- ChimeraX-users - RBVI Mailing Lists

Coot-like navigation?
by Murpholino Peligro 02 Jul '25

02 Jul '25

Can we navigate the protein model like in coot? spacebar jumps from residue i to residue i+1 shift-spacebar jumps from residue i to residue i-1 ctrl-g shows a tiny window where I can input 'a1' and the cofr goes to chain a residue 1 Can you point me in the right direction? Do I have to use aliases or is it something more complicated? Thanks

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rainbow separate color for each residue
by Rebecca Grace 02 Jul '25

02 Jul '25

Hello ChimeraX, Greetings! I've never asked a question, but I need to expedite solving this issue, so thought the time is now. :-) (I should also add, thank you for Chimera and then Chimera X, it has been so beneficial to my research and presentations!) Several months ago I used rainbow to color a range of residues on my structure. Now I am trying to recreate it on a different model and I can't seem to recapture the detail where every residue is delineated versus a continuous gradation across the selected region. I've searched and read several help emails etc, and maybe if I was a more expert user I would understand this from the usage/help entries about rainbow, but alas, I cannot recreate it. Please let me know how I did this?? Thanks for any help! Cheers, Bec Here is the past way that I want to recreate: *notice how each residue of tube helix has a separate color whereas the next image has no separations [image: image.png] And here is the way I can only seem to get the program to do today: [image: image.png]

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Model grouping and next/previous buttons
by Oliver Clarke 02 Jul '25

02 Jul '25

Hi, I use the next/previous buttons (sequential display controls) in the model panel quite a lot for quickly flicking between 3D classes - they are very handy for this! I would like to be able to use the same buttons for switching between model/map pairs, but there is no way to do this currently. I expected that if I grouped models by using the rename command to make (for example) the map a sub-model (e.g. model #1, map #1.1), then the next/prev buttons would switch between the model groupings, but this is not the case - it still treats the sub-models as independent models. Would it be possible to revisit this logic so that if a "base-level" model like #1 is selected, next/prev will switch between model groupings, while if a member of an ensemble is selected (say #1.1), it will cycle through members of the ensemble? Also, would it be possible at some point to add a GUI option for grouping models - perhaps a button in the model panel that allows for automatic grouping of the selected models? Cheers Oli

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Check waters with a full density map?
by Murpholino Peligro 01 Jul '25

01 Jul '25

Dear all I got a pdb and a mtz file (from phenix.maps) with: Number of columns: 11 label #valid %valid min max type H 23487 100.00% 0.00 56.00 H: index h,k,l K 23487 100.00% 0.00 39.00 H: index h,k,l L 23487 100.00% 0.00 26.00 H: index h,k,l 2FOFCWT 23337 99.36% 0.01 1113.30 F: amplitude PH2FOFCWT 23337 99.36% -180.00 180.00 P: phase angle in degrees 2FOFCWT_fill 23487 100.00% 0.01 1113.30 F: amplitude PH2FOFCWT_fill 23487 100.00% -180.00 180.00 P: phase angle in degrees FOFCWT 23337 99.36% 0.00 836.89 F: amplitude PHFOFCWT 23337 99.36% -180.00 180.00 P: phase angle in degrees ANOM 19860 84.56% 0.00 149.58 F: amplitude PHANOM 19860 84.56% -179.97 179.99 P: phase angle in degrees (as reported by phenix.mtz.dump) I open both in chimerax with open /home/murph/doc/pdbs/mol1/mol1.pdb open /home/murph/doc/pdbs/mol1/mol1_map_coeffs.mtz structureModel #1 (clipper already installed) If I do tools->structure analysis->check waters and choose the model (now id #1.2) and the 2fofc map (#1.1.1.2) I got a warning saying "Some (or all) atoms lie outside the volume, continue anyway?" If I continue anyway... some waters with density do have a 0 in the density column... This is, I think, because by default the density is not displayed around all atoms of the model (huge models would crash the computer, right?).. so maybe I just need to show the density around all the atoms in the model... How do I do that? (I thought that 'volume unzone' was the magic command but that only shows a bigger cube of density around the center of rotation, instead of the smaller sphere of density). Thanks

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BIOMT output
by Sui, Haixin (HEALTH) 01 Jul '25

