- ChimeraX-users - RBVI Mailing Lists

Re: [chimerax-users] [Chimera-users] xyz axis indicator
by Elaine Meng 01 Nov '22

01 Nov '22

Hi Xiang, I am guessing you are using ISOLDE with ChimeraX (not Chimera) so I am cross-posting this question to the chimerax-users(a)cgl.ucsf.edu list. I am not expert with ISOLDE so I am not sure about the answer. Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Oct 30, 2022, at 10:58 PM, Xiang Zhang via Chimera-users <chimera-users(a)cgl.ucsf.edu> wrote: > > Hi all, > > I was wondering how I could hide the xyz indicator in the center of window when I was viewing the X-ray density from mtz file? It only appears in crystal unit view mode but disappears in EM projection side view. > > Best, > Xiang > <1667192316818.png>_______________________________________________ > Chimera-users mailing list: Chimera-users(a)cgl.ucsf.edu > Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimera-users

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Co-centering maps and pub models
by mailman-bounces＠cgl.ucsf.edu 31 Oct '22

31 Oct '22

Dear ChimeraX users I have a density map and a pdb model opened in ChimeraX. How to move one of them to have a common axis (for both) , without disturbing the other. Stay safe & Regards Anindito Sen. Ph.D Microscopy and Imaging Center Texas A&M University 301 Old Main Dr College Station, TX 77843-2257 Office: ILSB Room 1133 <http://microscopy.tamu.edu/>Tel. 979-458-9881 fax: 979-847-8933 http://microscopy.tamu.edu <http://microscopy.tamu.edu/>

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Re: [chimerax-users] AlphaFold Prediction
by Tom Goddard 31 Oct '22

31 Oct '22

Hi Raihan, The maximum sequence length that can be predicted by AlphaFold is limited by GPU memory. The following table says that paid Google Colab services only offer at most 16 Gbytes of GPU memory (from https://blog.paperspace.com/alternative-to-google-colab-pro/ <https://blog.paperspace.com/alternative-to-google-colab-pro/>). Not sure if it is correct since the table is from a Google competitor. You can run sequence length 1000, sometimes 1200, with 16 GB of GPU memory as shown here https://www.rbvi.ucsf.edu/chimerax/data/alphafold-jan2022/afspeed.html Various cloud compute services offer modern GPUs like Nvidia A40, A100, A6000 with 48 GB, or 40 or 80 GB of GPU memory usually charging about $2-3 per hour. But ChimeraX can only currently use Google Colab for AlphaFold predictions. Tom > On Oct 31, 2022, at 2:45 PM, S.M. RAIHAN RAHMAN <smrrbtgeiu(a)gmail.com> wrote: > > Thank you. I saw the run times. Is it possible to run sequences of around 1200 in Google Colab pro plus paid service through ChimeraX? In the website link you shared, I only saw about Google Colab pro paid service. Please let me know. > > Regards, > Raihan > > On Mon, 31 Oct 2022 at 14:33, Tom Goddard <goddard(a)sonic.net <mailto:goddard@sonic.net>> wrote: > ChimeraX only runs AlphaFold on Google Colab. Because Google Colab provides 5 year old GPUs with little memory (16 GB) it can only run sequences of length about 1000 or less. With better equipment and your own AlphaFold installation you can run sequences up to length 3000 or 4000 although that can take 30 hours. Here are example run times > > https://www.rbvi.ucsf.edu/chimerax/data/alphafold-jan2022/afspeed.html <https://www.rbvi.ucsf.edu/chimerax/data/alphafold-jan2022/afspeed.html> > > Tom > > >> On Oct 31, 2022, at 2:28 PM, S.M. RAIHAN RAHMAN <smrrbtgeiu(a)gmail.com <mailto:smrrbtgeiu@gmail.com>> wrote: >> >> Thank you so much. Is there any alternative to Google Colab for running AlphaFold through ChimeraX? Please let me know. >> >> Regards, >> Raihan >> >> On Mon, 31 Oct 2022 at 14:22, Tom Goddard <goddard(a)sonic.net <mailto:goddard@sonic.net>> wrote: >> Hi Raihan, >> >> The ChimeraX AlphaFold prediction produces 5 models but it only automatically opens the best model. All 5 models are in the ~/Downloads/ChimeraX/AlphaFold/prediction directory after the job completes. There is no option to run fewer models. Running AlphaFold not through ChimeraX also produces 5 models. This is because AlphaFold works by running 5 slightly differently trained neural networks and the best is chosen. If you install your own AlphaFold (a somewhat difficult task, needs Linux and an Nvidia GPU and a few Tbytes of disk for databases) then you can modify the AlphaFold Python code to predict only one or a few models by choosing which of the 5 networks it should run. >> >> Tom >> >> > On Oct 31, 2022, at 1:39 PM, S.M. RAIHAN RAHMAN via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>> wrote: >> > >> > Hi! >> > Good Afternoon. I hope that you are doing well. I am facing a problem in running structure prediction of large protein sequence in AlphaFold prediction. Is there any way of predicting only 2 models of a given sequence in lieu of 5 models before providing the final model in AlphaFold prediction? Please let me know. Thank you. >> > >> > Regards, >> > Raihan >> > _______________________________________________ >> > ChimeraX-users mailing list >> > ChimeraX-users(a)cgl.ucsf.edu <mailto:ChimeraX-users@cgl.ucsf.edu> >> > Manage subscription: >> > https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users <https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users> >> >

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AlphaFold Prediction
by S.M. RAIHAN RAHMAN 31 Oct '22

