- ChimeraX-users - RBVI Mailing Lists

Mutated several residues (amino acids or nucleotides) at the same time
by Vorländer,Matthias Kopano 08 Mar '23

08 Mar '23

Hi there, I wondered if it would be possible to change several residues at the same time using the “swapna” and “swapaa” commands in order to change the model file so that it matches a target sequence. This would be extremely helpful for model building purposes. Many thanks, Matthias

3 3

Re: [chimerax-users] Some beginner's questions
by Elaine Meng 07 Mar '23

07 Mar '23

Hi Boaz, Glad you're getting acquainted with ChimeraX! Now I find it easier to use than Chimera. (1) no, it is not necessary to name the selection. The "save" command for PDB has an option to include selected atoms only, see: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/save.html#pdb> (2) do you mean the Side View tool? (ChimeraX does not have a per-model clipping gui currently). There is an icon in the Graphics tab of the toolbar across the top to show the Side View, or you can open it from the menu: Tools... General... Side View (3) if the surfaces are different, yes, that would be the reason for different min/max values found at surface vertices (4) Chimera's ~longbond command just hides the "missing segments" pseudobond group. In ChimeraX, you can look in the Model Panel (may need to use disclosure triangle on the model that contains it) to find the "missing structure" model. In that tool, you can just un-check the display box in the column under the eye icon to hide the whole model, or see what the model number is to use in a hide command, e.g. open 1www hide #1.1 (5) I would need more information: Are you trying to show isopotential surfaces, or to color the molecular surface by the potential value? If the latter, are you coloring the molecular surface of the protein or of the ligand? Do you have your own dx file already or do you just want to calculate Coulombic ESP and color by that? Coloring the protein surface by Coulombic ESP is as simple as clicking the icon in the Molecule Display tab of the toolbar. It is also covered in several tutorials, e.g. <https://www.rbvi.ucsf.edu/chimerax/docs/user/tutorials/binding-sites.html#e…> <https://www.rbvi.ucsf.edu/chimerax/data/mole-channel/mole-channel.html#esp> <https://www.youtube.com/watch?v=FEIJ0lmybXo> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Mar 7, 2023, at 9:12 AM, Boaz Shaanan via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu> wrote: > > Hi, > > I checked the commands-user guide but couldn't find answers: > • To write out a selection of atoms to a PDB, do I need to name the selection first? > • I couldn't find the clipping tool (after setting a pivot I see only small part of the model). > • The min/max values of a potential from APBS (.dx) seem to be different in Chimerax than they are in Chimera. I'm working on a tetramer and while in Chimera the whole tetramer surface is covered by the potential, in Chimerax it' shown for each monomer. Is that the source of the difference? > • What's the Chimerax equivalent of ~longbonds of Chimera? > • Just wondering, is there a demo for electrostatic potential surface around a ligand? I seem to be making progress on that but a demo would be most helpful. > Thanks, > > Boaz

2 2

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

2 2

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 >

2 2

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

2 1

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

2 2

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

2 1

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

2 3

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!

2 2

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

2 1