- ChimeraX-users - RBVI Mailing Lists

how to view Alphafold Run window
by James Raymond 02 Jun '23

02 Jun '23

Dear ChimeraX, I keep losing this window, whenever I click on it or move it. How do I get it back again? thank you Jim [image: image.png]

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Blast protein results
by postmaster＠cgl.ucsf.edu 02 Jun '23

02 Jun '23

From: Lynne Howell <howell(a)sickkids.ca <mailto:howell@sickkids.ca>> Subject: Blast protein results Date: June 2, 2023 at 2:18:42 PM PDT To: ChimeraX-users <chimerax-users-bounces(a)cgl.ucsf.edu <mailto:chimerax-users-bounces@cgl.ucsf.edu>> HI I’m a novice ChimeraX user and wondered whether there is a way of saving to an excel file the blastprotein results against the Alphafold database that appear in the session window? Was looking to capture all the information for cross reference to another file. Thanks in advance Lynne This e-mail may contain confidential, personal and/or health information(information which may be subject to legal restrictions on use, retention and/or disclosure) for the sole use of the intended recipient. Any review or distribution by anyone other than the person for whom it was originally intended is strictly prohibited. If you have received this e-mail in error, please contact the sender and delete all copies.

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MolecularDynamicsViewer
by Michael Patzschke 01 Jun '23

01 Jun '23

Dear colleagues, I would like to use the MolecularDynamicsViewr more often. My problem is, that I work with small metal organic systems and we never generate pdf files. What I do get a loot are multiple .xyz files. In these files the different images are just put one after the other without any extra new line or anything. Here are the first few lines from the optimisation “trajectory” for water as created by orca: 3 Coordinates from ORCA-job h2o E -76.051642020209 H 1.200000 0.000000 1.000000 H -1.200000 0.000000 1.000000 O 0.000000 0.000000 0.000000 3 Coordinates from ORCA-job h2o E -76.099647985008 H 1.102275 0.000000 0.980787 H -1.102275 0.000000 0.980787 O -0.000000 0.000000 0.038425 3 Coordinates from ORCA-job h2o E -76.150106142663 H 1.008335 0.000000 0.959926 H -1.008335 0.000000 0.959926 O 0.000000 0.000000 0.080147 Would it be possible to enhance the MolecularDynamicsViewr to accept such files? Thank you very much for your time and effort. Kind regards, Michael

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displaying different segmentations together
by Jesse Hansen 01 Jun '23

01 Jun '23

dear all, I have segmented different parts of my tomogram using different software packages. One outputs an MRC file which I Can display as either volume or surface. The other is exported from Dragonfly and I am unable to figure out how to export MRC so I have tried STL and OBJ. STL/OBJ will display in ChimeraX, but then if I try to load in the other segmentation MRC then the STL/OBJ will disappear. I cannot view both simultaneously. If I hide the mrc and "view all" then I can view the object. Conversely, if I hide the object and "view all" I can see the MRC. Any help would be appreciated. Is there any way to convert obj/stl to an mrc? thanks! Jesse

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Virus detected on Chimera X download
by Amy E. Kennedy 30 May '23

30 May '23

To whom it may concern: I downloaded the Windows executable from https://www.rbvi.ucsf.edu/chimerax/download.html this afternoon, and my antivirus software intercepted and neutralized a suspicious item when I opened the file. You may want to do a thorough check of your systems. Best, Amy Amy E. Kennedy (she/her) Doctoral Candidate, Mierke-Pellegrini Lab Biochemistry & Cell Biology, MCB, Guarini School of Graduate Studies PhD Innovation Fellow | E. E. Just Fellow

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Can I use autodock vina
by NAGANO Kyogo 30 May '23

30 May '23

Hello. I started using the ChimeraX from today. And, I want to use the autodock vina with ChimeraX. In the case of Chimera, Tools→Surface/Bindind/Analysis→Autodock vina. But,in the case of ChimeraX, I couldn't find it. So, I want to know how to use Autodock in ChimeraX. Thank you.

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Run Session Command Not Working
by Aashna Soni 30 May '23

30 May '23

Hi, I hope this email finds you well. I am trying to use the ChimeraX Python shell to run commands programmatically. When I try to run this command: run(session, "open <insert filepath>"), I am getting this error: "AttributeError: module 'chimerax.core.session' has no attribute 'models'." I have not written any import statements at the top (this is the first line in the Python shell). I am getting similar errors when I run any run(session, ...) command. Could you please help me resolve this issue? Thanks in advance. Warm regards, Aashna

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ChimeraX server problems
by Tom Goddard 25 May '23

25 May '23

ChimeraX web services (BLAST protein, Modeller, sequence alignment) are currently down. Also ChimeraX bug reporting is down. We updated our servers last week (CentOS 7 to Rocky 8) and are working on restoring these services. Thanks for your patience. Tom

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chimerax-users mailing list should be working
by Greg Couch 24 May '23

24 May '23

But the web interface to look at old messages will take some time to get to work. -- Greg

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chimerax-users mailing list will be down temporarily
by Greg Couch 23 May '23

23 May '23

We're upgrading the mailing list software. Should be back "soon".

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