January 2023 - ChimeraX-users - RBVI Mailing Lists

ISOLDE and secondary structure restraints
by Guido Hansen 17 Nov '23

17 Nov '23

Hi all, I just started model building in cryoEM maps and get great results using ISOLDE on AlphaFold2-derived initial models. I have a question which is mainly directed to Tristan I guess: Is is possible to use the command line/script to apply secondary structure restraints in ISOLDE? I would like to restrain the initial secondary structure assignment from Alphafold especially at resolution worse than 3.5 A. At the moment I select each and every residue range assigned to helix, parallel or antiparallel beta-strand one after the other and turn on the corresponding restrains in the ISOLDE GUI. Is there a better way via command line of script? Cheers, Guido -- PD Dr. Guido Hansen Group Leader UNIVERSITÄT ZU LÜBECK INSTITUT FÜR BIOCHEMIE Tel +49 451 3101 3122 Fax +49 451 3101 3104 E-Mail hansen(a)biochem.uni-luebeck.de www.biochem.uni-luebeck.de [1] Ratzeburger Allee 160 23562 Lübeck Links: ------ [1] http://www.biochem.uni-luebeck.de

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Feature request: replace residues in model with residues from other model
by Vorländer,Matthias Kopano 16 Nov '23

16 Nov '23

Dear ChimeraX team, Thanks a lot for developing the amazing tool that is ChimeraX! I use it extensively for model building, and would like to request a functionality to replace a residue selection in one model from residues in another model (similar to what is possible in coot via the replace fragment functionality). I am aware that this currently possible by a combination of delete, combine, and changechains, but it would be great if this could be shortcutted. Many thanks in advance, Matthias

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Trajectory smoothing
by Shubham Devesh Ramgoolam 15 May '23

15 May '23

Hi all, Does chimeraX has a command for trajectory smoothing? Based on previous similar questions, I know a script was written for trajectory smoothing in chimera/chimeraX. However, I cannot not access this script because it is not found on the server anymore. Shubham Sent from Mail<https://go.microsoft.com/fwlink/?LinkId=550986> for Windows

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Multi-chain single macromolecule .pdb file read as two molecules
by Lenye Dlamini 31 Jan '23

31 Jan '23

Hello, I have a homo-oligomeric model that I've refined using phenix and the ISOLDE tool in ChimeraX that's read during deposition as 2 separate molecules, a larger 14mer and a smaller tetramer. It's read as one molecule in Coot, Chimera and Pymol but read as two distinct molecules in ChimeraX exactly like the deposition. I found this curious and thought that perhaps you might have some idea of what's wrong with the file. There is nothing that appears obviously incorrect to me in the text of the .pdb file, all TER cards follow the chains and all amino acids and their identifiers are in sequence and correct. I'd appreciate any ideas you may have and I'm happy to send the file to you if you prefer. Thank you, Kind regards, Lenye Dlamini Disclaimer - University of Cape Town This email is subject to UCT policies and email disclaimer published on our website at http://www.uct.ac.za/main/email-disclaimer or obtainable from +27 21 650 9111. If this email is not related to the business of UCT, it is sent by the sender in an individual capacity. Please report security incidents or abuse via https://csirt.uct.ac.za/page/report-an-incident.php.

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Fwd: EMDB-SFF segmentation file: application of transform 0 for image-to-physical projection
by Eric Pettersen 30 Jan '23

