Protein Modeling C

[JonB]

When the fokI endonuclease protein is loaded on jmol, first we use the console to eliminate all amino acids besides 421-560. Then, we are left with two biomolecules. At first they appeared to be the same, however, when selecting one of them to view, jmol displays biomolecule 2 as have 53 more atoms than biomolecule 1. Does anyone know which biomolecule we are supposed to be modeling our protein after? Thank you!

You need to specify that you want chain A,
Restrict *A
Don't forget to capitalize the "A"

Thanks!

[Tony116]

I'm a bit confused about the protein we're supposed to model for the pre-build. The criteria says that we are including amino acids 421-560, and based on this, there are 140 amino acids, not 139 like the rule book says. So there is a one amino acid difference. Has anyone else noticed this? Clarification would be appreciated.

[bernard]

I'm a bit confused about the protein we're supposed to model for the pre-build. The criteria says that we are including amino acids 421-560, and based on this, there are 140 amino acids, not 139 like the rule book says. So there is a one amino acid difference. Has anyone else noticed this? Clarification would be appreciated.

In which section does it mention 139? I don't see it.

[Tony116]

I'm a bit confused about the protein we're supposed to model for the pre-build. The criteria says that we are including amino acids 421-560, and based on this, there are 140 amino acids, not 139 like the rule book says. So there is a one amino acid difference. Has anyone else noticed this? Clarification would be appreciated.

In which section does it mention 139? I don't see it.

Oh sorry i guess it's not mentioned in the rule book. I saw it on the pre-build visualization site, it literally said this: "This section is 139 amino acids long and will require a toober that is 278cm long at the scale of 1 amino acid = 2cm."

[EastStroudsburg13]

Both caps count as one amino acid I believe. That way when you mark the 2 cm lengths you end up with 140 amino acids, even though you have only 278 cm to work with.

[Tony116]

Both caps count as one amino acid I believe. That way when you mark the 2 cm lengths you end up with 140 amino acids, even though you have only 278 cm to work with.

Oh ok thank you. That makes more sense.

[ZESPLACHOLA]

Hey, I am having a lot of trouble importing the STRUCTURE OF RESTRICTION ENDONUCLEASE FOKI into the Jmol viewer, any advise?


HELP!

[JonB]

Hey, I am having a lot of trouble importing the STRUCTURE OF RESTRICTION ENDONUCLEASE FOKI into the Jmol viewer, any advise?


HELP!

go to rcsb.org
search FOKI Endonuclease
scroll down and select the 2FOK STRUCTURE OF RESTRICTION ENDONUCLEASE FOKI
on the top right side (next to 2FOK) click download
select PDB File (gz)
Then click the file button in jmol and search your downloads for the 2FOK.pdb file
The protein should open but then you have to restrict it to amino acids 421-560

If you are still having trouble, go onto scioly.org and read the wiki for Protein Modeling

[emmadej]

I have successfully gotten the endonuclease model into JMOL.

However, when i type in restrict 421-560, or select 421-560, it says 0 atoms selected.

How am I supposed to restrict it to the portion I am supposed to model?

[bernard]

I don't seem to have that problem. I've attached a screenshot so you can see if we are doing the same thing.