- Chimera-users - RBVI Mailing Lists

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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