April 2022 - ChimeraX-users - RBVI Mailing Lists

Re: [chimerax-users] palettes and color keys
by Martti Tolvanen 21 Apr '22

21 Apr '22

A followup question regarding palettes and color keys: Is there any way to create two color keys for two different properties or for two different models? My motivation to ask this stems from a dimer model I got from AlphaFold multimer. When I use the default alphafold palette, the individual monomers are hard to see, most of the interface being in the dark blue, marking highest confidence. I can apply a different palette to one of the chains, but it would be also nice to show the color keys for both palettes. Martti Tolvanen Lecturer in Bioinformatics U of Turku, Finland -----Original Message----- From: chimerax-users-request(a)cgl.ucsf.edu [mailto:chimerax-users-request@cgl.ucsf.edu] Sent: 12. huhtikuutata 2022 22:00 To: chimerax-users(a)cgl.ucsf.edu Subject: ChimeraX-users Digest, Vol 64, Issue 15 Send ChimeraX-users mailing list submissions to chimerax-users(a)cgl.ucsf.edu To subscribe or unsubscribe via the World Wide Web, visit https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users or, via email, send a message with subject or body 'help' to chimerax-users-request(a)cgl.ucsf.edu You can reach the person managing the list at chimerax-users-owner(a)cgl.ucsf.edu When replying, please edit your Subject line so it is more specific than "Re: Contents of ChimeraX-users digest..."

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ChimeraX command for rmsd color range in angstrom
by Dario Passos 20 Apr '22

20 Apr '22

Dear Chimera community, does anyone know how to add a range of values for the rmsd colors in Chimera X? Something like this (below) in angstrom: => *color byattribute seq_rmsd #1 palette blue:white:red threshold 0:3;6* Thanks, Dario

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Toolshed backend update
by Greg Couch 19 Apr '22

19 Apr '22

FYI, the ChimeraX toolshed will be down this evening (10 p.m PDT, 5 a.m. GMT) to upgrade the back-end. If all goes well, it will be back up within an hour. There should be no user visible changes after the update. However, the back-end change will allow Bundle developers to submit bundles that have commas in the dependencies. -- Greg

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Re: [chimerax-users] Render psuedobonds for RMF models?
by Tom Goddard 19 Apr '22

19 Apr '22

Hi Matthew, Yes. The coarse grain models made from reading RMF files create spheres that are actually atoms, and any atoms can be connected by pseudobonds. I don't know much about RMF in Chimera and ChimeraX. Ben Webb and Conrad Huang worked on that and Conrad retired 2 years ago. It may be that reading RMF creates pseudobonds that are specified in the RMF file. Another way to create pseudobonds is to open a pseudobond file https://www.cgl.ucsf.edu/chimerax/docs/user/pseudobonds.html#pbfiles <https://www.cgl.ucsf.edu/chimerax/docs/user/pseudobonds.html#pbfiles> For that you need to figure out the names of the "atoms" (which may represent coarse grain beads) you want to connect. You can open the RMF and hover the mouse over a sphere and a popup will show its name. Also the ChimeraX distance command can create pseudobonds https://www.cgl.ucsf.edu/chimerax/docs/user/commands/distance.html Tom > On Apr 19, 2022, at 8:41 AM, Hancock, Matthew wrote: > > This Message Is From an External Sender > This message came from outside your organization. > > Hi Tom, > > I am a UCSF graduate student in Andrej Sali's group and have a question about Chimera/ChimeraX functionality. I am curious if it is possible to render psuedobonds for multi-scale structures that are read from RMF files. Similar to how it can be done for pdb structures. > > Best > Matthew

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Chimera(X) in Centos stream 9
by Antonio Díaz Quintana 19 Apr '22

19 Apr '22

Dear all, I am unable to install Chimerax and Chimera—yes I still use the old one because its great tools—using the rpm package in Centos Stream 9, because lack of LibOSMesa package in this distribution. I tried using dnf, but a mesa-libGL library (21.3.4...) is already installed Similarly, it seems my OS distribution does not contain python Tk, nor I can get suitable python with Tk-devel from repository, so I get the following message. Could I get any help? Meanwhile I got it on my old Win10, 11 years-old laptop. Both programs work well there. Best, Antonio -- Dr. Antonio J. Díaz Quintana Instituto de Investigaciones Químicas Universidad de Sevilla - CSIC Avda. Americo Vespucio 49 41092 Sevilla Spain Phone: +34 954 48 9631

