August 2021 - ChimeraX-users - RBVI Mailing Lists

Apple silicon (M1 chip) native version?
by Jeffrey D. Hartgerink 28 Apr '22

28 Apr '22

Are there any plans for an Apple Silicon (M1 chip) native version of ChimeraX? While things work ok via the Rosetta emulator, it would be great to have the performance from a native app. -------------------------------------- Jeffrey D. Hartgerink, Ph.D. Prof. of Chemistry and Bioengineering Rice University, MS 602 6100 Main Street Houston, TX 77005 jdh(a)rice.edu / 713-348-4142 hartgerink.rice.edu

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A couple questions about programming in ChimeraX
by William Hofsøy 22 Sep '21

22 Sep '21

Hi, I'm currently working on a plugin that deals with a cmm-file model and have a few questions about how to do certain things. Mainly I would like to be able to modify the model by adding new markers and links to the model. I have managed to figure out how to make new markersets and add them to the session but not how to alter existing ones aka the model that I load from the cmm file. Additionally I am making use of the marker_extra_attributes info since the cmm file im reading has attributes there that I need, but as I read in the documentation these aren't saved in sessions and I wondered if there is a way to do just that. Lastly, I was wondering if it is possible to place any mesh in the scene, for instance a cube. -William

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Re: [chimerax-users] output mmCIF file
by Elaine Meng 02 Sep '21

02 Sep '21

> On Aug 31, 2021, at 1:50 PM, Liu, Xiangan <Xiangan.Liu(a)uth.tmc.edu> wrote: > > Hi, > I have issue to output the models I build in pdb formation to mmCIF formation. I did not provide the sequences in orginal pdb files. Could please let me know what is the problem and how to fix it? > Thanks, > Xiangan > ---------- > File "/usr/lib/ucsf-chimerax/lib/python3.8/site-packages/chimerax/mmcif/__init__.py", line 89, in save > mmcif_write.write_mmcif(session, path, **kw) > File "src/mmcif_write.pyx", line 145, in chimerax.mmcif.mmcif_write.write_mmcif > File "src/mmcif_write.pyx", line 149, in chimerax.mmcif.mmcif_write.write_mmcif > File "src/mmcif_write.pyx", line 542, in chimerax.mmcif.mmcif_write.save_structure > KeyError: ('a1', 'RPGMMDSQEFS') > > KeyError: ('a1', 'RPGMMDSQEFS') > > File "src/mmcif_write.pyx", line 542, in chimerax.mmcif.mmcif_write.save_structure Hi Xiangan, We recommend using the chimerax-users(a)cgl.ucsf.edu address for questions (CC'd on this message, so you don't need to do anything this time). The address you used is just for commercial licensing. Actually, if you get a traceback like this, you can usually use ChimeraX menu: Help... Report a Bug instead of sending e-mail. You may need to attach your session file so that we can reproduce the problem. I don't know the answer, so I'm using this address to share your question with the others. Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco

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ChineraX saves huge session files
by Dror Noy 31 Aug '21

31 Aug '21

Hi Recently, ChimeraX on my Mac (macOS Catalina) started saving very large session file. Regardless of the size of the pdb file I load - the session file is 124 MB even for small 2-3 MB pdb files. I’d appreciate any help. Thanks Dror

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Region-wise specific sub-coloring of SS elements
by Gupta, Arun 30 Aug '21

30 Aug '21

Dear ChimeraX team, Is there an easier way around by which we can do region-wise specific sub-coloring of secondary structural elements within a large protein instead of using the tedious way of identifying the secondary structural elements and then describing the residue wise specific selection of set of residues related to secondary structure elements? I am aware that we can do coloring of specific secondary structure elements in ChimeraX by following commands for e.g “color helix “darkcyan” targ c”. But, I am looking forward to do coloring, let’ say “all the helices within a protein from residues 1-300 as dark cyan and residues 300-500 as blue” Thanks!!! Arun Arun Gupta PhD, MRSC Research Fellow Challis & Lewandowski Group Chemistry Department University of Warwick Gibbet Hill Road Coventry CV4 7AL United Kingdom

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Adding labels in chimera X?
by rob.gruninger＠gmail.com 27 Aug '21

27 Aug '21

I am trying to figure out how to add labels to a figure in chimeraX. It was easy in the older Chimera using 2d labels but I can’t find a similar function in chimeraX and the website seems to be down so I can’t access documentation. Any direction for how I can do this? I’m wanting to add residue labels to some specific residue (catalytic and substrate binding site residues) I want to point out in a paper Thanks Sent from my iPhone

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ChimeraX site down?
by Jonathan Sheehan 27 Aug '21

27 Aug '21

It might be pointless to send this query to the list (if it runs on the same server), but are you aware of any problems with your webserver right now? I'm trying to get the files for the latest density-fitting tutorial here: www.cgl.ucsf.edu According to this site, I'm not the only one having trouble reaching it: https://www.isitdownrightnow.com/cgl.ucsf.edu.html It claims it's "Down for everyone" and "for more than a week." Thanks! -Jonathan

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Save cropped map visible coordinates
by Isabelle Phan 26 Aug '21

26 Aug '21

Hello, I have 2 maps that I want to combine into a single one. I cropped each map by reducing the box size. I now want to save the map that is displayed. Impossible?! “Save” fails to keep the relative orientation of the display. I get 2 cropped maps that are no longer correctly oriented with respect to each other. "volume add” also fails to preserve the relative orientation. The volume resample sounds like it could be helpful, but I don’t understand how to get the grid values that match the displayed box. I’ve now tried multiple options for over 5 hours solid and am at my wits’ end. Any hints greatly appreciated. Isabelle

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ChimeraX Bundle
by Mirko Plößer 26 Aug '21

26 Aug '21

Dear ChimeraX Team, my name is Mirko Ploesser, I am a Phd student in the Frankgakis group at the BMLS (Buchmann Institue for Molecular Life Sciences) in Frankfurt (Germany) and currently working on a ChimeraX bundle. Thanks to your detailed tutorial on how to develop bundles, I have already made a good progeress in doing so. Currently, however, I am stuck with a problem that I hanve't found a solution to yet. I would be very thankful if you could give me advice on how to progress. The problem is described as follows: I click a set of markers in a volume (tomogram as an EM file) and save the corresponding positions. At those positions I want to load different and smaller volumes (also EM Files). The information about those smaller volumes - position and rotation - I have saved in a different file (a motivelist in also an EM format). Now I am stuck with the problem on how to update the rotation angles when I use the tool "Rotate model" using the right mouse. I know that the corresponding rotation matrix is printed in the log. Is there any way that I can use the information given to the log in my bundle code? Also, since we already have a working version of the bundle in Chimera, I found the module "openModel" very useful. Unfortunately I haven't been able to find an equivalent module in ChimeraX. So I guess there is a different approach to this used in ChimeraX. I would be very happy if you could also help me out in this regard. Thank you very much in advance for your time and effort. I am looking forward to hearing from you soon. Best, Mirko Ploesser

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How to make nucleotides same color?
by Visvaldas K. 25 Aug '21

25 Aug '21

I couldn't find how to change the default coloring of the nucleotides in ChimeraX. I'd like the color of all nucleotides to be blue like in the "old" Chimera: multiple colors distract from the details I am trying to convey. Is it possible? Best regards, Visvaldas

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ChimeraX-users August 2021