July 2024 - ChimeraX-users - RBVI Mailing Lists

ChimeraX generated mmCIF files not suitable for PDB deposition
by Vorländer,Matthias Kopano 15 Jul '24

15 Jul '24

Dear ChimeraX team, Structure files in .cif format that are generated by ChimeraX are unfortunately not suitable for deposition to the PDB. This is due to lack of the column _entity_poly.pdbx_strand_id in the header. The column is usually found in the header in this table and contains the chain Identifier (i.e ‘A’ for chain A): loop_ _entity_poly.entity_id _entity_poly.nstd_monomer _entity_poly.type _entity_poly.pdbx_seq_one_letter_code_can Since ChimeraX does an excellent at converting PDBs to mCIFs otherwise, would it be possible to have ChimeraX include this column in the header of mmCIF files? This would greatly help to facilitate the tiresome process of depositing models to the PDB. Many thanks in advance, Best, Matthias

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AlphaFold Predicted Structures
by S.M. RAIHAN RAHMAN 15 Jul '24

15 Jul '24

Hi! Greetings. I hope you’re doing well. Recently, I did a structure prediction of a protein using the built-in AlphaFold of ChimeraX. Also, I downloaded the predicted structure of the same protein from the AF database. Surprisingly, when I superimposed these two structures, I found that they were pretty structurally different. However, the sequences are entirely similar. Could you please tell me what the reason for this is? And, is the built-in AlphaFold the AlphaFold2 or AlphaFold3? Thank you. Regards, Raihan

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Re: [Chimera-users] Covalent substrate modeling and minimization
by Elaine Meng 15 Jul '24

15 Jul '24

Hi Kelvin, First make sure of which program you are using. You sent this to the chimera-users mailing list which is for the program Chimera. However, the commands that you mention are for ChimeraX, so you must really be using chimeraX instead. In the future, please use chimerax-users(a)cgl.ucsf.edu for ChimeraX questions (CC'd here). I included both since the answer may involve both. Everything below is for ChimeraX unless stated otherwise: (1) Is this substrate included in the experimental structure? If the experiment was not done with the substrate bound, there is no reason to expect the density map to include density for it. 4kqo does not have a density map in EDS, so I guess you meant 4kq0. 4kq0 has plenty of density near the ligand residue MED, if that's what you meant by "substrate." You just need to use the slider in the Volume Viewer to change the isosurface level of the density ("volume" command below "level" option, but for interactive use, it is easier to use the slider in the GUI). To make it easier to view you can also limit the density to a zone near that ligand with the command "volume zone" open 1kq0 open 1kq0 from eds view ligand volume #2 level 0.01339 volume zone #2 near :MED The isosurface level in the example above is lower than what is shown initially when you open the map. However, I have no opinion as to what value exactly you should use. See help for "volume" and "Volume Viewer" <https://rbvi.ucsf.edu/chimerax/docs/user/commands/volume.html#general> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/volume.html#zone> <https://rbvi.ucsf.edu/chimerax/docs/user/tools/volumeviewer.html> (2) if you use "Join Models" section of "Build Structure" to create the bond (before combining) it will move one model to use your specified input bond distance and angles, and automatically combine the models. <https://rbvi.ucsf.edu/chimerax/docs/user/tools/buildstructure.html> If you combine first and then add a bond, it won't move the atoms and the bond distance and angles may be poor, but it depends on your situation as to which approach is better, i.e. I'm not saying the way you did it was wrong. You may also be interested in using the other sections in Build Structure (see link above): Adjust Bonds, Adjust Torsions You can also measure and change angles with "angle" and "torsion" commands. You can also rotate bonds manually using the "rotate bond" mousemode. <https://rbvi.ucsf.edu/chimerax/docs/user/commands/torsion.html> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/angle.html> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/ui.html#mousemode> (3) there isn't a simple minimization tool that handles nonstandard residues in ChimeraX yet. You could save a PDB file of the result from the above and use Chimera instead, which has a Minimize Structure tool. 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 Jul 12, 2024, at 3:26 AM, Kelvin Chung via Chimera-users <chimera-users(a)cgl.ucsf.edu> wrote: > > Good day > I am a researcher studying antibiotic interaction and trying to make a model with a substrate covalently bound to the active site. > There is a homolog with a crystal structure (PDB: 4KQO), and I am going to add the bound substrate in this pdb file to my target protein where the mode was generated by alphafold server. > > Although the workflow shall be simple, I still have some problems, could you kindly help? > > 1. Firstly, I would like to check whether the model of 4KQO is good enough for modeling, by examining the electron density map (open 4KQO, open 4KQO from eds). However, I found that it is a bit different from the tutorial (https://www.cgl.ucsf.edu/chimerax/docs/quickstart/index.html, pdb:1a0m) that the electron density of 4KQO did not cover the substrate molecule. I am totally ignorant in crystallography, so, how could I visualize the electron density of the substrate? by any symmetry operation / command so that I could check whether there is "electron density in the substrate" ? > > 2. I aligned 4KQO with the alphafold generated model, and I deleted the protein from 4KQO, and combined the two model, make a bond between the active residue with the substrate, however, I am not sure how to (1) check the bond length and angle is appropriately assigned, and (2) do energy minimization to reorientate side change to eliminate the crash with the substrate. > > Thank you very much for your help in advance > > Have a nice weekend

