- ChimeraX-users - RBVI Mailing Lists

How to show van der Waals surface
by 我就要柠乐 26 Apr '24

26 Apr '24

Dear Sir/Madam         Recently, I have been using ChimeraX for graphical analysis, and I find the software to be very user-friendly and efficient. I am currently facing a challenge where I want to display the van der Waals surface of a residue, similar to this illustration（https://doi.org/10.1038/s41467-022-31526-7）. However, I am not quite sure how to write the command correctly. I have looked up the commands on the official website and tried using these two:surface #1:230； surface style mesh. The bottom is open （the rad circle）, but I would like to have a complete van der Waals surface with closed openings, similar to what is typically seen in the literature. I would appreciate your assistance. Thank you！                                                                                                                       yours  sincerely                                                                                                                       yiwen 我就要柠乐 790639436(a)qq.com  

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Cinematographic effects in MD movie recording
by Enrico Martinez 26 Apr '24

26 Apr '24

Dear Chimera-X users ! I would like to add some cinematographic effects such as changing the camera angle back and forth during a short recording time of MD movies. Could you suggest some scripting tricks that I could add to the following coordset routine: # start recording movie record size 3840,2160 supersample 1 ## play movie from beginning to the end coordset #1 1,1000,1 wait 1000 etc Would it be possible to bend the camera automatically e.g. during the first 250 steps of recording ? Any other possibilities ? Yours with thanks Enrico

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Question about visualisation of DNA structure
by Enrico Martinez 26 Apr '24

26 Apr '24

Dear Chimera-X users, I have a question about the visualisation of the DNA structure obtained after tleap processing for Amber. As I have noticed, due to the renaming of the DNA residues, some of the sugar parts are not correctly recognised by Chimera-X (see the attached screenshot) and so these elements are only displayed as organic ligands. Would it be possible to change its style using some commands, assuming that the names of the residues located at the terminal parts of the DNA helix are DC5, DG3 and DT5, DT3 (so that Amber adds numbers to them)? Would it be possible to change the style of all the residues e.g. showing them ass ring fills or like a color bricks (default vizualisation which looks very cool!) using selection expressions like :DT*,DG*,DC*,DA* ? Many thanks in advance ! Enrico

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Add options to snapshot command
by Jaremko, Matt Joseph 26 Apr '24

26 Apr '24

Hello ChimeraX Team, Can you add option to snapshot command like transparentBackground and height to allow more customization of this convenient tool? Thank you, Matt Matt J. Jaremko, Ph.D. (He|Him) Senior Scientist | Protein & Structural Chemistry Merck Research Labs | 126 E Lincoln Ave | 80B 1012 | Rahway, NJ 07065 Cell: 808.741.6277 | Email: matt.jaremko(a)merck.com<mailto:matt.jaremko@merck.com> This e-mail message, together with any attachments, contains information of Merck & Co., Inc. (126 East Lincoln Ave., P.O. Box 2000, Rahway, NJ USA 07065) and/or its affiliates, that may be confidential, proprietary copyrighted and/or legally privileged. (Direct contact information for affiliates is available at - Contact us - MSD<https://www.msd.com/contact-us/>.) It is intended solely for the use of the individual or entity named on this message. If you are not the intended recipient, and have received this message in error, please notify us immediately by reply e-mail and then delete it from your system.

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palette command
by Cairns, Claudia Anna 26 Apr '24

26 Apr '24

Dear sir or madam, I try to apply the palette command to change the color range of the mlp command. Unfortunatelly i always get an error. For "palette rainbow" for example I get: rainbow Unknown command: palette rainbow Can you please help me? Sincerely, Claudia Cairns M.Sc. (Biotechnology) Department 'Applied and Molecular Microbiology' Institute of Biotechnology - TIB 4/4-1 Technische Universität Berlin Gustav-Meyer-Allee 25 D-13355 Berlin Phone: +49-(0)30-314-72827 E-mail: c.feurstein(a)tu-berlin.de<mailto:carsten.pohl@tu-berlin.de> Web: <http://www.mikrobiologie.tu-berlin.de> https://www.tu.berlin/mikrobiologie/

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Reconstruction of missed loop fragments
by Enrico Martinez 26 Apr '24

