Protein Modeling C

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Re: Protein Modeling C

Post by MacintoshJosh » February 6th, 2020, 8:12 pm

Have any of you found out how to calculate disulfide bonds? Typing "ssbonds on", "calculate ssbonds", "calculate disulfide bonds" or any other variation doesn't seem to work for me. I've just been looking at the amounts of Cysteines but that definitely isn't the best way.
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Re: Protein Modeling C

Post by Chameleon02 » February 6th, 2020, 8:24 pm

also how do I find the amount of total hbonds in the total molecule. I have been using a wierd roundabout way to solve it.
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Re: Protein Modeling C

Post by pb5754 » February 6th, 2020, 8:27 pm

Chameleon02 wrote:
February 6th, 2020, 8:24 pm
also how do I find the amount of total hbonds in the total molecule. I have been using a wierd roundabout way to solve it.
calculate hbonds?
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Re: Protein Modeling C

Post by Chameleon02 » February 6th, 2020, 8:33 pm

pb5754[] wrote:
February 6th, 2020, 8:27 pm
Chameleon02 wrote:
February 6th, 2020, 8:24 pm
also how do I find the amount of total hbonds in the total molecule. I have been using a wierd roundabout way to solve it.
calculate hbonds?
Lol I must have tried that before, I'll see it again tmrw. Also, (1) does anyone know how to calculate the X, Y, Z coordinates of an amino acid? And (2) how do you calculate how many struts can be added to the entire protein structure? Thanks! And I'm sorry for spamming questions, I have a competition next weekend :P
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Re: Protein Modeling C

Post by itsDerk » February 6th, 2020, 8:44 pm

Chameleon02 wrote:
February 6th, 2020, 8:33 pm
pb5754[] wrote:
February 6th, 2020, 8:27 pm
Chameleon02 wrote:
February 6th, 2020, 8:24 pm
also how do I find the amount of total hbonds in the total molecule. I have been using a wierd roundabout way to solve it.
calculate hbonds?
Lol I must have tried that before, I'll see it again tmrw. Also, (1) does anyone know how to calculate the X, Y, Z coordinates of an amino acid? And (2) how do you calculate how many struts can be added to the entire protein structure? Thanks! And I'm sorry for spamming questions, I have a competition next weekend :P
You should be able to get the x, y, z coordinates of an AA just by clicking on it. (It will show up in console at least in the standalone jmol program, it's a bit weirder with the in-browser version bc sometimes it just doesn't want to show up).

For the total structs, if you have everything selected you can just run "calculate struts" and the console should tell you.

Good luck at your competition next weekend.
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Re: Protein Modeling C

Post by sciencegirl03 » February 10th, 2020, 7:56 pm

Does anyone know how to display ions in Jmol? For example the central zinc atom in APOBEC3A? I came across a question on a test that asked the distance between the central iron atom and a proximal histidine at residue 93 in protein 1mbn.pdb. I tried commands such as select iron and select _fe and display _fe, but nothing is actually showing the ion. Thanks in advance!
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Re: Protein Modeling C

Post by exla23 » February 10th, 2020, 8:01 pm

sciencegirl03 wrote:
February 10th, 2020, 7:56 pm
Does anyone know how to display ions in Jmol? For example the central zinc atom in APOBEC3A? I came across a question on a test that asked the distance between the central iron atom and a proximal histidine at residue 93 in protein 1mbn.pdb. I tried commands such as select iron and select _fe and display _fe, but nothing is actually showing the ion. Thanks in advance!
One thing you could do is select the ion (I often use select ligands but select _fe and similar commands should also work) and then use the spacefill command to show it.
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Re: Protein Modeling C

Post by CookiePie1 » February 10th, 2020, 8:05 pm

exla23 wrote:
February 10th, 2020, 8:01 pm
sciencegirl03 wrote:
February 10th, 2020, 7:56 pm
Does anyone know how to display ions in Jmol? For example the central zinc atom in APOBEC3A? I came across a question on a test that asked the distance between the central iron atom and a proximal histidine at residue 93 in protein 1mbn.pdb. I tried commands such as select iron and select _fe and display _fe, but nothing is actually showing the ion. Thanks in advance!
One thing you could do is select the ion (I often use select ligands but select _fe and similar commands should also work) and then use the spacefill command to show it.
yes, the spacefill command is the only thing you were missing. then, double click on the ion to use the measure tool.
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Re: Protein Modeling C

Post by sciencegirl03 » February 11th, 2020, 6:48 am

CookiePie1 wrote:
February 10th, 2020, 8:05 pm
exla23 wrote:
February 10th, 2020, 8:01 pm
sciencegirl03 wrote:
February 10th, 2020, 7:56 pm
Does anyone know how to display ions in Jmol? For example the central zinc atom in APOBEC3A? I came across a question on a test that asked the distance between the central iron atom and a proximal histidine at residue 93 in protein 1mbn.pdb. I tried commands such as select iron and select _fe and display _fe, but nothing is actually showing the ion. Thanks in advance!
One thing you could do is select the ion (I often use select ligands but select _fe and similar commands should also work) and then use the spacefill command to show it.
yes, the spacefill command is the only thing you were missing. then, double click on the ion to use the measure tool.
Wow thanks guys! I can see the ion now :)
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Re: Protein Modeling C

Post by unknownuser2 » February 11th, 2020, 5:26 pm

Hi all,

My regional doesn't run protein modeling, so I'm in the midst of getting ready for the state-level as my first go around this year. Last year in NYS, the ES's used Jsmol to do the onsite build, is it likely that the visualization part of the test will also be in Jsmol as well, or should I expect them to switch over to Jmol for this year.

Doubt anyone has explicit answers, however any thoughts would be greatly appreciated.

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