June 2021 - ChimeraX-users - RBVI Mailing Lists

Surface dust command in the .cxc script
by 李泽 24 Feb '25

24 Feb '25

Hi all: I'm trying to use the .cxc script to run the software, I found that the "surface dust" command has never been executed in it. Have anyone met the same problem? Any suggestions. Thank you all. Best, Ze

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Get color code of a custom color
by Ahmad Khalifa 11 Feb '25

11 Feb '25

I created a custom color that I want to use in a different session. is there a way to do that besides trying to match colors by eye? Regards.

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Double and Triple Bond Stick Style
by Smith, Chase 05 Feb '25

05 Feb '25

Dear ChimeraX, I was just wondering why there is no way to represent a double or triple bond in either the ligands or the protein amino acids when viewing as a Stick or Ball-and-Stick representation? I sometimes use Chimera or ChimeraX to make visuals for my lectures, and the students often have difficulty in understanding due to the absence of the multiple bonds. I would love to have the ability to represent the double or triple bonds with multiple lines between the atoms. Thank you, Chase Smith ... ChaseSmith, PhD Chair, Department of Pharmaceutical Sciences & Associate Professor of Medicinal Chemistry School of Pharmacy MCPHS University 19 Foster Street | WorcesterMA01608 T 508.373.5717F 508.890.5618C 978.855.7203 chase.smith(a)mcphs.edu www.mcphs.edu MCPHS University Confidentiality Note: This e-mail, and any attachment to it, is intended to be confidential and might be legally privileged. It is intended solely for the use of the addressee. If you are not the intended recipient, you are hereby notified that reading, copying, disseminating or distributing this email is strictly prohibited. If you have received this e-mail in error, please immediately return it to the sender and delete it from your system. Thank you.

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Quest 2 Support?
by Blaine Hewitt 27 Dec '24

27 Dec '24

Hello, my name is Blaine Hewitt. Now I know that you have stated previously that you have no intention of bringing support to the Oculus Quest. Which is completely understandable since I know that not only would you have to develop around a completely new Operating System but another CPU architecture and much much more I assume. But with the soon release of the Oculus Quest 2 and it's new XR 2 chip-set makes a pretty good argument for it. As this would allow for much easier use in education (as is what I am attempting to do with it). I think it will be even easier now to push updates with SideQuest <https://sidequestvr.com/> being relatively simple to setup. I know that another (Naome <https://blog.matryx.ai/nanome-on-quest-public-beta-is-now-available-b546321…>) program is already available on the platform. But I do like your program a lot more since it is able to be used for free unlike Nanome Pricing <https://nanome.ai/pricing/> which is... as to say unappealing to public schools (such as mine). I was was also thinking (sorry if I am becoming annoying at this point) that if you do make a version of the Quest that you could make that GitHub branch available to the public. As for example while I may not be great at understanding complex protein structures I can help to make the whole experience more user friendly. Anyways if you read this far thank you for taking time from your day to read this. If you want to know who I am, my name is Blaine I am in my senior year of High School (Waynecsd <https://wh.waynecsd.org/>). I have to do a project by the end of the year where I have to present an area of study I want to pursue and I decided to research the effects of VR on the human's ability to learn and retain information. Budget..... None

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Apple silicon (M1 chip) native version?
by Jeffrey D. Hartgerink 28 Apr '22

28 Apr '22

Are there any plans for an Apple Silicon (M1 chip) native version of ChimeraX? While things work ok via the Rosetta emulator, it would be great to have the performance from a native app. -------------------------------------- Jeffrey D. Hartgerink, Ph.D. Prof. of Chemistry and Bioengineering Rice University, MS 602 6100 Main Street Houston, TX 77005 jdh(a)rice.edu / 713-348-4142 hartgerink.rice.edu

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How to Align Chromosome Models with Different Number of Atoms?
by Cardiff Jiang 30 Jul '21

30 Jul '21

Dear ChimeraX User List, How can I compare two chromosome 3D models (PDB files) that have different numbers of "atoms"? Matchmaker tool reports, "Reference and/or match model contains no nucleic or amino acid chains. Use the command-line 'align' command to superimpose small molecules/ligands." align #1 toAtoms #2 reports, "Unequal number of atoms to pair, 49 and 63." align #1 toAtoms #2 matchNumbering true reports, "Pairing dropped 49 atoms and 63 reference atoms. No atoms paired for alignment." align #1:1-40 to #2:1-40 reports, "No atoms paired for alignment." How should I compare two chromosome 3D models below? Thank you. [image: image.png] Best regards, Zichen "Cardiff" Jiang

