September 2023 - 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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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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inquire about the capabilities of the UCSF Chimera software in visualizing bond atoms in a spring mode
by Wee Zhang 11 Sep '23

11 Sep '23

Dear RBVI Team, I hope you are doing well. I am writing to inquire about the capabilities of the UCSF Chimera software in visualizing bond atoms in a spring mode, similar to the exemplary images I have enclosed for reference. I have been using UCSF Chimera for various molecular visualization and analysis tasks, and I am particularly interested in exploring this feature for my research and projects. The visualizations I am referring to are those that effectively represent covalent bonds as springs connecting atoms in a molecular structure. These spring-like representations can provide valuable insights into the flexibility and dynamics of molecules, which are crucial aspects of my research in materials science. I have attached images that illustrate the visualizations I want to achieve with UCSF Chimera for your reference. These images serve as excellent examples of dynamic and informative representations that I believe could greatly enhance my research. I would appreciate it if you could provide information on whether UCSF Chimera can generate bond atom visualizations in a spring mode, and if so, any guidance on how to achieve this would be beneficial. Additionally, if any specific plugins or settings are required to create such visualizations, please let me know. Furthermore, if any workshops, tutorials, or resources can assist me in mastering this feature, I would be eager to participate in or access them. Thank you in advance for your time and assistance. I look forward to hearing from you regarding the feasibility of incorporating the spring mode bond atom visualization into UCSF Chimera and any guidance you can provide on achieving this. Please feel free to contact me via email at [your email address] or by phone at [your phone number] if you require additional information or clarification. Sincerely,

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Chimera will not start
by Secor, Maxim 06 Sep '23

06 Sep '23

Hello, I am a postdoc in the Lin lab at Tufts. We use Chimera for everything. Thank you for such wonderful software. Last week Chimera stopped working on my machine. I tried (1) restarting my machine (2) Updating my OS (3) reinstalling Chimera (4) Installing the daily release of Chimera. Nothing works… Thankfully ChimeraX is a good substitute. However, (A) I cannot seem to find all the features that I want in ChimeraX that I loved in Chimers, for example minimization tools, and (B) would really like the Chimera GUI to work. Any thoughts? Maybe there is a corrupted hidden cache file that I need to delete somewhere. Best Max

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Very big THANKS FOR SENT ME ACCESS to ;st version by CHIMERA X.IT IS FANTASTIC!!!Boris
by Boris Atanasov 02 Sep '23

02 Sep '23

-- Prof. BORIS ATANASOV <borisatanasov2(a)gmail.com> Institute of Organic Chemistry, Bulgarian Academy of Sciences, SOFIA 1113, Bulgaria

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Chimera-users September 2023