id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 6527 RFE: option to always draw a specific model on top Elaine Meng Tom Goddard "Mauricio Losilla would like an option to draw a specific model on top, as per these earlier messages on chimerax-users: Hi, I am new to ChimeraX, thank you for making this great software available. I loaded a pdb file that has 2 amino acid chains aligned (chimerax.png). These chains are a model (gray) and template (purple). As you can see, the two chains look weaved or blended. I would much prefer to display the uninterrupted template around to model, to visually represent their fit. Is there a way to do this? I am attaching a second image (ideal_display.png, generated elsewhere) with the visual outcome I am after (the purple chain is the template, the rainbow-colored chain is the model). Thank you *Mauricio Losilla, PhD* Integrative Biology; and Ecology, Evolution, & Behavior Michigan State University he, him, his ... my first answer suggesting making one transparent and the other one fatter: ...and subsequent request and further clarification from Mauricio From: Mauricio Losilla via ChimeraX-users Subject: Re: [chimerax-users] display options for model with 2 chains Date: April 1, 2022 at 8:17:42 AM PDT To: ChimeraX Users Help Reply-To: Mauricio Losilla Hi Elaine, I am sorry, I didn't explain myself well, I will try to do it here. I was able to use all your tips successfully: I split the chain in two models, and tweaked the thickness, width, and transparency at will. It worked great! I am attaching the result [result.png]. I think it accomplishes my original goal fairly well: to visually represent the fit of the gray protein to the purple template. However, the purple chain still looks sewed into the gray chain. In the image, this is better seen in the horizontal beta sheets at the center. The ideal display I was after is that of the image with the rainbow-colored chain and the purple template I sent in my original email. There, the purple chain always looks ""on top"" of the rainbow chain. That is what I meant yesterday with ""the ability to superimpose the view of one chain"". In case it is helpful, the reference image and the PDB file came from I-TASSER. I am new to ChimeraX (and to 3D shapes of molecules in general), so I apologize if I am not making much sense. Thank you! " enhancement closed moderate Graphics not a bug losillam@… all ChimeraX