01 Jul '25

Hello Is there a way to write out the BIOMT matrices associated with the input symmetry symbol in the output PDB file saved by Chimerax? Thank you Haixin -- Haixin Sui, Ph.D Pronouns: he, his, him (What's This<https://oer.ny.gov/system/files/documents/2023/11/personal-pronouns.pdf>?) Principal Investigator Wadsworth Center NY State Department of Health Biggs Lab C311, Empire State Plaza Albany, NY 12237 (518) 474-4235 (o) haixin.sui(a)health.ny.gov<mailto:haixin.sui@health.ny.gov> www.wadsworth.org/research/laboratories/sui-laboratory/sui-laboratory<http://www.wadsworth.org/research/laboratories/sui-laboratory/sui-laboratory>

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zone ID
by Denton, Jerod S 01 Jul '25

01 Jul '25

Hi, We are trying to see/export a list of amino acids that are within 5 angstroms of a docked ligand. Can you please tell me how to do this if possible? Thanks, Jerod Denton Vanderbilt

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Query for Volume viewer
by Akash Singh 01 Jul '25

01 Jul '25

Hi, I'm a researcher from India. I have been trying to make some EM fitting image with model protein. There is no Volume viewer option for Line smoothening, surface smoothening or square mesh to triangle mesh conversion. Also surface smoothening problem. I have been trying to execute through the command line, but it doesnt work . Can you help me regarding command line code for following Mesh Line smoothing Mesh surface smoothening Dim transparency The suite is ChimeraX or ChimeraX 1.9 Regards, Akash Singh

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Filling gaps in selection
by Bruno Hay Mele 30 Jun '25

30 Jun '25

Hi all, I'm trying to evaluate salient differences within a specific topological domain across a set of protein structures. My workflow is as follows: I choose a reference structure, and use MatchMaker to align all other structures to it. Then, I use the Contacts tool with distance 0 and overlap 0 to select CAs of residues that are perfectly aligned to the reference selection (i.e. the topological domain). This approach works well in conserved regions, but it results in gaps where insertions or small variations occur. I've tried to use sel up to fill these gaps, but my attempts have failed miserably. Is there a way to fill in gaps within a discontinuous selectionbi.e., to make it continuousbwithout extending the selection outward beyond the domain of interest? Ideally, I'd like to interpolate or bridge only the missing parts, without picking up unrelated residues. cheers, -- Bruno Hay Mele, PhD 2D-20, Biology Dept., University of Naples Federico II https://github.com/bhym/ | +39 081 67 9118

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rotating 2dlabels?
by coyote_v2002＠yahoo.com 30 Jun '25

30 Jun '25

Is there a way to rotate 2dlabels within ChimeraX? The only way I found to add such labels is in an external program like Inkscape. Vis

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Re: interrupted beta-strands
by Elaine Meng 29 Jun '25

29 Jun '25

Hi Maria, For ChimeraX questions, it is better to use the chimerax-users(a)cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu> address CC'd here. The chimera-users address is for Chimera and we don't want people to get confused between the two. In ChimeraX: Probably you also need to set ss_id to indicate they are all in the same strand, instead of two consecutive strands, which would always be shown with a short connector instead of as a continuous strand. Please see <https://rbvi.ucsf.edu/chimerax/docs/user/attributes.html#residue> ... and previous posts, such as these talking about helices but probably the same problem as your strands: <https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu…> <https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu…> 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 29, 2025, at 8:02 AM, Maria Sola i Vilarrubias <maria.sola(a)ibmb.csic.es> wrote: > > Dear colleagues, > > I would like to know how to solve a problem that I encountered several times in ChimeraX , which is a disruption of beta strands. I attach a figure. This is a beta-hairpin of a model that ChimeraX showed as a coil, but previous data showed that this region corresponds to a beta-hairpin. I imposed a beta-strand fold for each of the corresponding segments with ChimeraX (setattr #3/a:40-52,59-66) res ss_type 0) but the strands appear interrupted between consecutive residues. I guess it's a problem of the polypeptide bond, but nevertheless Chimera can solve the problem. How can I solve this in ChimeraX? > > Thank you for your time and best regards, > Maria > > -- > Maria Solà > Dep. Structural Biology IBMB-CSIC > Barcelona Science Park (Helix Building) > Baldiri Reixac 15 > 08028 BARCELONA > Spain > Tel: (+34) 93 403 4950 >

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