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Modify a pdb structure
by GAETANI, LUCIA (PGR) 15 Jul '24

15 Jul '24

Hi, I am a PhD student at the University of Warwick (UK). I am contacting you to know if I can modify a pdb structure in ChimeraX. I would need to create a covalent bond between the epsilon -NH2 group of a Lys residue and the hydroxyl group of fructose to make a bond like R-CH2-NH-R'. Is this modification possible in Chimera X? If so, how can I do this? Best wishes, Lucia

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stereo
by Krishnan Raman 12 Jul '24

12 Jul '24

Hi guys, How to reverse the sequential stereo in chimerax using camera command? Thanks Krish Krishnan Raman Executive Director, Structural Biology BioCryst Pharmaceuticals CONFIDENTIALITY NOTICE This email, including any attachments, may contain confidential or legally privileged information that is intended only for the individual or entity to whom it is addressed. If you are not the intended recipient, please be advised that any dissemination, distribution or copying of this email and any attachment is strictly prohibited. If you have received this email in error, please reply to the sender so that BioCryst Pharmaceuticals, Inc. can take corrective measures and then permanently delete this email and any attachment, including any printed copies. Thank you.

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3d glasses free monitors from acer....
by Krishnan Raman 12 Jul '24

12 Jul '24

https://www.acer.com/ee-en/spatiallabs maybe we can see chimerax😊 in 3d in these… they do have a plugin for unity.. Iam trying get one of these to try things out. Krishnan Raman Executive Director, Structural Biology BioCryst Pharmaceuticals CONFIDENTIALITY NOTICE This email, including any attachments, may contain confidential or legally privileged information that is intended only for the individual or entity to whom it is addressed. If you are not the intended recipient, please be advised that any dissemination, distribution or copying of this email and any attachment is strictly prohibited. If you have received this email in error, please reply to the sender so that BioCryst Pharmaceuticals, Inc. can take corrective measures and then permanently delete this email and any attachment, including any printed copies. Thank you.

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Re: Same residues look different
by Guillaume Gaullier 12 Jul '24

12 Jul '24

Hi Adinda, You will get answers faster if you send your questions to the list, so keep it in CC. 😊 I also observe this difference in coloring when using the button or your command. Note that the log reports a slightly different command when using the toolbar button. But I don't know why these two commands produce such different results. Try reading the documentation (the command "help coulombic" will open the relevant page). Regarding your second question, this is explained in the documentation (and in physical chemistry textbooks): "Coulombic electrostatic potential is calculated from atomic partial charges and coordinates according to Coulomb's law: φ = Σ [qi / (εdi)] φ is the potential (which varies in space), q are the atomic partial charges, d are the distances from the atoms, and ε is the dielectric, representing screening by the medium. The resulting potential is in units of kcal/(mol·e) at 298 K. A distance-dependent dielectric is sometimes used to approximate screening by implicit solvent. By default, distDep true and dielectric 4.0 are used" What is represented on the surface of the protein as a red-blue gradient are the values of this electrostatic potential, which is continuous in space. So, your example aromatic residue appears blue because there must be a positively charged residue sufficiently close in space (look around, you should find it). This is not too surprising: lysine and arginine often make cation-pi interactions with aromatic residues. See https://en.wikipedia.org/wiki/Cation%E2%80%93%CF%80_interaction for more info. I hope this helps, Guillaume ________________________________ From: ADINDA <adinda.fitri.falinka(a)gmail.com> Sent: Friday, July 12, 2024 9:27:12 AM To: Guillaume Gaullier Subject: Re: [chimerax-users] Same residues look different Dear Dr Guillaume, Thank you for your prompt response. I have another question. * How does the ESP colouring work? When you click on molecular display and click "electrostatic" after that, it shows you the charges on the surface protein display (blue for positive, red for negative). But if you run the command "coulombic protein surfaces #sample", you'll get a different view, with the positive and negative parts becoming more pronounced. <https://preview.redd.it/need-help-with-chimerax-v0-loexjv50glbd1.png?width=…> [r/labrats - this is the view I get when I just click electrostatic in the molecular display bar (PDB: 2j1a)] this is the view I get when I just click electrostatic in the molecular display bar (PDB: 2j1a) <https://preview.redd.it/need-help-with-chimerax-v0-vmusn036glbd1.png?width=…> [r/labrats - this is what I get when I run the command "coulombic protein surfaces" (PDB: 2j1a)] this is what I get when I run the command "coulombic protein surfaces" (PDB: 2j1a) * Why is tryptophan/phenylalanine (actually any hydrophobic a.a for that matter) "positively charged" when I turn on ESP? (it's coloured blue when it should be white) <https://preview.redd.it/need-help-with-chimerax-v0-3fmfb2rjglbd1.png?width=…> [r/labrats - my mouse is hovering at the light blue area next to phenylalanine label] my mouse is hovering at the light blue area next to phenylalanine label Best, Adinda On Fri, Jul 12, 2024 at 2:50 PM Guillaume Gaullier <guillaume.gaullier(a)kemi.uu.se<mailto:guillaume.gaullier@kemi.uu.se>> wrote: Hello Adinda, These two lysines look different because one displays the hydrogen atoms while the other one doesn’t. The one that doesn’t show them probably doesn’t have them in the coordinate file (omitting them is a common practice when doing model building), but you can add them with the command "addh". Once they are added, or with a coordinate file that already had them, you can hide them from the display with the commande "hide H". The other reason these two lysines look different is because they have different rotamer conformations. As far as I can tell, they seem to be from different structures, so this is normal. These conformations depend on the underlying experimental data that were used to build these atomic models (an electron density map from a crystallographic dataset, or a cryoEM map). If you display the map overlayed on the atomic model, you can determine how well these rotamers are supported by the data. But lysines exposed at the surface, like these ones, often show poor density (because they are flexible), so the rotamer modeled in the atomic model is unlikely to fully account for the real conformations. I hope this helps, Guillaume On 12 Jul 2024, at 06:35, ADINDA via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu<mailto:chimerax-users@cgl.ucsf.edu>> wrote: Dear developers, I have a few questions about how residues are visualised on your software. <image.png> <image.png> They're both lysine but look different. What can I do to solve this? Best, Adinda VARNING: Klicka inte på länkar och öppna inte bilagor om du inte känner igen avsändaren och vet att innehållet är säkert. CAUTION: Do not click on links or open attachments unless you recognise the sender and know the content is safe. _______________________________________________ ChimeraX-users mailing list -- chimerax-users(a)cgl.ucsf.edu<mailto:chimerax-users@cgl.ucsf.edu> To unsubscribe send an email to chimerax-users-leave(a)cgl.ucsf.edu<mailto:chimerax-users-leave@cgl.ucsf.edu> Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/ När du har kontakt med oss på Uppsala universitet med e-post så innebär det att vi behandlar dina personuppgifter. För att läsa mer om hur vi gör det kan du läsa här: http://www.uu.se/om-uu/dataskydd-personuppgifter/ E-mailing Uppsala University means that we will process your personal data. For more information on how this is performed, please read here: http://www.uu.se/en/about-uu/data-protection-policy VARNING: Klicka inte på länkar och öppna inte bilagor om du inte känner igen avsändaren och vet att innehållet är säkert. CAUTION: Do not click on links or open attachments unless you recognise the sender and know the content is safe.