26 Apr '24

Dear Chimera-X user! I am preparing a model of GPCR protein for the molecular dynamics simulation. In this structure there is a loop fragment of 10-20 residues which is missed. Is it possible to reconstruct it (e.g. based on the sequence information or alternatively just add manually the missing fragment) using some tool of Chimera-X e.g. combining with the bond command ? Many thanks in advance ! Enrico

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Greek characters
by Marta Martinez 25 Apr '24

25 Apr '24

Hi guys, I just downloaded a pdb file from AlphaFold DB (AF-P69905-F1-model_v4.pdb). After modifying it with ChimeraX (version 1.6.1 (2023-05-09)) I've saved the modified atomic structure as a cif file. The original pdb file contains this line: COMPND 2 MOLECULE: HEMOGLOBIN SUBUNIT ALPHA; After saving the file as cif format ALPHA is not longer a string but a GREEK character: _entity.pdbx_description "hemoglobin subunit α" Is there any flag in the save command that disables this conversion from plain ASCII to UTF-8? Thank you very much for the answer in advance: MARTA -- Marta Martinez Gonzalez Biocomputing Unit (Lab B13) National Center for Biotechnology-CSIC Darwin, 3. Campus de la Universidad Autonoma de Madrid 28049 Madrid. Spain Tel:+34 915854510 Fax:+34 913720112 E-mail: mmmtnez(a)cnb.csic.es

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atom serial_number is inconsistent with PDB serial numbers in multi-chain structure
by Daniel David Richman 25 Apr '24

25 Apr '24

Hi all, I’ve been debugging an off-by one error in a ChimeraX script I’m working on, which I’ve traced to a apparent inconsistency between the serial_number reported by ChimeraX for an atom and the actual serial number of that atom read/written in PDB format. To reproduce: open 5MJ7 select #1/B:6@CA info atoms sel attribute serial_number ==> atom id /B:6@CA serial_number 2548 but the correct serial number for this atom in 5MJ7.pdb is 2549. Maybe this is because the TER record for chain A takes up one serial number in the PDB file, but ChimeraX doesn’t include it as a numbered atom? Regardless, how can I query ChimeraX for the actual serial number that will be written if I write out a PDB file? Thanks, Daniel

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How to make an MD template for ISOLDE?
by Guillaume Gaullier 25 Apr '24

25 Apr '24

Hi Tristan and chimerax-users, Some time ago I asked the list about modeling PTM and got several helpful answer, including this one: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu… Now, I am working on a structure containing chlorophyll A molecules (residue code CLA) and realized that it won’t work for MDFF in ISOLDE because there is no MD template for it. After trying to manually fit one of these molecules rigidly, I concluded that I would rather spend the rest of the month learning how to make an MD template for it (than next month painstakingly fitting every single molecule manually rigidly). From the message linked above, I think this should be doable because this time it is not a covalent modification on an otherwise parameterized residue, but simply a new ligand (ok, maybe the coordinated Mg2+ makes it a bit more complicated?). I looked up ANTECHAMBER, and also some documentation from OpenMM, but that got me nowhere, mostly because I have little clue what the task really entails. My guess is that I need some program to take the CLA residue in PDB or mmCIF format (which I can easily save from a previous PDB entry) and write out an OpenMM XML file like the one you sent me back then for KCX. Is this correct? The ANTECHAMBER documentation mentions many programs and formats, and I got totally confused. If you have time to elaborate a bit on the specific practical steps to take (including how to supply the final XML file to ISOLDE), that would be super helpful! I can do with pointers to documentation, not afraid to read, but I need help getting oriented. Thank you in advance! Guillaume 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

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Realsense issues
by Casey Eubanks 24 Apr '24

24 Apr '24

Hey guys, You all helped me a week or so ago getting the Realsense package updated to the new version of chimerax, which I can now download so thats great! But I am now having an issue with running its command "Realsense on" I receive the following errors attached to this email It is having errors processing the trigger and it says it cant resolve the requests. Let me know if I am doing anything wrong or need to make any changes! Thanks, Casey Eubanks Service Desk Specialist MOBILE (205) 617-0581 time zone United States, Central Time Zone (CST) [cid:image001.png@01DA9660.03D4DE80]<https://www.biocryst.com/> "Go Fast, Patients are waiting" If you need immediate IT support please submit a ticket to ITsupport(a)biocryst.com<mailto:ITsupport@biocryst.com> 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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