September 2024 - ChimeraX-users - RBVI Mailing Lists

Select multiple rotamer conformations for a single amino acid
by Alexander Lee 09 Sep '24

09 Sep '24

Hi! I was able to select and use multiple rotamer conformations simultaneously for a single amino acid using the Rotamers tool, saved as alternate locations within a pdb file. Is there a way to do that using swapaa or from the command line?

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Ribbon style editor
by Alessio Nocentini 09 Sep '24

09 Sep '24

Hello, I have been an academic user of chimera for years. I have just downloaded chimerax but I cannot find the ribbon style editor. Can you please help? Best regards Alessio -- Dr. Alessio Nocentini University of Florence Neurofarba Department Via Ugo Schiff 6, 50019 - Sesto Fiorentino (Firenze), Italy Phone: +39-055-4573685 *NEUROFARBA Dipartimento di **ECCELLENZA 2023-2027*

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Re: [Chimera-users] morph command in chimerax
by Elaine Meng 09 Sep '24

09 Sep '24

Hi Bryan, Since this is a ChimeraX question, I've CC'd chimerax-users(a)cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu> --- in the future please use that mailing list for ChimeraX questions, because we don't want to confuse users between the two programs, for which the answers may be different. This answer is for ChimeraX: The "morph" command is for atomic structures, not maps. That's why it keeps saying you need structures! This is mentioned in the first sentence of the help page: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/morph.html> To instead morph maps, see the "volume morph" command: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/volume.html#morph> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Resource for Biocomputing, Visualization, and Informatics Department of Pharmaceutical Chemistry University of California, San Francisco > On Sep 9, 2024, at 7:29 AM, Hansen, Bryan (NIH/NIAID) [E] via Chimera-users <chimera-users(a)cgl.ucsf.edu> wrote: > > Hi, > I’m using ChimeraX v 1.8 (2024-06-10) and I’m having a problem with the morph command. No matter how I format the command I’m getting the same error message of “Require at least 2 structures for morph” I’ve tried > morph #3,4 core 0.1 frames 75 wrap t > and > morph #3#4 core 0.1 frames 75 wrap t > These are 2 electron density maps so there’s no sequence info docked in yet. Thanks for any tips or advice on what I’m doing wrong. > Bryan Hansen

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MD Trajectory
by Mcguire, Kelly 07 Sep '24

07 Sep '24

What is the largest MD trajectory file (i.e. DCD) ChimeraX can handle? VMD is designed for very large MD trajectory visualization and analysis. Is ChimeraX for smaller trajectories? Kelly McGuire PhD Postdoc - Herzik Lab University of California - San Diego

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colored stl file for 3d printing
by Haydar Witwit 06 Sep '24

06 Sep '24

Dear ChimeraX team, I'd like to know if it is possible to save a colored file of pdb into stl, because when I save the file as stl, chemierax saves it as a monocolor structure. Actually, my intention was to 3d print a hydrophobic structure of small protein but labeled with one letter code label and position of the amino acids. Something similar to the following image: [cid:4c34bc91-300a-456c-8583-ab4de7f1b1d9] Kind regards Haydar

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Re: Optimizing ChimeraX Performance for Multiple Subtomo Maps
by Tom Goddard 06 Sep '24

06 Sep '24

Hi Wang, Glad to hear ArtiaX helps showing your subtomogram averaged particles. An important feature of that extension written by Utz Ermel optimizes the display of thousands of particles by not using a separate ChimeraX model for each one. I tried opening 1500 maps of size 20 x 20 x 20 grid points in ChimeraX 1.8 on a Mac Studio M2 Ultra with much less powerful graphics than an Nvidia 4090, displaying all as surfaces, full lighting, and they rotated, zoomed and translated usably fast at 9 frames per second. So I am surprised you had a problem and I don't know why it is slow for you. Tom > On Sep 6, 2024, at 3:01 AM, 王光磊 <wangguanglei20(a)mails.ucas.ac.cn> wrote: > > Hi Tom, > > > Thank you for your prompt response. > > It seems that the performance issue was caused by the excessive number of subtomo maps. In my case, I loaded approximately 1,500 subtomo maps using the subtomo2chimera script, and displayed them in surface mode. This led to ChimeraX freezing for several seconds after any rotation or zoom of the view. Loading an extra tomograph did not affect performance. > > I tried using AriaX to load the subtomo maps, and now the scene runs smoothly. Thank you for your advice! > > Thanks, > > Wang GuangLei > > > > -----原始邮件----- > 发件人:"Tom Goddard" <goddard(a)sonic.net> > 发送时间:2024-09-06 03:34:59 (星期五) > 收件人: 王光磊 <wangguanglei20(a)mails.ucas.ac.cn> > 抄送: chimerax-users(a)cgl.ucsf.edu > 主题: Re: [chimerax-users] Optimizing ChimeraX Performance for Multiple Subtomo Maps > > Hi Wang, > > I think your Nvidia 4090 should handle the large tomogram fine, and probably the slowdown is because having 1000-2000 open model of any kind, even if they are small like your subtomo maps, is more than ChimeraX was designed to handle. I am surprised though that rotating the view becomes slow because that should just move the camera which should not depend on the number of models shown. Do I understand correctly that you just open the tomogram and 1000-2000 subtomograms, display them all, and rotate and it updates slowly? How slowly, like 1 frame per second, or does it freeze for ten seconds? What display style do you use for the subtomograms, surface or volumetric? > > You might be interested in the ArtiaX ChimeraX extension which is for looking at particles in tomograms. You would get it using ChimeraX menu Tools / More Tools.... > > Tom > > >> On Sep 5, 2024, at 1:15 AM, 王光磊 via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu> wrote: >> >> >> >> Hi, >> >> I'm using chimerax to display my tomograph and multiple subtomo averages in surface mode. Specifically, I need to visualize a 1440*1022*250 tomograph, along with 1000-2000 subtomo maps, sized at 32x32x32 and 16x16x16. However, loading such a large number of maps has significantly slowed down ChimeraX, particularly when rotating the view. Is there any settings to improve interactive performance or increase hardware utilization? I hope to avoid cropping the tomograph. >> >> My system specifications are as follows: >> >> Dual Intel Xeon 5317 processors(a)3.00GHz >> RTX 4090 GPU >> 128GB RAM >> Operating System: CentOS Stream 9 >> GNOME Version: 40.4 >> GPU Driver Version: 550.54.15 >> I would greatly appreciate any suggestions. >> >> Thanks, >> >> Wang GuangLei >> >> _______________________________________________ >> ChimeraX-users mailing list -- chimerax-users(a)cgl.ucsf.edu >> To unsubscribe send an email to chimerax-users-leave(a)cgl.ucsf.edu >> Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/ >

