July 2022 - Chimera-users - RBVI Mailing Lists

Question about save images
by Chang, Jufang 29 Apr '24

29 Apr '24

Hi, there, I used Chimera for a very short period of time. When I just started using Chimera I was able to save image by going to "file" and "save image" to save the image on the display window. For some reason, this stopped working. Now, after I did the same thing, the image I saved has complete blackness (attached). I wonder whether I might get be able to get help from you. I also tried using command line to save image. The result is the same. The exact procedure I used are: Go to "Presets", choose "publication 1" , then go to "File" and "save image" I used window system. Thank you J ________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.

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Question about equivalent command in Chimera
by Thu Nguyen 28 Jul '22

28 Jul '22

Good afternoon, I want to ask if we have any command in Chimera that is similar to the command "volume cover" in ChimaraX. My goal is to create a map and pdb file of individual chains from the whole structure. For example: > open 12554 from emdb > open 7ns0 > volume cover #1 atomBox #2/A1 pad 1.0 > save 12554_A1.mrc models #3 Could you tell me how I can do this using Chimera commands? Thank you very much. Best regards, Thu

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Re: [Chimera-users] How to show hydrophobility clearly
by Elaine Meng 27 Jul '22

27 Jul '22

Hi Kenji In this latest message, you are using one method that shows the pocket surface only, like in the tutorial. Your image after step 1 of what you tried looks OK to me: But if you are not happy with that, I am guessing you do not want this method. If you want it to look more like this example image with the labeling "hydrophobic pocket" and "allosteric tunnel" ...then you need to use a DIFFERENT method that includes clipping: showing the whole surface of the protein and then using clipping to slice. We already discussed this method, and you were already using this method the first time you asked the question: <https://www.rbvi.ucsf.edu/pipermail/chimera-users/2022-July/018741.html> <https://www.rbvi.ucsf.edu/pipermail/chimera-users/2022-July/018746.html> With that method, all you can do is to move and rotate the structure and move the clipping (either global clipping plane with Side View tool or surface-only clipping with Per-Model Clipping, both mentioned in previous replies) to try to get a good view. However, different pockets are different shapes and depending on the shape of your pocket it may not be possible to make an image that clearly shows what you want. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Jul 26, 2022, at 6:40 PM, Kenji MATSUI <s214903z(a)st.go.tuat.ac.jp> wrote: > > Dear Chimera > > Thank you for taking the time to answer my question the other day. > > 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(third) > > If you know of any, could you please let us know? > > I tried to show what you mentioned in your email.(clip off, mclip) > > I apologize for asking this question so often in your busy schedule, but I would appreciate it if you could confirm it for me. > > <image.png> <image.png> > > The picture I want to show > <image.png> > > Tried thing > 1. clip off +~ribbon > <1edf41f0-9f2e-4921-92fe-19399979fd97.png> > > 2.m clip > <image1.png> > > > > > . > --------------------------------------------------------------------------- > > > 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 > <Hydrohobility_1P8D_LXR_LBD_mono_24,25-epoxycholesterol.pyc>

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Help with Fetch ID from UNIProt
by Tina Wright 26 Jul '22

26 Jul '22

Hi there, I have worked my way through the majority of the Chimera tutorials and thought I would try to Fetch ID of Human SP-B (P07988) from UNIProt but unlike the tutorials, it will not upload an image. Can you please help? Many thanks Tina Wright

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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 08 Jul '22

08 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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Chimera-users July 2022