- Chimera-users - RBVI Mailing Lists

How to examine the hydrophobicity and hydrophilicity around the ligand
by Kenji MATSUI 21 Jul '22

21 Jul '22

Dear Chimera Thank you for taking the time to answer my question the other day. I also apologize for contacting you outside of business hours due to the time difference. I'm Kenji Matsui, a second-year master's student at a national university in Japan. I am looking at ligand-protein interactions and how they affect binding affinity. Therefore, I would like to examine the hydrophobicity and hydrophilicity around the ligand in the figure below（second photo,）. [image: image10.png] [image: image.png] second photo Methods Tried select→ligand→Focus This method causes some parts of the surface to be difficult to see. As shown in the second photo, it is difficult to see the degree of hydrophobicity around the ligand. [image: image.png] Please confirm. --------------------------------------------------------------------------- Kenji Matsui Graduate School of Tokyo University of Agriculture and Technology M2 2-24-16, Nakamachi, Koganei-shi, Tokyo 184-8588, Japan Mail: s214903z(a)st.go.tuat.ac.jp

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VolumeViewer in python
by Yumeng Yan 20 Jul '22

20 Jul '22

Hi all, I tried to fit some models into a large density map using python script for chimera. Do you know how to set the VolumeViewer module in python script to show all the surface of the density map like command line” volume #1 style surface region all level 0.15 step 1”? Here is my python code: Import chimera import FitMap import VolumeViewer model_list = chimera.openModels.open("test.pdb") em_map = VolumeViewer.open_volume_file("test.mrc")[0] “python code ” for “volume #1 style surface region all level 0.15 step 1” model = chimera.selection.ItemizedSelection([model_list[0]]) listfit = FitMap.fitcmd.fitmap(model, em_map, resolution=5.0, metric="correlation") Thanks and best wishes, Yumeng

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imod
by Aaran Vijayakumaran 13 Jul '22

13 Jul '22

Dear all, I was wondering if it was possible to measure the distance of structures within an IMOD segmentation file. For instance, measuring the length of microtubules lets say? Thank you in advance for any assistance. Bests, Aaran Vijayakumaran PhD Researcher Medical Research Council Toxicology Unit University of Cambridge, Gleeson Building, Tennis Court Road, Cambridge CB2 1QR av623(a)cam.ac.uk<mailto:Av623@cam.ac.uk> [A picture containing text, screenshot Description automatically generated] [cid:image001.png@01D84DAF.64335190]

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IOError for non-existing ViewDock_Accelerator.py when executing Chimera
by 夏前程 07 Jul '22

07 Jul '22

Hi, Recently I've received an error message from CLI each time I executed chimera as before. Although it does not affect the normal use of chimera, I am still curious what's the issue and how to get rid of it? The error message is as below: Error executing accelerators file $HOME/Downloads/Chimera/ViewDock_Accelerator.py: IOError: [Errno 2] No such file or directory: '$HOME/Downloads/Chimera/ViewDock_Accelerator.py' File "$HOME/opt/UCSF-Chimera64-1.15rc/share/Accelerators/__init__.py", line 103, in load_accelerators execfile(path, dict) See reply log for Python traceback. With Regards, Qiancheng Xia, 2022/07/07

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Coloring model by b-factor
by 师扬 07 Jul '22

07 Jul '22

Dear developer, I am trying to color a model by b-facor and used the command like : color by bfactor #4/A palette red:green:blue range 35,45. However, the range setting was not working. So my question is how to color with a user-defined palette and a user-defined range. Best wishes, Yang

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Mask Question in windows Chimera
by Zhang, Ruojing 04 Jul '22

04 Jul '22

To whom it may concern, Hello, this may sound like a silly question. May I ask how to use Mask in Volume? For some unknown reasons, I could not find the Mask button in Volume Viewer and neither in the tool taskbar. The input files are pdb and mrc file. I used Fit in Map to align structure and map. Then I selected the whole structure. When I went back to mask the map, I could not find the Mask button in Volume Viewer. When I tried to run in the command line (mask), it shows "missing required arguments: Volume, SurfaceSpec". Could you please help? Thank you Jing

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ChimeraX Version 1.4 on CentOS/RHEL 7
by Long Gui 01 Jul '22

01 Jul '22

Dear Chimera community, We are interested in the new version of the ChimeraX/1.4 but we could not find the installation file of ChimeraX/1.4 on our CentOS/RHEL 7 system. Only ChimeraX/1.3 supports CentOS/RHEL 7. So we would like to ask if there is a way to install ChimeraX/1.4 on our CentOS/RHEL 7 system? In addition, our computational source would prefer to install the program using docker. Currently I only find this docker file supports ChimeraX/1.3 https://github.com/maduprey/chimerax-docker/ ? Have anyone tried it for ChimeraX/1.4 yet? Thanks! Long Long Gui, Ph.D. Postdoc Researcher, Nicastro Lab University of Texas Southwestern Medical Center Long.Gui(a)utsouthwestern.edu Tel: (214)-645-1561 ________________________________ UT Southwestern Medical Center The future of medicine, today.

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AutoDock Vina error on Chimera
by Utkarsh Narsaria 30 Jun '22

30 Jun '22

Dear Team, I am using chimera for a typical protein-ligand docking study. The ligands were prepared in chimera itself using the dockprep options using gasteiger charges and amber ff14SB force field. While docking the same using AutoDock Vina function in Chimera , we encountered few errors for some of the ligands. The errors are explained as follows : 1. "" Ho" is not a valid dock type AutoDock atom types are case-sensitive." 2. Autodock Vina Error on Chimera: "ValueError: Could not find an atomic number for Hc Hc" Any inputs regarding these will be helpful in resolving the issues. Regards, Utkarsh

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Save trajectory file to PDB
by Yan Yi Li 24 Jun '22

24 Jun '22

Hello, I have a question about saving specific frame from trajectory file to PDB. Instead of using MD movie, is there any module/command available so that I can convert the file format directly with python script? Regards

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How to show hydrophobic interactions
by Kenji MATSUI 17 Jun '22

17 Jun '22

Dear Chimera Thank you for taking the time to answer my question the other day. I also apologize for contacting you outside of business hours due to the time difference. I'm Kenji Matsui, a second-year master's student at a national university in Japan. I have shown hydrophobic interactions between ligands and amino acid residues, how should I display them? I refer to these methods. But, I did not know where to find Examine residues. Therefore, could you please tell me the location of Examine residues? If possible, we would appreciate it if you could attach a diagram after the operation so that we can confirm the operating procedure. *A:Find hydrophobic interactions* Select >> Residue(s) (either in entire structure or within a selected set (see above $ or %)) >> Amino acid category >> hydrophobic >> Action >> Atoms/Bonds >> Show >> Examine residues >> Mouse over atoms or Left click on them to identify them --------------------------------------------------------------------------- 松井健治東京農工大学大学院工学府産業技術専攻修士 2年〒184-8588 東京都小金井市中町2-24-16 Kenji Matsui Graduate School of Tokyo University of Agriculture and Technology M2 2-24-16, Nakamachi, Koganei-shi, Tokyo 184-8588, Japan Mail: s214903z(a)st.go.tuat.ac.jp

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