30 Jan '23

> Begin forwarded message: > > From: Tom Goddard <goddard(a)sonic.net> > Subject: Re: [chimerax-users] EMDB-SFF segmentation file: application of transform 0 for image-to-physical projection > Date: January 30, 2023 at 11:54:02 AM PST > To: Paul Korir > Cc: Martin Schorb > > Hi Paul, > > ChimeraX does not specify what distance units the open models use. For atomic structures and cryoEM map it is usually Angstroms. For light microscopy images it is often microns. For medical image scans (MRI, CAT) it is I think meters. The file formats for the data define the physical distance units, not ChimeraX. So if EMDB SFF provides a segmentation for say an MRC or CCP4 density map file the scaling of that density map in the ChimeraX graphics is taken from the file header which has a field "cell dimensions in Angstroms". If a segmentation of that density map is made that is say a bounding surface it might use x,y,z coordinates in Angstroms or it might use grid index units when it writes out a file, that would depend on the segmentation file format and the software that is writing the segmentation. In ChimeraX it always tries to scale the data into physical units so that different data sets, like an atomic structure and 3D image data have the correct relative scale. So ChimeraX never displays images using grid index units. > > So from what you say about EMDB SFF the first transform goes from grid index units to physical units and ChimeraX should apply that transformation to the segmentation data so that it has the same scaling as the map data that the segmentation was derived from. I see there is a function in the ChimeraX EMDB SFF file reader called "guess_scale_and_shift" that is trying to figure out what transform to apply, but it is just a hack and looks for any non-identity transform. > > https://github.com/RBVI/ChimeraX/blob/da72f2cd9b23c0c35a66122b7edc453d593ea… <https://github.com/RBVI/ChimeraX/blob/da72f2cd9b23c0c35a66122b7edc453d593ea…> > > And another comment in the code suggests it is doing that hack because it was needed for EMDB SFF test data EMDB 1547. > > If I understand you correctly ChimeraX should instead always apply the first transform from transforms_list. I can make that change. The main thing will be to test it on pairs of EMDB SFF segmentations and corresponding maps to make sure it produces the correct alignment. > > Tom > > >> On Jan 30, 2023, at 2:20 AM, Paul Korir via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu> wrote: >> >> Hi Tom/ChimeraX admin, >> >> Just to clarify: what are the units of physical space in ChimeraX: Å or nm? >> >> Kind regards, >> >> Paul K. Korir, PhD >> 3D Visualisation Lead >> CS3DB >> EMBL-EBI >> >> On 30/01/2023 08:51, Paul Korir wrote: >>> Hi Tom, >>> >>> To the best of my understanding, ChimeraX displays images and associated segmentations in physical space not image space. However, segmentations are performed in image space. EMDB-SFF uses the first transform in the transforms_list field (with id=0) as the image-to-physical transform. (https://emdb-empiar.github.io/EMDB-SFF/v0.8.0.dev1/segmentation_da_xsd.html… <https://emdb-empiar.github.io/EMDB-SFF/v0.8.0.dev1/segmentation_da_xsd.html…>) >>> >>> I've tested with two files having the same segmentation but different values for transform 0 and they render the same. >>> >>> Could you please implement this feature in ChimeraX? >>> >>> Kind regards, >>> >>> -- >>> Paul K. Korir, PhD >>> 3D Visualisation Lead >>> CS3DB >>> EMBL-EBI >>> >> _______________________________________________ >> ChimeraX-users mailing list >> ChimeraX-users(a)cgl.ucsf.edu >> Manage subscription: >> https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users >

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EMDB-SFF segmentation file: application of transform 0 for image-to-physical projection
by Paul Korir 30 Jan '23

30 Jan '23

Hi Tom, To the best of my understanding, ChimeraX displays images and associated segmentations in physical space not image space. However, segmentations are performed in image space. EMDB-SFF uses the first transform in the transforms_list field (with id=0) as the image-to-physical transform. (https://emdb-empiar.github.io/EMDB-SFF/v0.8.0.dev1/segmentation_da_xsd.html… <https://emdb-empiar.github.io/EMDB-SFF/v0.8.0.dev1/segmentation_da_xsd.html…>) I've tested with two files having the same segmentation but different values for transform 0 and they render the same. Could you please implement this feature in ChimeraX? Kind regards, -- Paul K. Korir, PhD 3D Visualisation Lead CS3DB EMBL-EBI

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How to license AlphaFold with ChimeraX
by Asma Rehman 28 Jan '23

28 Jan '23

Hi, I'm currently a chimeraX user and would like to also use AlphaFold along with it. I was wondering if you could help us with directions. I appreciate your support. Thanks, Asma

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Isolde in with VR Headset ?
by Thibault TUBIANA 27 Jan '23

27 Jan '23

Dear all, I tried to use my Occulus Quest with ChimeraX Isolde Pluggin, while it works amazingly, the "tugging" function doesn't work. I thought that maybe it is the mouse mode that is node configured, so I tried "vr button trigger select" or 'vr button trigger "isolde tug atom"' but nope... It is not a request of course, just a question to know if someone already tried it ^^ Best regards, Thibault Tubiana. -- Thibault Tubiana, PhD Postdoctoral Fellow @ [ https://www.i2bc.paris-saclay.fr/equipe-interactions-and-assembly-mechanism… | IMAPP ] Institute for integrative biology of the cell ( [ https://www.i2bc.paris-saclay.fr/ | I2BC ] ) - CNRS UMR 9198 CEA Saclay, 91191 Gif sur Yvette - Bât 532 pce 34 Web Site: [ http://www.tubiana.me/ | http://www.tubiana.me/ ]

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Select ring atoms of ligand using python in chimerax
by Dr. Vijay Masand 26 Jan '23

26 Jan '23

Dear all I am looking for an efficient method to select ring atoms of ligands using python in chimeraX. Also, is there any python code/method to get the sum of charges on ligand atoms only? Thanks in advance. From Vijay With Warm Regards *Dr. Vijay H. Masand* Department of Chemistry, Vidya Bharati College, Amravati, 444 602 Maharashtra, India. Phone number- +91-9403312628 https://sites.google.com/site/vijaymasand/

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Re: [chimerax-users] recent query
by Rangarajan, Amith 26 Jan '23

26 Jan '23

Dear Eric, thanks for taking time to answer my query. It was very detailed and i am beginning to understand how bundles work on chimerax. i am working on a methods paper that uses sidechain center of masses as a representation of mutation position and generates clusters to intrepret the impact of the mutations. i tried scripting this, but i realised that pandas library is not present in chimerax (?) and i did not proceed further. is there a way to include scikit learn , pandas libraries in chimerax script? thanks once again for all your support ! best amith

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ChimeraX-users January 2023