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error in the documentation?
by Bourguet,Pierre 06 Sep '24

06 Sep '24

Dear ChimeraX support, First of all, thank you for developing & maintaining such an easy-to-use software. I am not trained as a structural biologist, but I looking at more and more structures thanks to alphafold. The journey is much nicer since I switched to ChimeraX! I have noticed the following inconsistency in the documentation. https://rbvi.ucsf.edu/chimerax/docs/user/commands/alphafold.html#contacts "If one set of entities is higher-confidence (lower in pLDDT<https://alphafold.ebi.ac.uk/faq#faq-12>) than the other, it is usually best to specify them as the aligned set so that the coloring will show the error values of the lower-confidence set." My understanding is that it should say "(higher in pLDDT)". Hopefully that helps! Best, Pierre Pierre Bourguet Postdoc Gregor Mendel Institute of Molecular Plant Biology GmbH Dr. Bohr-Gasse 3, 1030 Vienna, Austria pierre.bourguet(a)gmi.oeaw.ac.at http://www.gmi.oeaw.ac.at [cid:gmi_48f983b7-0679-4d21-99bc-bda376e5bf6b.png]

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Optimizing ChimeraX Performance for Multiple Subtomo Maps
by 王光磊 05 Sep '24

05 Sep '24

Hi, I'm using chimerax to display my tomograph and multiple subtomo averages in surface mode. Specifically, I need to visualize a 1440*1022*250 tomograph, along with 1000-2000 subtomo maps, sized at 32x32x32 and 16x16x16. However, loading such a large number of maps has significantly slowed down ChimeraX, particularly when rotating the view. Is there any settings to improve interactive performance or increase hardware utilization? I hope to avoid cropping the tomograph. My system specifications are as follows: Dual Intel Xeon 5317 processors(a)3.00GHz RTX 4090 GPU 128GB RAM Operating System: CentOS Stream 9 GNOME Version: 40.4 GPU Driver Version: 550.54.15 I would greatly appreciate any suggestions. Thanks, Wang GuangLei

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Discrepancy: plDDT laphafold3 and ChimeraX version 1.9.dev202405310031 (2024-05-31)
by Khawar Siddiqui 03 Sep '24

03 Sep '24

Dear Tom and ChimeraX team I recently did some protein structures using AF3. I found that the plDDT color prediction given by AF3 differs from when I opened the downloaded file in ChimeraX. Both photos are below. Can you please guide me to where I am making the mistake? Some adjustments may be needed. The AF3 coloring (right) shows prominently Blue-cyan (70-90% confidence) whereas after opening the same file in ChimeraX (left) shows many regions as yellow (50% confidence). Thanks again for the help. sohail Dr Khawar Sohail Siddiqui, [cid:3f847f24-9a1b-47bc-bb56-1704e8bd8ac3] [cid:2c952f1f-e76e-458e-a444-8242f6bdab3a] [cid:0089dce1-a9be-4009-93b9-d158c31cee29]hoo.com

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I found that the phosphodiester bond has broken.
by Yan ZHANG 张艳 03 Sep '24

03 Sep '24

Dear ChimeraX Team, I am writing this letter due to an issue I have encountered. I have adjusted the phosphodiester bonds of the RNA chain using Coot for structure correction. However, when I opened it in ChimeraX, it appears to be in a broken state, even though the distance between the two atoms is 1.6 angstroms. I am unsure what the reason for this could be. I have attached an image below. The dashed line should originally be a P-O bond. Could you please suggest any solutions to this problem? I look forward to receiving your reply as soon as possible. [cid:image001.png@01DAFDEC.77532DA0]

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