- Chimera-users - RBVI Mailing Lists

saving selected residues
by Dieter Blaas 28 Nov '23

28 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 ------------------------------------------------------------------------

2 4

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).

2 2

Announcement: Release of DOCK 6.11
by Scott Brozell 16 Nov '23

16 Nov '23

We are pleased to announce the release of DOCK 6.11. DOCK is a suite of programs for molecular docking. The source code for DOCK 6.11 is available for download and free for academic users at http://dock.compbio.ucsf.edu/DOCK_6/index.htm This is a release of the new descriptor-driven de novo design method DOCK_D3N which takes advantage of the integration of the open source toolkit RDKit into DOCK6. DOCK_D3N tailors ligand growth towards desirable regions of chemical space by calculating cheminformatic descriptors at each stage of ligand construction. For full information on what is new in DOCK 6.11, please visit: http://dock.compbio.ucsf.edu/DOCK_6/new_in_6.11.txt Sincerely, The DOCK Team Please visit us at the DOCK Web site. http://dock.compbio.ucsf.edu

1 0

Unable run Modeller: [Errno 13] Permission denied
by naghmehn85＠gmail.com 27 Oct '23

27 Oct '23

Hello, I was trying to use the Modeller (run it locally) on Chimera UCSF but I encountered this error: Unable run Modeller: [Errno 13] Permission denied. I, as well, received this error when I wanted to load PDB files from my local MacOs. Would you mind please telling me what the issue is? Thank you so much.

3 2

Chimera(X) website and web services down Oct 30-31
by Elaine Meng 26 Oct '23

26 Oct '23

Dear users, Due to system upgrades, the Chimera and ChimeraX websites, associated web services hosted by the UCSF RBVI (Modeller, Blast Protein, etc.), and the ChimeraX Toolshed will be unavailable -- the estimated downtime is from Monday, Oct 30 8:00 am PDT through Tuesday, Oct 31 11:59 pm PDT. Please pardon the inconvenience, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco

1 0

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*

2 1

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

2 3

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

2 2

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

2 1

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.

2 4