- ChimeraX-users - RBVI Mailing Lists

Re: Boltz pae contacts
by Tom Goddard 21 Apr '26

21 Apr '26

Hi Nathan, The error message "No alphafold specified for alphafold contacts" is goofed up -- it should say "No atoms specified for alphafold contacts". This means your structure has no chain A, so your command "alphafold contacts /A to /B distance 5 maxpae 6" needs to be modified to use the actual chain identifiers in your structure. You can hover the mouse over the chains in your structure and it will popup some text indicating the chain id under the mouse. Yes the "Alphafold Error Plot" in ChimeraX works for Boltz 1 and 2, AlphaFold 2 and 3, OpenFold 3, and ESMFold predictions. I plan to rename it Predicted Aligned Error Plot so it will be clearer that it is not specific to AlphaFold. It currently has the AlphaFold name because when I added AlphaFold 2 support about 4 years ago there were no other prediction programs writing PAE. I have fixed the text of the error message in the daily build. Thanks for reporting the problem. Tom > On Apr 21, 2026, at 4:41 PM, Nathan Davis <ndavis18(a)uwyo.edu> wrote: > > I get the error: No alphafold specified for alphafold contacts. I attached my chimerax session. Should I be using alphafold error plot for the pae? > > On Apr 21, 2026, at 11:06 AM, Nathan Davis via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>> wrote: > > Hi, I'm Nathan. I have been using ChimeraX to assess protein-protein interfaces. One of the commands I use is alphafold contacts, usually with something like this: alphafold contacts /A to /B distance 5 maxpae 6. I started looking at boltz runs as well and realized that this command does not work for boltz models. Is there a similar command that would work for boltz? Also, I'm importing boltz models that I ran on my local cluster. > > Thank you! > Nathan

1 0

Boltz pae contacts
by Nathan Davis 21 Apr '26

21 Apr '26

Hi, I'm Nathan. I have been using ChimeraX to assess protein-protein interfaces. One of the commands I use is alphafold contacts, usually with something like this: alphafold contacts /A to /B distance 5 maxpae 6. I started looking at boltz runs as well and realized that this command does not work for boltz models. Is there a similar command that would work for boltz? Also, I'm importing boltz models that I ran on my local cluster. Thank you! Nathan

2 1

Sequence selection and export tools
by Samuel Haysom 21 Apr '26

21 Apr '26

Hi, Not sure if I'm missing this but there are a few sequence selection and export tools that I can't seem to find an easy way to do: 1. Is there a way to select two locations on a protein chain and then expand the selection to include all the residues between those two points? 2. If a continuous stretch of residues is selected, is there a way to print the sequence to the log or to copy it to the clipboard? 3. In the sequence view, is there a way to select a stretch of residues and then copy that to the clipboard? In general it would be really nice if copy worked in the sequence view window on selected residues I'm aware that I could script this functionality but it does seem to the sort of thing that might be possible in the vanilla installation. KR, Sam Samuel Haysom Senior Scientist • Protein Sciences Nxera Pharma +44 (0)1223 949201 • Steinmetz Building, Granta Park, Great Abington Cambridge, CB21 6DG, United Kingdom The information in this e-mail is confidential and may be legally privileged. It is intended for the exclusive attention of the addressee stated above and should not be copied or disclosed to any other. If you have received this transmission in error, please contact the sender immediately, make no use of its contents and delete this message from your system. Nxera Pharma UK Limited. Registered Office: Granta Park, Great Abington, Cambridge, Cambridgeshire, CB21 6DG. Company No: 06267989

3 2

Chimera X color question
by Michael Moos 14 Apr '26

14 Apr '26

Hello, I try to color different parts of a molecular chain and am stuck with the problem that I can not define the fill color individually for the selected parts. The color is valid for the selected sticks but fill color changes for the whole molecule. Is there a solution for this problem? It works if I cut the molecule in different parts but I would like to keep it as whole. The program itself is very nice and I prefer to use it for displaying long molecules. A color code would be necessary for marking the different parts of the molecule for better visualization (see attached file). Kind regards, Michael -- Dipl. Chem. Michael Moos Universität Würzburg Institut für Organische Chemie Lehrstuhl für Physikalische Organische Chemie AK Prof. Lambert Am Hubland C1 97074 Würzburg Phone: +49931 31 88764 Fax: +49931 31 88764-0 Web: https://www.chemie.uni-wuerzburg.de/oc/lambert-group/

