- ChimeraX-users - RBVI Mailing Lists

Build Structure - peptide
by Jeffrey D. Hartgerink 06 Mar '23

06 Mar '23

Hello, I’m trying to build a series of related peptides with ChimeraX’s Build Structure - peptide tool. The way it currently works is simple and easy to use. However it is cumbersome to input phi/psi angles repeatedly, especially if the peptide sequences is anything more than very short. I am wondering if there is a way for this tool to take in either a text file list containing (Amino Acid, Phi, Psi), to paste in the same data into the input window, or any other related way to more efficiently generate peptide structures for starting points. This would greatly reduce the time needed to compare a variety of related sequences and conformations. Thank you very much for your time and consideration! -Jeff ---------------------------------------------- Jeffrey D. Hartgerink, Ph.D. Prof. of Chemistry and Bioengineering Rice University jdh(a)rice.edu / 713-348-4142 https://hartgerink.rice.edu

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Fwd: Request for Help with Chimerax and Protein Visualization
by Eric Pettersen 02 Mar '23

02 Mar '23

> Begin forwarded message: > > From: Ratchanont Viriyakitkosol <ratchanont.vir(a)gmail.com> > Subject: Request for Help with Chimerax and Protein Visualization > Date: March 2, 2023 at 12:26:42 AM PST > To: pett(a)cgl.ucsf.edu > > Dear Eric Pettersen, > > I hope this email finds you well. I am a medical school undergraduate student, and I have been using Chimerax to visualize protein structures that I predicted using AlphaFold. I am reaching out to you as I have encountered some difficulties with visualizing chemical bonding interactions in Chimerax, and I was hoping you could provide some guidance. > > Firstly, I have been using the "contacts" command in Chimerax to visualize chemical bonding interactions that interact with a single amino acid. However, I am not sure if this is the correct command to use. The visualization only shows blue dashlines, which I assume are hydrogen bonds. However, I am not sure if it is showing all direct interactions, including polar and nonpolar, favorable and unfavorable (including clashes). I want to know what is meant by "favorable and unfavorable" interactions in this context. > > Secondly, I have been unable to find a command to show disulfide bonds within a protein in Chimerax. I know that Pymol can show disulfide bonds in the same model, but I find Chimerax easier to use. Could you please let me know how to visualize disulfide bonds in Chimerax? > > As an undergraduate student with limited knowledge of structural analysis, I want to ensure that the bonding I use in my manuscript is shown correctly. I would greatly appreciate any advice or guidance you could provide. > > Thank you for taking the time to read my email, and I look forward to your reply. > > > > Best regards, > > James >

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Inquiry about bond type generated by the "contacts" command with default settings for AlphaFold-generated protein structure
by stomp.pumped0g＠icloud.com 02 Mar '23

02 Mar '23

Dear UCSF ChimeraX team, I hope this email finds you well. I am writing to inquire about the bond type generated by the "contacts" command with all default settings in UCSF ChimeraX for a protein structure that was generated using AlphaFold. I am particularly interested in understanding the nature of the blue line that is generated after running this command. As a reminder, my protein structure was generated using AlphaFold, and I would like to know if the bond type is a hydrogen bond, salt bridge, disulfide bond, or another type of bonding. Any information or insight you could provide on this matter would be greatly appreciated. Thank you for your time and assistance. Best regards, James

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Discrepancies in SASA values between chimera and chimeraX
by Prathvi Singh 01 Mar '23

01 Mar '23

Hi Elaine, I compared the SASA values generated by chimera and chimeraX for a few PDB files and I noticed that whenever the SASA value of a residue is reported to be zero by chimera, the same residue's SASA value is reported to be -1.42 by chimeraX. Few examples are 18.A and 38.A of the PDB ID 1A62. *Method used to calculate SASA of residues in chimera: *Tools > Structure analysis > Render by attribute *Method used to calculate SASA **of residues** in chimeraX: *I ran the following commands: measure sasa protein;info residues attribute area Why is this happening? Kindly help. -- Prathvi Singh, Research Fellow, Department of Biological Sciences & Bioengineering, Indian Institute of Technology, Kanpur-208016

