- Chimera-users - RBVI Mailing Lists

Request for Mathematical Details or Source Code for Helix Axis and Interhelical Distace/Angle Calculations in Chimera
by pupadhyay21 24 Jun '25

24 Jun '25

Respected Sir/Madam, My name is Prashant Upadhyay, and I am currently pursuing a Ph.D. in Bioinformatics and Molecular Dynamics Simulation at the Indian Institute of Technology Kanpur (IIT Kanpur), India. As part of my research, I am analyzing the structural dynamics of helical membrane proteins using molecular dynamics simulations. I have been using UCSF Chimera extensively for structural analysis. Specifically, I have been utilizing the Structure Analysis → Axes/Planes/Centroids tool to calculate the helix axes of selected helices in my protein of interest. When I select two helices, the Reply Log provides the interhelical distance and angle between the computed axes. This functionality has been incredibly useful for analyzing static structures. To extend this to a dynamic context, I am interested in applying the same axis and angle calculation to each frame of an MD trajectory. For this, I would greatly appreciate it if you could share the mathematical methodology or the relevant portion of the source code that Chimera uses to compute: 1)The helix axis from selected residues 2)The angle and the shortest distance between two helix axes My aim is to replicate this analysis programmatically over the entire simulation trajectory. Any guidance, reference, or code snippet you could provide would be immensely helpful. Thank you, Prashant Upadhyay Ph.D. Student Department of Biological Sciences and Bioengineering Indian Institute of Technology Kanpur (IIT Kanpur)

3 3

Request for Mathematical Details or Source Code for Helix Axis and Interhelical Distace/Angle Calculations in Chimera
by pupadhyay21 22 Jun '25

22 Jun '25

Respected Sir/Madam, My name is Prashant Upadhyay, and I am currently pursuing a Ph.D. in Bioinformatics and Molecular Dynamics Simulation at the Indian Institute of Technology Kanpur (IIT Kanpur), India. As part of my research, I am analyzing the structural dynamics of helical membrane proteins using molecular dynamics simulations. I have been using UCSF Chimera extensively for structural analysis. Specifically, I have been utilizing the Structure Analysis → Axes/Planes/Centroids tool to calculate the helix axes of selected helices in my protein of interest. When I select two helices, the Reply Log provides the interhelical distance and angle between the computed axes. This functionality has been incredibly useful for analyzing static structures. To extend this to a dynamic context, I am interested in applying the same axis and angle calculation to each frame of an MD trajectory. For this, I would greatly appreciate it if you could share the mathematical methodology or the relevant portion of the source code that Chimera uses to compute: 1)The helix axis from selected residues 2)The angle and the shortest distance between two helix axes My aim is to replicate this analysis programmatically over the entire simulation trajectory. Any guidance, reference, or code snippet you could provide would be immensely helpful. Thank you, Prashant Upadhyay Ph.D. Student Department of Biological Sciences and Bioengineering Indian Institute of Technology Kanpur (IIT Kanpur)