2 4

Re: [Chimera-users] Built-in residue specific annotations in mmCIF?
by Oliver Clarke 13 Apr '26

13 Apr '26

Hi all, Bringing back a long-forgotten thread from the dead... Would it be possible to incorporate self-contained annotations into mmCIF in ChimeraX (reading/writing)? I recently added a primitive little widget to do this in coot1-trimmings: https://bsky.app/profile/olibclarke.bsky.social/post/3micblpuoxc2u This adds the notes as base64 in a loop at the end, so they are persistent and can be read/written/modified by multiple users, with timestamps & 3D coordinates for each note: _cootnote_annotation_meta.version 1 _cootnote_annotation_meta.program coot-trimmings loop_ _cootnote_residue_note.id _cootnote_residue_note.auth_asym_id _cootnote_residue_note.auth_seq_id _cootnote_residue_note.pdbx_PDB_ins_code _cootnote_residue_note.label_comp_id _cootnote_residue_note.author_b64 _cootnote_residue_note.modified_utc _cootnote_residue_note.note_b64 1 A 162 ? GLY T2xp 2026-03-31T17:06:58Z dGhpcyBnbHljaW5lIGlzIHdlaXJk 2 A 196 ? GLU T2xp 2026-03-31T17:07:41Z VGhpcyBpcyBhIGdsdXRhbWF0ZS4gVGhpcyBpcyBhIHJlYWxseSBsb25nIG5vdGUuIFRoaXMgaXMgYSByZWFsbHkgbG9uZyBub3RlLiBUaGlzIGlzIGEgcmVhbGx5IGxvbmcgbm90ZS4gVGhpcyBpcyBhIHJlYWxseSBsb25nIG5vdGUuIFRoaXMgaXMgYSByZWFsbHkgbG9uZyBub3RlLiBUaGlzIGlzIGEgcmVhbGx5IGxvbmcgbm90ZS4gVGhpcyBpcyBhIHJlYWxseSBsb25nIG5vdGUuIFRoaXMgaXMgYSByZWFsbHkgbG9uZyBub3RlLiBUaGlzIGlzIGEgcmVhbGx5IGxvbmcgbm90ZS4gVGhpcyBpcyBhIHJlYWxseSBsb25nIG5vdGUuIFRoaXMgaXMgYSByZWFsbHkgbG9uZyBub3RlLiBUaGlzIGlzIGEgcmVhbGx5IGxvbmcgbm90ZS4gVGhpcyBpcyBhIHJlYWxseSBsb25nIG5vdGUuIFRoaXMgaXMgYSByZWFsbHkgbG9uZyBub3RlLiBUaGlzIGlzIGEgcmVhbGx5IGxvbmcgbm90ZS4gVGhpcyBpcyBhIHJlYWxseSBsb25nIG5vdGUuIFRoaXMgaXMgYSByZWFsbHkgbG9uZyBub3RlLiBUaGlzIGlzIGEgcmVhbGx5IGxvbmcgbm90ZS4gVGhpcyBpcyBhIHJlYWxseSBsb25nIG5vdGUuIFRoaXMgaXMgYSByZWFsbHkgbG9uZyBub3RlLiBUaGlzIGlzIGEgcmVhbGx5IGxvbmcgbm90ZS4gVGhpcyBpcyBhIHJlYWxseSBsb25nIG5vdGUuIFRoaXMgaXMgYSByZWFsbHkgbG9uZyBub3RlLiBUaGlzIGlzIGEgcmVhbGx5IGxvbmcgbm90ZS4gVGhpcyBpcyBhIHJlYWxseSBsb25nIG5vdGUuIFRoaXMgaXMgYSByZWFsbHkgbG9uZyBub3RlLiBUaGlzIGlzIGEgcmVhbGx5IGxvbmcgbm90ZS4gVGhpcyBpcyBhIHJlYWxseSBsb25nIG5vdGUuIFRoaXMgaXMgYSByZWFsbHkgbG9uZyBub3RlLiBUaGlzIGlzIGEgcmVhbGx5IGxvbmcgbm90ZS4gVGhpcyBpcyBhIHJlYWxseSBsb25nIG5vdGUuIFRoaXMgaXMgYSByZWFsbHkgbG9uZyBub3RlLiBUaGlzIGlzIGEgcmVhbGx5IGxvbmcgbm90ZS4gVGhpcyBpcyBhIHJlYWxseSBsb25nIG5vdGUuIFRoaXMgaXMgYSByZWFsbHkgbG9uZyBub3RlLiBUaGlzIGlzIGEgcmVhbGx5IGxvbmcgbm90ZS4gVGhpcyBpcyBhIHJlYWxseSBsb25nIG5vdGUu 3 C 3006 ? K T2xp 2026-03-31T17:08:08Z VGhpcyBpcyBvbmUgb2YgdGhlIHBvdGFzc2l1bXM= The nice thing about this is it is very flexible, and it means the structure itself can contain a record of modifications, interesting sites, disease mutations, etc - and can also become a kind of "track changes" or discussion forum for the structure - facilitating conversations between collaborators, for example. If there is interest, it might be good to identify a shared format for such a loop, so notes written in Coot could be read/navigated in ChimeraX, & vice versa? Cheers Oli > On Nov 12, 2015, at 7:08 PM, Greg Couch <gregc(a)cgl.ucsf.edu> wrote: > > Noted. I've added this to the list of things to do for ChimeraX (formerly known as Chimera2). > > -- Greg > > On 11/12/2015 02:21 PM, Oliver Clarke wrote: >> Relating to this, I wonder whether it is possible to find a home for attributes calculated in Chimera 2 in one of the mmCIF fields? >> >> I mean that's the advantage of mmCIF in theory right, that it is extensible and can support attributes beyond just position and B-factor? >> >> This would make transferring custom defined or