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Ring fill color
by Luca Pellegrini 01 Mar '23

01 Mar '23

Is it possible to color differently the ring fill for sugar and base in DNA? When I select just the bases or just the riboses and then apply color using the ‘ring fill’ option, they both change to the new color. Thanks, Luca Luca Pellegrini, PhD Department of Biochemistry University of Cambridge Cambridge CB2 1GA UK

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Update pdb model in cxs session
by 张一小 28 Feb '23

28 Feb '23

Hi, I'm using ChimeraX to prepare figures. I saved a session containing several pdb files and maps. (The pdb files were saved in the CXS file right?) Now, I manually adjusted one of the models in Coot. Is there a way to update the old model with the new one in the session so that all the settings, such as colors, views, showing residues, hidden ribbons can be kept and applied?" Thanks, Yixiao

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Rotating/moving a chain to a different site
by Lohry, David 27 Feb '23

27 Feb '23

Hello! I am working with a protein dimer with DNA from a crystal structure. The dimer is composed of 2 chains (chain A and chain B) I would like to be able to place one of the chains on a different region of DNA and at a slightly different position. The only tool that I could find was the Movement Mouse Mode in Chimera original. Is there a way to do this a bit more mathematically (keeping the chain in tact)? Move 50 angstroms in the x direction, rotate chain by 30 degrees, etc . Also, I need it to update the actual coordinates in the PDB when saved so it can't be something that just affects the visual output. Thank you!

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Question!
by Matthew Wengler (TSL) 26 Feb '23

26 Feb '23

Hello, I am a PhD student studying the downstream signalling events of a kinase in a fungal plant pathogen. We have differential phosphopeptide data of the kinase itself over a time course during plant infection (i.e., four residues on this kinase are differentially phosphorylated during stages of infection). I had a vision of showing a movie that incorporated the phosphorylated residues x phosphorylation abundance x time on the kinase’s tertiary structure and was wondering if this could be possible with Chimera X: * The tertiary structure would be displayed in grey * The phosphorylated residues would be highlighted in blue * A movie would be played and the highlighted residues would change colour based on phosphopeptide abundance over a time course (ranging from 0-100% abundance = blue -> red) I was wondering if this was currently possible. Alternatively (and maybe this is really the easiest way), because we only have ~6 time points, I could have 6 different stills of the protein with the residues highlighted corresponding to the phosphopeptide abundance values (blue-red 0-100%) and then piece them together in a 6 frame video that will loop…? I think I would prefer the colours to blend slower together dynamically than 6 harsh frames. Would there be a way to do this in Chimera? Thank you, Matt Wengler

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some question about the use of chimera x 1.4
by 游宠昭 24 Feb '23

24 Feb '23

Dear developers, Sorry to bother you. Recently, I notice that chimera x display the DNA/RNA in a different way from that in chimera, and I find that there is a option in chimera called ribbon spline containing two options:B-spline and cardinal which explain why DNA/RNA is displayed in different ways in two softwares. However, I can not find the related actions in chimera x: "ribbon spline" in chimera refers to what in chimera x and how can I adjust this parameter. Sincerely, Chongzhao You

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Help Generating a Volume to use for 2D classification template generation
by Joshua Denson 22 Feb '23

22 Feb '23

Hi, I’m trying to take an alpha fold model of my complex, generate a low resolution map of the model using molmap, and then use it for 2D template generation in CryoSparc. I am able to generate the low resolution map just fine, but the resulting map is in a rectangular volume (48x64x51) and I need it to be a cubic volume for CryoSparc to accept it. Ideally it would have dimensions of 64x64x64. Is there a way to generate a low resolution map in a cell with specific dimensions while maintaining the protein complex dimensions? (eg. I don’t want to simply scale it into a cube) I am using ChimeraX 1.5. Best Josh Joshua M. Denson PhD Candidate (Johnson Group) Dept. of Chemistry and Biochemistry Utah State University

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