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Re: [chimerax-users] Generating surfaces from a specific selection
by Eric Pettersen 01 Jul '21

01 Jul '21

Hi Diego, If there are interior voids within the structure your main surface is enclosing, there will be "bubbles" like what you're seeing, where solvent (or possibly larger things) could theoretically be contained. If you want to only create the outermost surface and not any of the interior void surfaces then add "visiblePatches 1" to your surface command, and only the single largest surface will be created. --Eric > On Jun 30, 2021, at 8:32 AM, Diego Amaya <diaamayaram(a)unal.edu.co> wrote: > > Hi Eric, > > Thanks for your fast reply. The script works but I identify a "weird behavior" in some surfaces. In some cases, you can find "isolated spheres" and if you superimpose them with the corresponding entire surface, these spheres are buried in the structure. All the pdb files have the same atom order and there are no waters, ions or other molecules. The structure is composed of two protein chains. I tried several probeRadius and gridSpacing values but the problem stays. Any suggestions ? > > Best regards, > > > > > El mar, 29 jun 2021 a las 22:58, Eric Pettersen (<pett(a)cgl.ucsf.edu <mailto:pett@cgl.ucsf.edu>>) escribió: > Hi Diego, > It's impossible to be 100% certain without knowing exactly which line it crashed in, but my strong suspicion is that the long atom spec you generate overran some limit in the atom spec or command parser and resulted in a crash. I will be investigating in more detail later, but working off that assumption I would change your script to directly select the atoms in Python rather than via a command. I'm going to assume the atoms in your PDB files are always in the same order, and that the structure is the only model open. If so, change these lines in the 'if' block: > > cur_sel = selected_atoms(session).unique_structures[0].atoms.serial_numbers > for a in cur_sel: > list_atoms.append('@@serial_number='+str(a)) > sel_atoms = ' | '.join(list_atoms) > > to: > > selected = session.models[0].atoms.selecteds > > and these lines in the 'else' block: > > rc(session, 'sel {}'.format(sel_atoms)) > rc(session, 'surface {} enclose #1'.format(sel_atoms)) > to: > > session.models[0].atoms.selecteds = selected > rc(session, 'surface sel enclose #1') > --Eric > > Eric Pettersen > UCSF Computer Graphics Lab > > >> On Jun 29, 2021, at 10:00 AM, Diego Amaya via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>> wrote: >> >> Hello, >> >> I have a pdb trajectory of 50 frames (in separated pdb files). I want to generate only the solvent accessible surface around amino acid 31 within a radius of 15 A. I want to use the same set of atoms when generating each surface with respect to the first frame of the trajectory. I'm using the python script here below but it doesn't work, I get a segmentation error in the else block. It works if I use "rc(session, 'surface zone #1.1 nearAtoms :{} distance {}'.format(resid, radius))" in the else block but in that way I don't use exactly the same atoms each time. Any suggestions? >> >> Thanks in advance. >> >> Here the code : >> >> ########################################################### >> from chimerax.core.commands import run as rc >> >> def get_surfaces(resid, radius): >> from chimerax.core.commands import run as rc >> from chimerax.atomic import selected_atoms >> >> with open('list_pdbs.txt', 'r') as list_pdbs: >> flag = 0 >> for pdb_file in list_pdbs: >> if flag == 0: >> list_atoms = [] >> rc(session, 'open ' + pdb_file.strip()) >> rc(session, 'sel :{} @<{}'.format(resid, radius)) >> cur_sel = selected_atoms(session).unique_structures[0].atoms.serial_numbers >> for a in cur_sel: >> list_atoms.append('@@serial_number='+str(a)) >> sel_atoms = ' | '.join(list_atoms) >> rc(session, 'surface #1 enclose #1') >> rc(session, 'surface zone #1.1 nearAtoms :{} distance {}'.format(resid, radius)) >> rc(session, '~ribbon') >> rc(session, '~disp') >> rc(session, "save {}_resid_{}_radius_{}.stl format stl".format(pdb_file.strip()[:-4], resid, radius)) >> rc(session, 'surface close') >> rc(session, '~sel') >> rc(session, "close all") >> flag = 1 >> else: >> rc(session, 'open ' + pdb_file.strip()) >> rc(session, 'sel {}'.format(sel_atoms)) >> rc(session, 'surface {} enclose #1'.format(sel_atoms)) >> rc(session, '~ribbon') >> rc(session, '~disp') >> rc(session, "save {}_resid_{}_radius_{}.stl format stl".format(pdb_file.strip()[:-4], resid, radius)) >> rc(session, '~sel') >> rc(session, 'surface close') >> rc(session, "close all") >> >> resid = 31 >> radius = 15 >> >> get_surfaces(resid, radius) >> rc(session, "quit") >> ############################################################# >> >> >> -- >> Diego A. Amaya Ramírez >> >> Aviso legal: El contenido de este mensaje y los archivos adjuntos son confidenciales y de uso exclusivo de la Universidad Nacional de Colombia. Se encuentran dirigidos sólo para el uso del destinatario al cual van enviados. La reproducción, lectura y/o copia se encuentran prohibidas a cualquier persona diferente a este y puede ser ilegal. Si usted lo ha recibido por error, infórmenos y elimínelo de su correo. Los Datos Personales serán tratados conforme a la Ley 1581 de 2012 y a nuestra Política de Datos Personales que podrá consultar en la página web www.unal.edu.co <http://www.unal.edu.co/>. Las opiniones, informaciones, conclusiones y cualquier otro tipo de dato contenido en este correo electrónico, no relacionados con la actividad de la Universidad Nacional de Colombia, se entenderá como personales y de ninguna manera son avaladas por la Universidad. >> _______________________________________________ >> ChimeraX-users mailing list >> ChimeraX-users(a)cgl.ucsf.edu <mailto:ChimeraX-users@cgl.ucsf.edu> >> Manage subscription: >> https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users <https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users> > > > > -- > Diego A. Amaya Ramírez > > Aviso legal: El contenido de este mensaje y los archivos adjuntos son confidenciales y de uso exclusivo de la Universidad Nacional de Colombia. Se encuentran dirigidos sólo para el uso del destinatario al cual van enviados. La reproducción, lectura y/o copia se encuentran prohibidas a cualquier persona diferente a este y puede ser ilegal. Si usted lo ha recibido por error, infórmenos y elimínelo de su correo. Los Datos Personales serán tratados conforme a la Ley 1581 de 2012 y a nuestra Política de Datos Personales que podrá consultar en la página web www.unal.edu.co <http://www.unal.edu.co/>. Las opiniones, informaciones, conclusiones y cualquier otro tipo de dato contenido en este correo electrónico, no relacionados con la actividad de la Universidad Nacional de Colombia, se entenderá como personales y de ninguna manera son avaladas por la Universidad.