calculated attributes between different chimera sessions much easier I think, if they were inherent to the file containing the coordinates, and again would at least allow for the possibility of data exchange with other programs. >> >> Oliver. >> >> On Thu, Nov 12, 2015 at 4:49 PM, Oliver Clarke <olibclarke(a)gmail.com <mailto:olibclarke@gmail.com>> wrote: >>> I see what you mean Greg... it is not at all clear how to use this now that I look at it in more detail. >>> >>> A hack using this entry as a handle for persistent notes would certainly be useful in the medium term, but in the longer term it would be nice to have a established syntax, so that notes written in Chimera could be read and displayed in Coot, for example (see here for discussion: https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=coot;8213db52.1511) >>> >>> But I guess this might require some discussion with the PDB - according to their FAQ old-school PDB files will become obsolete next year and mmCIF/PDBx will be the only game in town... >>> >>> Cheers, >>> Oliver. >>> >>> On Thu, Nov 12, 2015 at 4:22 PM, Greg Couch < <mailto:gregc@cgl.ucsf.edu>gregc(a)cgl.ucsf.edu <mailto:gregc@cgl.ucsf.edu>> wrote: >>>> That is an excellent suggestion. Currently the mmCIF files from the PDB provide the free-form text for the footnote, but do not provide the data that is supposed to be in the associated conformer_family_coord_set category. And without that data, it will be difficult to figure out and show exactly which atoms/residues are associated with the footnote. It looks like that part of the mmCIF specification is unused because it is not well thought out. The conformer_family_coord_set data category makes references to CIF save frames, but currently " mmCIF does not support references to save frames or the use of save frames for purposes other than for encapsulating dictionary definitions" [ <http://mmcif.wwpdb.org/docs/tutorials/mechanics/pdbx-mmcif-syntax.html>http://mmcif.wwpdb.org/docs/tutorials/mechanics/pdbx-mmcif-syntax.html] And since there are no examples, so it is unclear how the mmCIF committee was expecting this to work. >>>> >>>> So until atom_sites_footnote's are "fixed", is getting access to the text okay? We could probably extract the relevant residues from the free-form text most of the time, but it would be a hack. >>>> >>>> -- Greg >>>> >>>> >>>> On 11/11/2015 10:11 AM, Oliver Clarke wrote: >>>>> Hi all, >>>>> >>>>> As discussed on the ccp4bb ( <https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ccp4bb;2223469c.1511>https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ccp4bb;2223469c.1511) the mmCIF format incorporates an atom_sites_foornote record ( <http://mmcif.wwpdb.org/dictionaries/mmcif_nmr-star.dic/Categories/atom_site…>http://mmcif.wwpdb.org/dictionaries/mmcif_nmr-star.dic/Categories/atom_site…) which allows for the direct association of specific comments/annotations with particular atoms/residues. >>>>> >>>>> As part of expanding mmCIF support in Chimera2, would it be possible to consider incorporating the capacity to read, write, and display these records as labels or notes? This could be a great way of incorporating built-in-annotations in a structure pertaining to specific features that could potentially be readable by other software such as Coot and pymol. >>>>> >>>>> Cheers, >>>>> Oliver. >>>>> >>>>> >>>>> >>>>> _______________________________________________ >>>>> Chimera-users mailing list >>>>> Chimera-users(a)cgl.ucsf.edu <mailto:Chimera-users@cgl.ucsf.edu> >>>>> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users >>>> >>> >> >

