April 2025 - Chimera-users - RBVI Mailing Lists

Error with color byattribute
by svle＠tiscali.it 13 Apr '25

13 Apr '25

Hi, I'm using the Attribute Assignment Files tutorial with the commands: open [1] 1pho open [2] kdHydrophobicity.defattr [3] color byattribute [4] kdHydrophobicity palette ^RdYlBu select [5] ::kdHydrophobicity>2.0 I've only substituted 1pho with 1caz. For the command: color byattribute [6] kdHydrophobicity palette ^RdYlBu I receive the error "color byattribute is undefined" with different version of chimera. Any suggestions? Thanks. Saverio

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Exporting PDB in correct coordinate system
by James Nettles 11 Apr '25

11 Apr '25

Hello, I have built a Chimera model of N-term and C-term folding associated with a particular dimeric crystal structure associated with HCV. The crystal structure (1zh1) is our reference and we identified theoretical low-energy folds that correlate well with our biological data. We want to be able to upload pdb’s of our folding models with the data presented in the paper so that readers can also see the interactions in 3D. I used the writePDB function and chose to Save relative to 1zh1 in Model Panel, but the results come out misaligned. I’m obviously doing something wrong, have tried various things but have not been able to figure this out. Any tips? Thanks, Jim _____________________ James Nettles, PhD nettlesconsulting(a)gmail.com +01.404.966.4617

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Save PDBs relative to each other
by Elaine Meng 11 Apr '25

11 Apr '25

On Apr 11, 2025, at 9:35 AM, James Nettles <nettlesconsulting(a)gmail.com> wrote: > > Hi Elaine, I tried submitting a new question to the list, but received a response that I’m not a list member. > > I am trying to output some models in PDB format and am having problems getting the coordinates of the sports to align properly when read back in. > > I haven’t been able to figure what I'm doing wrong. > > Your help will be appreciated. > > Jim Hi Jim, That message is probably caused by sending the message from a different address than what is signed up to the list. If so, your question has to be approved by the moderator (not me) but usually it is within a day. Otherwise we would be inundated with spam messages from addresses that aren't list members. Re your question: If you moved one model relative to the other and want to maintain their relationship, you need to use the save "relative" option. Doesn't matter which model is relative to which, as long as they are all relative to the same model. This is in both the File... Save dialog and the "write" command. <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/write.html> These are the address for managing list subscriptions (Chimera and ChimeraX users) <https://mail.cgl.ucsf.edu/mailman/mailman3/lists/chimera-users.cgl.ucsf.edu/> <https://mail.cgl.ucsf.edu/mailman/mailman3/lists/chimerax-users.cgl.ucsf.ed…> ChimeraX has an analogous relative saving option for PDB files in both the File... Save dialog and the "save" command (instead of Chimera's "write" command). Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Resource for Biocomputing, Visualization, and Informatics Department of Pharmaceutical Chemistry University of California, San Francisco

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Inquiry about Using UCSF Chimera for Biology Olympiad
by Oliwier Różański 02 Apr '25

02 Apr '25

Dear UCSF Chimera Team, I am a student participating in the *Biology Olympiad* and would like to ask if I am allowed to use *UCSF Chimera* for this competition. Could you please confirm if this is permitted and if there are any specific licensing requirements? Thank you for your assistance.

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Re: UCSF Chimera Download
by Elaine Meng 31 Mar '25

31 Mar '25

The recommended address for asking questions about Chimera is chimera-users(a)cgl.ucsf.edu <mailto:chimera-users@cgl.ucsf.edu> ... you do not need to send another message, I have CC'd that address on this message so that somebody else can answer. I don't know the details of Windows download. My only guess is to wait for a few minutes to be sure the download is finished before you try to open it. Maybe there is a temporary filename for the partial download that changes after the download is complete. Regards, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Resource for Biocomputing, Visualization, and Informatics Department of Pharmaceutical Chemistry University of California, San Francisco > On Mar 31, 2025, at 2:52 PM, Ki Kim <pkhkim(a)gmail.com> wrote: > > Hello, > I am trying to download and install the UCSF Chimera Program. I used the download site as shown below: > > > This is what I have in my download folder: > > > Now, this doesn;t seem to be the right exe file. Did I do something wrong? > I have a Window 11 and 64-bit. > Thank you for your help. > Ki > >

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