1 0

ChimeraX menu
by Elaine Meng 13 Jun '25

13 Jun '25

Hi Mariela, Your picture #1 is Chimera. Picture #2 is ChimeraX. These are two different programs. To get ChimeraX, you have to go to the ChimeraX website and download it: <https://www.rbvi.ucsf.edu/chimerax/download.html> If you meant that you do already have ChimeraX, but the Toolbar with icons is not shown, use ChimeraX menu: Tools... General... Toolbar to show it. See ChimeraX window and Toolbar help: <https://rbvi.ucsf.edu/chimerax/docs/user/window.html> <https://rbvi.ucsf.edu/chimerax/docs/user/tools/toolbar.html> If you have ChimeraX questions, please use address chimerax-users(a)cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu> CC'd here. The other address chimera-users[...] is for Chimera. I hope this helps, 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 Jun 13, 2025, at 5:34 AM, Mariela Urrutia via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu> wrote: > > Hi Eric > I send you the menu I have (adjunto 1) and the menu I would like to have in my CPU (adjunto 2). > Could you tell me please how can I add it? > Thanks you. > Mariela > > De: Eric Pettersen <pett(a)cgl.ucsf.edu> > Enviado: Jueves, 12 de Junio de 2025 14:14 > Para: Mariela Urrutia <murrutia(a)cedie.org.ar> > CC: chimera-users(a)cgl.ucsf.edu <chimera-users(a)cgl.ucsf.edu>; Alexis Rohou via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu> > Asunto: Re: [Chimera-users] query > Hi Mariela, > I don’t really know what a “superior menu” is. Maybe you could clarify? If you mean a popup menu, you get that by clicking the right button on your mouse (or the equivalent on a trackpad). > Since this is a ChimeraX question, I have cc’ed the chimerax-users list and directed replies there. Chimera and ChimeraX are separate programs and have separate mailing lists. > > --Eric > > Eric Pettersen > UCSF Computer Graphics Lab > > > On Jun 12, 2025, at 9:23 AM, Mariela Urrutia via Chimera-users <chimera-users(a)cgl.ucsf.edu> wrote: > > Hello, > Could you give me direction to add the superior menu in ChimeraX 1.9 (2025-3-6)? > Thanks you in advance! > Mariela > Dra. Mariela Urrutia > Investigadora > Centro de Investigaciones Endocrinológicas “Dr. César Bergadá” (CEDIE) > CONICET – FEI – División de Endocrinología, Hospital de Niños Ricardo Gutiérrez > Gallo 1330 – C1425EFD Buenos Aires – Argentina > Tel. (+54-11) 4963-5931 int 290 > murrutia(a)cedie.org.ar 🌎 www.cedie.org.ar 👥 Facebook Instagram > _______________________________________________ > Chimera-users mailing list -- chimera-users(a)cgl.ucsf.edu > To unsubscribe send an email to chimera-users-leave(a)cgl.ucsf.edu > Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimera-users@cgl.ucsf.edu/ > > _______________________________________________

1 0

query
by Mariela Urrutia 12 Jun '25

12 Jun '25

Hello, Could you give me direction to add the superior menu in ChimeraX 1.9 (2025-3-6)? Thanks you in advance! Mariela Dra. Mariela Urrutia Investigadora Centro de Investigaciones Endocrinológicas “Dr. César Bergadá” (CEDIE) CONICET – FEI – División de Endocrinología, Hospital de Niños Ricardo Gutiérrez Gallo 1330 – C1425EFD Buenos Aires – Argentina Tel. (+54-11) 4963-5931 int 290 murrutia(a)cedie.org.ar<mailto:murrutia@cedie.org.ar> 🌎 www.cedie.org.ar<https://cedie.conicet.gov.ar/> 👥 Facebook<https://www.facebook.com/CEDIE-Centro-de-Investigaciones-Endocrinol%C3%B3gi…> Instagram<https://www.instagram.com/cedie.conicet/>

3 2

Chimera on RHEL10 or Fedora 42 with Wayland
by Ben Webb 10 Jun '25

10 Jun '25

RedHat Enterprise Linux 10 has dropped Xorg in favor of Wayland, and Fedora 43 will likely do the same. Fedora 42 already uses Wayland by default. Is Chimera expected to work with Wayland? ChimeraX works fine in our environment with Wayland, but I have folks that still want to use Chimera. And they're getting a Togl failure at startup: "Display misconfiguration. Please increase the color quality (24 bit color or greater), update your display (graphics) driver, and/or upgrade your graphics card. Also see chimera installation instructions." I would love to tell them that "the Chimera folks say it doesn't work with Wayland so you need to switch to ChimeraX" (we can eke out another six months or so with Fedora 42 using Xorg) but if you think it *should* work, any clues as to where to look to tweak our configuration? Other than using the NVIDIA drivers (570.133.07), we are using a stock Fedora and Wayland install.

3 6

Add sequence logo to view
by Alexander Lee 05 May '25

05 May '25

Dear ChimeraX community, I have a consensus sequence + logo done in an outside program. Is there a way to superimpose this onto a crystal structure? When hovering my mouse over a residue in the structure viewer (or sequence viewer), I would like the logo to come up. Is there a similar feature available? Regards, Alex

2 1

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

3 2

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

2 2

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

2 1

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.

2 1