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matchmaker question: restrict moving parts to selection?
by Vorländer,Matthias Kopano 18 Apr '22

18 Apr '22

Hi everyone, Is it possible to align parts of a model to another while only moving the specified residues but not the rest of the molecule? A use case would be having an alphafold model from one species where the individual domains are correctly predicted, but don't agree with the relative orientation of the domains observed in a reference structure from another species. I envision this similar to the "fitmap" option "moveWholeMolecule false". Example: Mm #1:100-200 to #2/100-200 MoveWholeMolecule false This should leave the residues 1-99 in model #1 unchanged. I hope my question is clear. Thanks a lot in advance, Matthias Get Outlook for Android<https://aka.ms/AAb9ysg>

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Saving multiple MRC with derivative names
by Nebojsa Bogdanovic 18 Apr '22

18 Apr '22

Hi, I was looking into the possibility of saving 5 mrc maps after batch z-flipping them. The commands would looks something like this: 1. cd /folder/with/maps 2. open *.mrc 3. volume flip #1-5 4. save [name]*-zflip*.mrc models #6-10 Ideally, the script would save each new (flipped) map as a new .mrc with the suffix "-zflip" or whichever suffix user specifies in the script line 4. Is there such an option if it's implemented? Thank you for the awesome ChimeraX Best regards, Nebojša Bogdanović, Ph.D Department of Physiology and Biophysics, School of Medicine, Case Western Reserve University

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0417_1
by 泡沫 17 Apr '22

17 Apr '22

How do you make similar pictures 发自我的iPhone

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Hello
by Brandon Palmer 13 Apr '22

13 Apr '22

My name is brandon palmer I work with Biocryst and came across your software. So far been reading through and I enjoy it's features, and I had a question. Would you happen to have apk version for the use of a Vive 3 Headset? 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: [chimerax-users] [Chimera-users] Chimera X color by attribute middle range value
by Elaine Meng 12 Apr '22

12 Apr '22

Hi Marcell! In ChimeraX, you can control which colors go with which values in the "palette" option of the "color byattribute" command. This option can take color/value pairs, and the "range" option is not needed in your situation (if I understand correctly). As you found, if you only give the range, it will spread out the colors evenly. Here's an example of value,color pairs if you want to color by attribute named "blah" using dodger blue for 0.2, red for 1.0, and gold for 4.0: color byattr blah palette 0.2,dodgerblue:1.0,red:4.0,gold <https://rbvi.ucsf.edu/chimerax/docs/user/commands/color.html#byattribute> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/color.html#palette-options> There are lots of named colors, although you could use hex codes instead if the named ones aren't quite what you want. <https://rbvi.ucsf.edu/chimerax/docs/user/commands/colornames.html> ChimeraX does not yet have a color-by-attribute GUI although that is something we would like to have eventually. The Color Key tool is just for drawing a color key to explain the coloring, but does not itself affect the structure coloring. By the way, you may be interested in the chimerax-users(a)cgl.ucsf.edu mailing list (CC'd on this reply) for questions/discussion specifically about ChimeraX. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Apr 11, 2022, at 5:07 PM, Zimanyi, Marcell via Chimera-users <chimera-users(a)cgl.ucsf.edu> wrote: > > Hello Chimera Community, > > I have a .defattr file where I have assigned a value to a few residues on my protein. I'd like to set the range to be 0.2, 1, and 4 so that values with 1.0 will be the middle color. I currently don't see a way to set the middle value for the range. In Chimera, I could set the middle range value in the define attribute GUI. In Chimera X, I'm using color byattribute range 0.2,4 because the range argument will only accept two values. I see that I can bring up the color key gui, but when I change the color key I don't see a way to update the coloring on the residues themselves. > > Could you please help me figure out how to set attribute range with 3 values as in Chimera? > > Thanks, > Marcell

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