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Same residues look different
by ADINDA 11 Jul '24

11 Jul '24

Dear developers, I have a few questions about how residues are visualised on your software. [image: image.png] [image: image.png] They're both lysine but look different. What can I do to solve this? Best, Adinda

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Generating long fibrils
by Binh Nguyen 11 Jul '24

11 Jul '24

Dear all, Is there a way in chimeraX that I can use to generate a long fibril, say 20 chains, from a single chain with a twist angle of -1.4 degree and the rise (distance between layers) of 4.75 Angstrom. Some thing like this: [cid:4fb0d318-2ddd-4570-99a9-99846b9ee27c] I normally used Coot and manually add a single layer into density. Thanks, B ________________________________ UT Southwestern Medical Center The future of medicine, today.

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Install ChimeraX on Linux without sudo
by Roden Deng Luo 10 Jul '24

10 Jul '24

Dear ChimeraX Team, The install notes for all the current distributions for the Linx system require sudo. I wonder is it possible without sudo? On Rocky Linux VERSION 9.4 (Blue Onyx), I tried the following. $ flatpak --user install ChimeraX-1.8.flatpak error: The application edu.ucsf.rbvi.ChimeraX/x86_64/master requires the runtime org.freedesktop.Platform/x86_64/23.08 which was not found $ rpm -ivh ucsf-chimerax-1.8-1.el9.x86_64.rpm error: Failed dependencies: fftw-libs-single is needed by ucsf-chimerax-1.8-1.el9.x86_64 mesa-libOSMesa is needed by ucsf-chimerax-1.8-1.el9.x86_64 sqlite is needed by ucsf-chimerax-1.8-1.el9.x86_64 xcb-util-cursor is needed by ucsf-chimerax-1.8-1.el9.x86_64 xcb-util-image is needed by ucsf-chimerax-1.8-1.el9.x86_64 xcb-util-keysyms is needed by ucsf-chimerax-1.8-1.el9.x86_64 xcb-util-renderutil is needed by ucsf-chimerax-1.8-1.el9.x86_64 xcb-util-wm is needed by ucsf-chimerax-1.8-1.el9.x86_64 Thanks, Roden -- This message and its contents, including attachments are intended solely for the original recipient. If you are not the intended recipient or have received this message in error, please notify me immediately and delete this message from your computer system. Any unauthorized use or distribution is prohibited. Please consider the environment before printing this email.

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