- ChimeraX-users - RBVI Mailing Lists

Selection by segid
by CUNIASSE Philippe 28 Oct '22

28 Oct '22

Dear all, Is there a way in ChimeraX to make a selection by segid (column 73-76 in pdb format from CHARMM of XPLOR)? Thanks in advance. Philippe Cuniasse. ----------------------------------------------- Philippe Cuniasse, PhD/HDR. Institut de Biologie Integrative de la cellule. UMR 9198 CNRS-CEA-Univ Paris Sud Bat 144 CE-Saclay 91191 Gif-sur-Yvette Cedex France Tel: (33) 1 69 08 56 35 Fax: (33) 1 69 08 47 12 Email: philippe.cuniasse(a)cea.fr<mailto:philippe.cuniasse@cea.fr> Web: http://biodev.cea.fr/rasmot3d/ [signature_700846419][signature_2907812893][signature_966493179] -----------------------------------------------

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Re: [chimerax-users] ChimeraX sequence alignment score?
by Elaine Meng 27 Oct '22

27 Oct '22

> On Oct 27, 2022, at 4:46 PM, Budayr, Omar Mahdi <obudayr(a)vols.utk.edu> wrote: > > Dear Dr. Meng, > > I looked through the documentation for ChimeraX and I still cannot figure out what the value for sequence alignment score indicates. I aligned two b-adrenergic receptors from PDB (2RH1 and 3NH8) and it gives a value of 2423.9. What does this value actually represent? The documentation refers to it but never gives specifics besides the parameters in the table that matchmaker generates > > Sincerely, > Omar Budayr Dear Omar Budayr, The value itself is not at all important. The reason to have a score is that the alignment process tries to maximize it for the pair of sequences that it is given. By changing parameters for scoring you can change the relative importance of the different parts of the score, and thus what is most important for the alignment method to align. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco P.S. we recommend sending questions to the chimerax-users(a)cgl.ucsf.edu address (CC'd here) so that others can benefit from the answers and/or help to answer the questions - thanks!

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Selecting residues in two chains
by McClean, Phillip 27 Oct '22

27 Oct '22

Hi Everyone, I have a .pdb file created using AF2 Multimer. It consists of two chains, B and C. Chain B is a protein with 315 residues, while Chain C is a protein with 662 residues. Each chain is modeled with structured and unstructured regions. I would like to only show residues 19-24 of Chain B and residues 1-190 of Chain C in the display window. I have tried using the information provided on the "Command-Line Target Specification" page, but I have not had any success with just displaying those ranges of residues in the display window. My goal is to highlight specific features of those ranges of residues to display their interaction. Thanks for any information you can provide. Phil McClean

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segmented tomogram density in chimeraX
by Jesse HANSEN 25 Oct '22

25 Oct '22

hi all, I have segmented a tomogram in Amira and exported to chimera for visualization. I first opened the .rec file in chimera and re-saved as .mrc. Okay, the segmentation output gives a fully filled volume cube except for the regions of segmentation. Obviously things are inverted. Also, the volume viewer shows clear sharp peaks (delta functions) rather than continuous density, as volume slider moves to the right new segmentation features appear. So I used volume filter with "scale" to -1, and I turned off "displayed subregions only". This fixed the inversion problem and now as I slide toward the right I see more segmented densities. However the threshold values are all negative (-250 on the far left to -240 on the far right). This, combined with the densities being sharp peaks, makes it impossible to use this volume like a regular volume for surface coloring, filtering, segger, etc. Any suggestion on how to go from this step to a usable density would be appreciated. thanks! Jesse ================================= Dr. Jesse Hansen Schur Group Institute of Science and Technology Austria Am Campus 1 3400 Klosterneuburg Austria

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Useful tools ideas/requests
by Shayne Quinn 21 Oct '22

21 Oct '22

Hello, I have been using ChimeraX for a few years now for multidimensional cell bio-imaging and cannot thank the team and developers enough for such an amazing program. I am not sure where to ask for other useful tools so I am starting here. These may already exist but I was unsuccessful in finding them in the user guide so my apologies if I missed them. 1) Is there an option to color the different axis for the 'showOutlineBox' feature for volumes? For example box lines in x-blue, y-green and z-red to help keep orientation (I have included a mock version in the attachment) 2) I work specifically with Lattice Light Sheet Data which requires our 3D cells to be placed on glass coverslip that do not show up in the captured data but are useful for referencing orientation. Is there a feature in place already that would allow me to create a mock coverslip. So far I resorted to importing a throwaway volume (Volume 4 in attachment) and made the threshold for a surface ~0, set it to grey, and made it fill the bottom 5 pixels or so, shown in the attachment. 3) Is there a time stamp feature similar to the scale bar function that has already been implemented? Thank you so much for all the time and effort that has been put in and for creating such an amazing visualization tool! Cheers, Shayne Quinn

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Installing ChimeraX on Ubuntu 16.04 or openSuse Leap 15.2
by Miguel 19 Oct '22

19 Oct '22

Hello, I am trying to install ChimeraX on Ubuntu 16.04 or openSUSE Leap 15.2 without success. Is it possible? If so, what would be the procedure? Thanks, Miguel

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Center of the erase sphere
by Tianming Qu 19 Oct '22

19 Oct '22

Hi ChimeraX developers, Is there any way I can know the center of the erase sphere in CHimeraX? Best, Tianming

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Generate surface from a model using user defined color
by HONG ZHAN 17 Oct '22

17 Oct '22

Dear all, I would like to generate surface using my model but I want to keep the color as I defined. My protein contains only one chain so that when I ran Surface command, it generated surface with one color... Is there a way to generate surface to keep my defined color? Super thanks! Hong

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chimeraX clipper install
by Gutierrez, Dominique 17 Oct '22

17 Oct '22

Hello, I tried to install clipper with the popup window but it takes forever. I downloaded it directly from the website. Where do I put it .whl file? Best Regards, Dominique Gutierrez

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Re: [chimerax-users] [chimera-dev] ChimeraX pyhton script
by Elaine Meng 17 Oct '22

17 Oct '22

> On Oct 17, 2022, at 7:26 AM, Jan Hofmann via Chimera-dev <chimera-dev(a)cgl.ucsf.edu> wrote: > > To whom it may concern, > I want to write a python script to open a pdb file, then load a .xplor file in as well. After one rotation which I also want to do via the script I want to export the output file as a .png file. > Could you provide any advice to me on how to write such a script? I am having troubles loading any python script into ChimeraX. Eventually I want to use this script to batch wise output structures including guest adsorption where the guest species is introduced via the .xplor from previous analysis and the structure is provided by a .pdb file. I really would need some advice/tutorial at this stage so I would be more than happy to hear back from you. > Many thanks and kind regards, > Jan Hofmann, M.Sc. > PhD Student, Department of Chemistry > Chapman Group > Stony Brook University > jan.hofmann(a)stonybrook.edu > Office: Room 563, Chemistry Hi Jan, This is the Chimera list, maybe you wanted to send to chimerax-users(a)cgl.ucsf.edu instead? (Cc'd) Maybe it can be done at least partly with ChimeraX command script instead of a python script. If you do these steps interactively in ChimeraX, it should show the corresponding commands in the Log . A ChimeraX command script is just the same commands you would enter in the Command Line, except in a plain text file named something.cxc as explained here: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/usageconventions.html#cxc…> There is also a "forEachFile" option of the "open" command to read a ChimeraX command file and apply it to a series of input files, e.g. all the .pdb files in some folder. If you name the .xplor files to match the corresponding .pdb files, maybe you can use the $ mechanism described for that option, see: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/open.html#forEachFile> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco

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