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Having multiple marker files
by SHIQING LIAO 30 Jun '21

30 Jun '21

Hi! I’m trying to have multiple marker files because I would like them to have different radius and coloring distance. I figured out that I can create new marker files by “marker #5 1,1,1 radius 100”, for example. However, if I add new markers, the new marker always goes to the first marker file, instead of the selected marker file that I want. Any help is really appreciated! Best, Shiqing

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Python API Inquiry
by Nathan Wood 30 Jun '21

30 Jun '21

To Whom it May Concern, My name is Nathan Wood and I am currently a Google Summer of Code Intern with the OpenChemistry Group. Currently I am currently in the process of replacing Visualizing Molecular Dynamics (VMD) with ChimeraX as a means to visualizing computationally generated electrostatic potential diagrams. To accomplish this I am having to use the Python API in a script. However, I am having difficulties enabling the Python API. When I execute a Tutorials example found in the online developer's documentation, I receive the error: /ImportError: No module named chimerax.core.commands// / which suggests that the python modules were never installed properly. I also recieve similar errors when attempting to import the toolshed. Otherwise, the ChimeraX GUI and its shell work properly and I am unsure how to resolve the API error. I am currently using the Generic Linux 64 Bit Daily Release and can provide more information if necessary. Any assistance would be greatly appreciated ------------------------------------------------------ Very Respectfully, Nathan Wood Undergraduate Year 3, GSOC Intern University of Florida

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Fit crystal structure into mrc
by SHIQING LIAO 30 Jun '21

30 Jun '21

Hi, I am trying to build an illustration using marker/color zone. I successfully colored my mrc file. Now, I want to fit a crystal structure I downloaded from pdb into the mrc. But they apparently have different sizes. I tried voxelSize to scale up my mrc, but then all my markers don’t fit with the enlarged mrc. However, voxelSize doesn’t seem to work with the crystal structure (.pdb1) as I got an error message “no volumes specified” when I indeed wrote “volume #5 voxelSize 2”. I am wondering is there any function like voxelSize to scale down the crystal structure? Thank you!

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