Xia National Institute of Biological Sciences Beijing, China 2023/10/20

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Questions about phosphorylating residues on proteins
by Hoang-Long Bui 16 Oct '23

16 Oct '23

Hello, My name is Andy and I am a student researcher at San Jose State University with the Grazioli Research Group. I am trying to research a section of a protein using your software and was wondering if I could phosphorylate certain residues of the protein, and how. Thank you! Andy Bui

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ChimeraX Redistribution Policy Question
by Patrick Rynkiewicz (RIT Student) 09 Oct '23

09 Oct '23

Hello! I am a co-developer on a molecular dynamics software package that relies on UCSF ChimeraX, and am looking to package this software in a docker container. It's unclear to me from the licensing process what the policy is for ChimeraX redistribution, such as including the .deb package in a docker build. Can you please clarify if I would be able to cite and redistribute ChimeraX 1.6, Ubuntu 22.04 to* non-commercial users* in my software package, or does each individual user need to accept the non-commercial license agreement separately? Thanks! Pat Rynkiewicz

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Circular DNA Construction and DNA Origami in Chimera 1.17.3
by fatemeh F 29 Sep '23

29 Sep '23

I am writing to inquire about the capabilities of Chimera 1.17.3 for constructing circular DNA and DNA origami, and to seek guidance on saving PDB output files for future use in GROMACS with the AMBER force field. Firstly, I am interested in constructing circular DNA using Chimera 1.17.3. Could you please provide information or guidance on whether this version of Chimera supports circular DNA construction? If so, I would appreciate any instructions or resources that can help me achieve this. Additionally, I would like to explore the possibility of building DNA origami structures using Chimera 1.17.3. Could you please inform me if this version of Chimera has the functionality to create DNA origami structures? If it does, any pointers or documentation on how to get started with DNA origami in Chimera would be highly valuable. Lastly, my goal is to save the PDB output files generated in Chimera for subsequent use in GROMACS with the AMBER force field. Could you provide guidance on the best practices for saving PDB files from Chimera for compatibility with GROMACS and the AMBER force field? Any specific settings or considerations to ensure seamless integration would be greatly appreciated.

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Disulfide bond recognition in Chimera
by wangyizhen＠nibs.ac.cn 28 Sep '23

28 Sep '23

Dear developers of UCSF chimera, I am interested in the reason why chimera recognize the disulfide bond only by the CONNECT record in PDB files. Why not use the bond identification algorithm as used on other heavy atoms (sum of the covalent bond radii and tolerance 0.4A) to show the bond? Is there any special considerations for this? Thanks in advance for any help. Yizhen

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Re: Question about Selecting Structure Parts in Chimera
by Tom Goddard 25 Sep '23

25 Sep '23

Hi Maytha, The most basic way to select parts of an atomic model within a map is to ctrl-click with the left mouse button on an atom or ribbon residue. Then the up-arrow key on the keyboard will expand the selection to the containing helix or strand, and pressed again to the whole chain. Maybe you don't have an atomic model -- hard to tell from your question. Tom > On Sep 24, 2023, at 1:05 PM, MAYTHA ALSHAMMARI <malsh009(a)odu.edu> wrote: > > Dear Goddard, > > I hope you're well. I have a quick query about selecting parts of a structure within a boxed map in Chimera. Can you provide some guidance or instructions on how to do this effectively? Your help is much appreciated. > > Best regards, > Maytha

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Chimera X menu "View" vs. "Focus"
by C. Klein 25 Sep '23

25 Sep '23

Dear Chimera Team first of all, thank you very much for your important and good work on the Chimera software. Two comments: I did some recent work with Chimera X. The menu item "Focus" was changed to "View", which I find less suitable. The term "View" is often applied in other contexts, in particular if a certain residue should be shown vs. not shown. In contrast, "Focus" is not ambiguous, it is not related to showing vs. hiding certain parts of the molecular representation but exactly indicates what is done by the command. The direct pdb download from rcsb or whatever repository is a highly useful tool which is more difficult to access than it used to be. Ok I know it is there, I type "open xxxx" and I use the command line quite a lot anyway, but for others who start with the menus it does not appear to be accessible. Perhaps I also missed something, but then others may not find it as well. Thank you and best wishes Christian Klein

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Cannot Minimize the Water Molecules
by Gourav Das 13 Sep '23

13 Sep '23

Dear all, I am trying to minimize the crystal structure of a protein using Chimera. But the program could not minimize the water molecules of the protein. I added hydrogen atoms to the whole structure. But during the minimization, it is showing the following error: No MMTK name for atom "H" in standard residue "HOH" It would be very helpful for me if you can suggest what changes I should make. Thank you! Sincerely Gourav Das Research Scholar Department of Chemistry IIT Kharagpur India

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Any plan to support sdf as 3D molecules output format?
by Francois Berenger 11 Sep '23

11 Sep '23

Dear Chimera hackers, This might be nice, because mol2 is not supported by rdkit while sdf is. It would ensure that molecules saved from chimera can be properly read in by rdkit (hopefully). Regards, F.

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