3 7

Help with command-line orientation of structure in ChimeraX
by Nusrat Tazkia 13 Apr '26

13 Apr '26

Dear ChimeraX Support Team, I hope you are doing well. I am currently working with spike protein structures in ChimeraX and would like to orient them in a consistent and reproducible way using command-line instructions. Specifically, I am trying to “straighten” the structure so that the receptor-binding domain (RBD) is oriented upwards, without relying on manual mouse adjustments. The RBD in my structure corresponds to residues 319–541 (chains A, B and C). I have been using commands such as 'measure inertia', 'view', and 'turn', but I am having difficulty determining the exact sequence needed to achieve a clean and consistent orientation. I have attached a .cxs session file showing my current structure and preferred manual orientation. I actually have many similar .cxs files, so I am looking for a command-line approach that will reliably produce the same orientation across all of them. Additionally, when I use 'movie encode' to generate a rotation, I notice that the structure slightly tilts to the left or right during rotation. I would like the structure to remain perfectly straight and spin cleanly along a single axis (ideally the y-axis), without any unintended tilt. Would it be possible for you to suggest the appropriate commands (or workflow) to reproduce this view consistently and achieve a stable, axis-aligned rotation? Thank you very much for your time and support. Kind regards, Nusrat Tazkia

3 6

Orbital Viewer - Gaussian formatted checkpoint
by Matthias Bremer 08 Apr '26

08 Apr '26

Dear All, when trying to render molecular orbitals from a Gaussian .fchk file, I get the following error message: WARNING AaronTools.fileIO.FileReader.read_fchk could not create Orbitals, try increasing the max. array size to read from FCHK files I used the 6-31+G(d) basis. How can I fix this? Best regards Matthias Bremer

2 1

vseries movie recording with frame labels
by Rayees Mattoo 06 Apr '26

06 Apr '26

Hi, I want to record a vseries movie, a total of 20 frames (frame 0-19). I used the below script. I want to include a frame label (Frame 0 to 19) as the movie oscillates across frames. The frame numbers should appear in sync with the movie frames. How can I include that and record with vseries? movie record; vseries play #1 direction oscillate loop true; wait 200; movie encode ~/Desktop/vseries_movie1.mp4 Best Rayees

2 2

Visualizing contact sites on structures larger than atoms
by Wilson, Melissa (NIH/NINDS) [F] 03 Apr '26

03 Apr '26

Hello, I am currently using ChimeraX to reconstruct mitochondria undergoing autophagy. I am interested in visualizing contact sites between the mitolysosome, surrounding mitochondria, and endoplasmic reticulum. The clashes/contacts command<https://www.cgl.ucsf.edu/chimerax/docs/user/commands/clashes.html#options> is all in the context of atoms. Can this command be used for the purpose of larger structures? Or is there another method in ChimeraX to achieve such a visualization? All of my models are surfaces. Best, Melissa Wilson

2 1

Issue with SVG export in CircosContacts plugin: Interface residues missing !
by Arun Gupta 03 Apr '26

03 Apr '26

Dear ChimeraX Team, Today I tested the CircosContacts plugin in ChimeraX to generate Circos plots for the peptide–MHC interface. The plugin works as expected in the CircosContacts HTML webpage, where I can see the interface residue/atom contact details between the peptide (Chain Id - C) and MHC chain (Chain Id- A). However, I am not able to observe the interface residues in the exported contacts_circos.svg file. The SVG export appears to be missing the interface residue annotations that are visible in the HTML view. I have attached the exported contacts_circos.svg file for reference. For reproducibility, I used the following command: circoscontacts #1/A restrict #1/C outputDir /Users/arungupta/010426_contacts_1 interModel true intramol false Could you please let me know whether this is expected behavior, or if there is a workaround to ensure that the interface residues are included in the exported SVG file as well or if this is a known limitation of the current version of the plugin ? Thank you for your time and for developing such a useful plugin. Best regards, Arun Arun Gupta PhD, MRSC Sr. Post Doctoral Research Assistant Gillespie/McMichael Group Nuffield Dept. of Clinical Medicine, University of Oxford, Centre for Immuno-Oncology Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7DQ

4 4