31 Oct '22

Hi! Good Afternoon. I hope that you are doing well. I am facing a problem in running structure prediction of large protein sequence in AlphaFold prediction. Is there any way of predicting only 2 models of a given sequence in lieu of 5 models before providing the final model in AlphaFold prediction? Please let me know. Thank you. Regards, Raihan

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Copy a part of a model ?
by mailman-bounces＠cgl.ucsf.edu 31 Oct '22

31 Oct '22

Hi :) I wanted to duplicate only one part of a model and I haven't found a copy function (I found this old thread tho https://www.rbvi.ucsf.edu/pipermail/chimerax-users/2020-January/000783.html <https://www.rbvi.ucsf.edu/pipermail/chimerax-users/2020-January/000783.html>) For now my strategy is to duplicate the model with "combine #1 close false" and then delete what I don't want on the new model like for example (to delete helices) "delete ~helix & #2" I know you are always super busy with ChimeraX dev, but I thought this could be a good "quick way" to create a "copy" function of example (if there are no alternative that I missed of course). Have a great day! Best regards, Thibault. -- Thibault Tubiana, PhD Postdoctoral Fellow @IMAPP <https://www.i2bc.paris-saclay.fr/equipe-interactions-and-assembly-mechanism…> Institute for integrative biology of the cell (I2BC <https://www.i2bc.paris-saclay.fr/>) - CNRS UMR 9198 CEA Saclay, 91191 Gif sur Yvette - Bât 532 pce 34 Web Site: http://www.tubiana.me/gallery <http://www.tubiana.me/>

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Re: [chimerax-users] [Chimera-users] Question regarding protein-protein interactions in ChimeraX
by Elaine Meng 31 Oct '22

31 Oct '22

Hi Camille, ChimeraX does not move the proteins to predict how they might bind each other, although you could move one relative to the other "manually" (with the mouse) yourself, or use some other program to do protein-protein docking. ChimeraX is just showing the coordinates in the Protein DataBank data files that you opened, i.e. whatever the authors deposited. If you are using ChimeraX, for future questions you may want to use ChimeraX mailing list chimerax-users(a)cgl.ucsf.edu CC'd here instead of the Chimera one. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Oct 30, 2022, at 3:26 PM, Lake, Camille (NIH/NIAID) [C] via Chimera-users <chimera-users(a)cgl.ucsf.edu> wrote: > > Hello, > > My name is Camille Lake and I have used ChimeraX to model proteins. I was wondering - if I load two completely separate proteins from PDB, what is the nature of their interaction as shown by ChimeraX? The two proteins I'm interested in, TIM-3 (5f71) and CEACAM1 (5dzl), are predicted to interact in the literature, but if I load them separately into ChimeraX, is this predicted interaction what displays automatically? It seems that they are, but I can't find anywhere on the web whether this is automatically done in ChimeraX. Other proteins I randomly add in generally keep far away from each other in space. > > Thank you, > > Camille

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can not download
by keqing yin 29 Oct '22

29 Oct '22

Hello, There is no reaction after I clicked the save as the CSV when I want to download the clipper from tools/more tools . I would be very appreciate if you could solve this problem. [cid:image003.png@01D8EAFB.ECAB74A0] 从 Windows 版邮件<https://go.microsoft.com/fwlink/?LinkId=550986>发送

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How do I visualize an amber nc file in ChimeraX?
by Yasmene Wang Elhady 28 Oct '22

28 Oct '22

Hello, I'm new to molecular modeling, and new to Chimera. I'm trying to visualize an AMBER .nc output file from an AMBER tutorial ( http://ambermd.org/tutorials/basic/tutorial0/) and I have a topology file that in VMD is the type AMBER7 Parm. How can I visualize this in ChimeraX? I saw another thread suggesting to use the MD movie tool, but I don't see that option in ChimeraX. Is this something I need to add? If so, where can I get it from, and how do I add it? Thanks in advance, Yasmene

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Selection by segid
by CUNIASSE Philippe 28 Oct '22

28 Oct '22

Dear all, Is there a way in ChimeraX to make a selection by segid (column 73-76 in pdb format from CHARMM of XPLOR)? Thanks in advance. Philippe Cuniasse. ----------------------------------------------- Philippe Cuniasse, PhD/HDR. Institut de Biologie Integrative de la cellule. UMR 9198 CNRS-CEA-Univ Paris Sud Bat 144 CE-Saclay 91191 Gif-sur-Yvette Cedex France Tel: (33) 1 69 08 56 35 Fax: (33) 1 69 08 47 12 Email: philippe.cuniasse(a)cea.fr<mailto:philippe.cuniasse@cea.fr> Web: http://biodev.cea.fr/rasmot3d/ [signature_700846419][signature_2907812893][signature_966493179] -----------------------------------------------

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Re: [chimerax-users] ChimeraX sequence alignment score?
by Elaine Meng 27 Oct '22

27 Oct '22

> On Oct 27, 2022, at 4:46 PM, Budayr, Omar Mahdi <obudayr(a)vols.utk.edu> wrote: > > Dear Dr. Meng, > > I looked through the documentation for ChimeraX and I still cannot figure out what the value for sequence alignment score indicates. I aligned two b-adrenergic receptors from PDB (2RH1 and 3NH8) and it gives a value of 2423.9. What does this value actually represent? The documentation refers to it but never gives specifics besides the parameters in the table that matchmaker generates > > Sincerely, > Omar Budayr Dear Omar Budayr, The value itself is not at all important. The reason to have a score is that the alignment process tries to maximize it for the pair of sequences that it is given. By changing parameters for scoring you can change the relative importance of the different parts of the score, and thus what is most important for the alignment method to align. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco P.S. we recommend sending questions to the chimerax-users(a)cgl.ucsf.edu address (CC'd here) so that others can benefit from the answers and/or help to answer the questions - thanks!

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