- ChimeraX-users - RBVI Mailing Lists

using chimerx on unix
by Barak Yariv 11 Dec '22

11 Dec '22

Dear Chimera team, I'm from the ConSurf webservere https://consurf.tau.ac.il/consurf_index.php We have been working with chimera for many years and we want to update to chimerax. We have trouble installing chimerax on our unix system. We did manage to install it on our local computers in windows but when installing on unix we get an error: missing library PyQT6 Can you help us? Barak

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Specify unmodelled residues
by Jaremko, Matt Joseph 09 Dec '22

09 Dec '22

Hello ChimeraX Team, What information in the PDB file specifies the unmodelled residues (in black box)?: [cid:image001.png@01D90BDD.3983D7C0] I’d like to have this information in my own PDB files. Thank you, Matt Matt J. Jaremko, Ph.D. (He|Him) Senior Scientist | Protein & Structural Chemistry Merck Research Labs | 2000 Galloping Hill Rd. | Kenilworth, NJ 07033 Office: 908.740.5613 | 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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Perframe and distance
by Simonson, Benjamin Thomas 09 Dec '22

09 Dec '22

Hello! I am trying to measure the distance between two atoms in my trajectory in every 10th frame. My approach was to use the perframe command paired with the distance command. Below was my attempt: perframe "distance /D:15@NH1 /B:42@OD1;distance save dist$1.txt;~distance /D:15@NH1 /B:42@OD1" interval 10 However, it instead simply outputs the distance of the currently displayed frame over and over again. Any help would be appreciated! Ben ......................................... Benjamin Simonson MCIBS PhD Candidate Penn State University

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How do I NOT "show disjoint surfaces"?
by Sungwook Woo 06 Dec '22

06 Dec '22

Hi I've been using UCSF Chimera and recently encountered ChimeraX -- I really like the modern look and feel! One feature I cannot find in the X version, though, is editing the attributes of an MSMS surface model, where I was able to disable (make 'false') the 'show disjoint surfaces' setting, in the original version. Most of the time dealing with models I don't need it, but sometimes I like to 3D print molecular models to really get a 'grip' on the models, and that feature of not showing disjoint surfaces has been useful to remove internal 'bubbles', which I learned about through this posting: https://www.cgl.ucsf.edu/pipermail/chimera-users/2009-May/003903.html . If internal bubbles are not removed, they waste printing material and increase printing time. Is there any way to disable showing disjoint surfaces, or otherwise achieve a similar goal in the X version? Thanks! Best, Sungwook

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swapna in ChimeraX
by Shahid, Taha (Dr.) 01 Dec '22

01 Dec '22

Hi all, Does ChimeraX have swapna functionality? I can find the swapaa command but not swapna. Is there another way to achieve its effects? If not, I think it would be useful addition. Kind regards, Taha

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ChimeraX 1.5 release not visible on website
by Shahid, Taha (Dr.) 01 Dec '22

01 Dec '22

Dear ChimeraX Team, I would like to update, but can't see either the ChimeraX 1.5 release candidate or production release on the USCF ChimeraX download page (only ChimeraX 1.4 and the daily build are available). Many thanks, Taha Dr Taha Shahid Postdoctoral Research Associate Leicester Institute of Structural and Chemical Biology Henry Wellcome Building | University Road | Leicester | LE1 7RH | UK e: ts387(a)leicester.ac.uk<mailto:XXXX@leicester.ac.uk> w: https://www2.le.ac.uk/institutes/liscb Follow us on Twitter<https://twitter.com/leicstructbio> [cid:D64185E6-9A9E-47F3-98A6-A33685D0B03A]

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chimerax freezing
by HOH Francois 30 Nov '22

30 Nov '22

Hi I had to change my hard drive and reinstall everything. When launching chimerax, it starts but freeze. Have to kill it. OS ubuntu 22.04. No special message in the log when using chimerax --debug Any idea ? Thank's FH ________________________________________ Hoh François, PhD Research Engineer Team BSME: Biologie structurale multi-échelles Centre de biochimie Structurale de Montpellier CNRS UMR 5048 - UM - INSERM U 1054 29 rue de Navacelles 34090 MONTPELLIER Cedex - FRANCE http://www.cbs.cnrs.fr Tel: (33) 04 67 41 77 29

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ChimeraX 1.5 release
by Elaine Meng 30 Nov '22

30 Nov '22

UCSF ChimeraX version 1.5 has been released! ChimeraX includes user documentation and is free for noncommercial use. Download for Windows, Linux, and MacOS from: https://www.rbvi.ucsf.edu/chimerax/ Updates since version 1.4 (Jun 2022) include: - AlphaFold search/fetch uses database v4 (fixes ~4% of v3 entries) - show AlphaFold residue-residue errors (PAE) with colored lines - Axes/Planes/Centroids tool to define objects, use in measurements - transform surface models (scale, shift, rotate) - add hydrogens GUI - calculate and assign charges, including for nonstandard residues - dock prep command - renumber residues, change chain IDs - crosseye and walleye stereo - cleaner close session (reverts more settings) - UniProt sequence fetch updated to work with UniProtKB's new API - DICOM browser shows patient-study-series hierarchy in medical image data For details, please see the ChimeraX change log: https://www.rbvi.ucsf.edu/trac/ChimeraX/wiki/ChangeLog

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Ribbon coloring
by F.Xavier Gomis-Rüth 30 Nov '22

30 Nov '22

Hi Elaine, when coloring a helix differently from the attached coils, is there a means to prevent the first short segment of the coil to get the color of the helix? It seems to me there was some kind of "halfbond"-mode one... Best, Xavier --

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Re: [chimerax-users] Placing a ligand in a protein structure from PDB
by Elaine Meng 30 Nov '22

30 Nov '22

> On Nov 30, 2022, at 7:41 AM, Amit Kugler <amit.kugler(a)kemi.uu.se> wrote: > > Hej Elaine, > > I found you on the ChimeraX website, and I have a question. > > I have a PDB file of my protein, but not showing a ligand. > > I am wondering if there a way I can add a ligand to the active site of the protein and write out the new PDB file on ChimeraX? > > Best regards, > Amit > Hi Amit, We recommend sending questions to chimerax-users(a)cgl.ucsf.edu (CC'd here) to make it more likely you get a response. Not sure what you mean by add a ligand. Sure you can open a file of a ligand and open a file of the protein, and then combine them into one model, and then save. But probably you want to put the ligand in some sensible position, which could be done by moving it individually by hand, or by using some docking program. ChimeraX does not do docking. You would have to use some docking program (Glide, DOCK, Gold, Autodock, Autodock Vina, etc.) and then open the output from that docking program in ChimeraX. Moving models by hand, see this previous post: <https://www.rbvi.ucsf.edu/pipermail/chimerax-users/2017-November/000157.html> There is a "combine" command to combine the two separate models into a new single model, and "save" (or menu File... Save) to save the resulting combined model as a PDB file. <https://rbvi.ucsf.edu/chimerax/docs/user/commands/combine.html> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/save.html#pdb> Or maybe you don't have a structure of the ligand. If there is some other PDB structure that contains it you can open that structure and delete all the rest of the atoms, or if you can find it in PubChem you can try fetching by PubChem ID into ChimeraX, e.g. command open pubchem:12120 <https://rbvi.ucsf.edu/chimerax/docs/user/commands/open.html#fetch> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco

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