- Chimera-users - RBVI Mailing Lists

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 30 Sep '23

30 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 29 Sep '23

29 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 12 Sep '23

12 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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