UCSF Chimera: Structure Comparisons

[@AmitSingh-le5xn]

The Match->Align option is not available in my ChimeraX installed on windows system. Please suggest an alternative for percentage sequence identity. Thank you.

[@sonicbouy]

thanks, could you also do dock prep and energy minimization , molecular dynamics too

[@leixiao169]

I wonder what is the "R" sign under the lower right panel?

[@rashamoustafa427]

Great lecture🎉🎉🎉❤❤❤❤

[@tantrilestari4897]

Hi I couldnt find Tool>structure comparison menu in my windows chimera X . may I know how to view this tool

[@dr.ravikumar9481]

Can someone provide the link of the website?

[@1p53gen]

when we model a protein with Chimera with the option modeller, how to decide what model is better with the value zDOPE. If I have only positives values. What is the best? The highest number or the nearer to cero?

[@madorkas5400]

how do you determine c vs n terminal end in chimera? thank you!

[@firatkurt4289]

"named selection" does not appear when the steps followed in the video... ???

[@diptendusarkar1912]

i am also facing same problem

[@firatkurt4289]

@@diptendusarkar1912 follow these steps. After matching two structures as it was done in video, you first go to "Select"-"Chain"-choose"D". Then "Select"-"Selection Mode"-"Append". Again, "Select"-"Chain"-"A"-"1mbo" At this juncture you have two ways to follow choose whichever you like: FIRST: After appending the 1mbo, you go to "Select"- "Invert (Selected Models)", and then "Actions"-"Ribbon" -"Hide" Second: "Select"-"name selection"- (a window appears! name it as you like. For example 1mbo-4hhb) hit ok. "Select"- "Invert (Selected Models)", and then "Actions"-"Ribbon" -"Hide" The advantage of the second method is that If you touch anywhere on the screen on chimera and loose your selection, this is guarantee way to bring your selection back. I hope, this explanation helps...

[@simranahuja5980]

@@firatkurt4289 Thank you so much for this!

[@sivecheachhay8704]

After the structure comparison matchmaker, I can’t do the named selection

[@durdonamalikova4915]

Thanks a lot. I'm from Uzbekistan

[@abidabilal4111]

How to determine other molecular interactions other than hydrogen bonding?

[@shylajanaciyar8394]

How to superimpose three structures?

[@brianwiley6349]

you can select the chains for instance for the first model #0 at the command line with 'select #0 :.A-C' and then name it with command "namesel 4hhb-ABC". Got this from link below. www.cgl.ucsf.edu/pipermail/chimera-users/2019-January/015384.html and the namesel command from the cheat sheet www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/quickref.pdf

[@diptendusarkar1912]

how to work on it? When I am following the same, it is not appearing

[@simranahuja5980]

Hey, it didn't work for me too

[@TeamXenash]

Didn't show how he name the selection to select ABC got lost a bit there

[@simranahuja5980]

Yes, same happened with me..I even named the selections but still it didn't happen that way.

[@rupindersayal]

Great tutorial, thanks!

[@nain9038]

Hi..how can we save a file in pdb format using chimera?????plzzzzz would you explain???

[@nikitaabramenko4490]

File, Save ODB

[@nikitaabramenko4490]

Sorry, File, Save PDB

[@bankimmondal4337]

Very nice! Thanks a lot!

[@7kidstudio]

Merci

[@sarahrodriguez6783]

Thank you

[@IslamSafwat--]

Thanks::)