Protein Modeling C

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Re: Protein Modeling C

Postby JonB » September 22nd, 2014, 2:44 pm

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!

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Re: Protein Modeling C

Postby Tony116 » October 3rd, 2014, 2:23 pm

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.

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Re: Protein Modeling C

Postby bernard » October 3rd, 2014, 7:24 pm

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.
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Re: Protein Modeling C

Postby Tony116 » October 4th, 2014, 2:36 pm

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."

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Re: Protein Modeling C

Postby EastStroudsburg13 » October 5th, 2014, 6:01 am

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.
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Re: Protein Modeling C

Postby Tony116 » October 5th, 2014, 8:27 am

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.

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Re: Protein Modeling C

Postby ZESPLACHOLA » October 10th, 2014, 12:51 pm

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


HELP!

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Re: Protein Modeling C

Postby JonB » October 10th, 2014, 2:01 pm

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

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Re: Protein Modeling C

Postby emmadej » October 12th, 2014, 3:04 pm

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?

:cry:

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Re: Protein Modeling C

Postby bernard » October 13th, 2014, 2:21 am

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