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Re: Protein Modeling C

Posted: February 15th, 2020, 11:02 am
by CookiePie1
Chameleon02 wrote:
February 15th, 2020, 12:43 am
Hey guys. How do I find out how many chains are in a structure?
How do I find the widest width of a protein?
How do I find how many polymers a structure contains?
Thanks!
when you load a pdb file, open the console. It will say, "found biomolecule 1: [something]". the number of letters is the number of chains. for the width question, you can type "boundbox on" and "show boundbox". you'll have to subtract all three length values and see which one is longest.

I'm not quite sure what you mean by how many polymers, is that not the same thing as the number of chains?

Correction: the first set of coordinates is the center of the boundbox, and the second set of coordinates is the distance from the center to the outside of the box along each axis (x,y,z). to find the length, subtract and multiply by 2.

Re: Protein Modeling C

Posted: February 20th, 2020, 12:20 pm
by voisinet22
Are there any good sites/books to learn the different crispr types and systems?

Re: Protein Modeling C

Posted: February 20th, 2020, 2:01 pm
by CookiePie1
voisinet22 wrote:
February 20th, 2020, 12:20 pm
Are there any good sites/books to learn the different crispr types and systems?
Try reading some papers on PMC: https://www.ncbi.nlm.nih.gov/pmc/
You can also use google scholar but most of the ones on PubMed are free to read.

Wikipedia is always a great resource for scioly. You can also just use regular google to try and find some reputable sources, but be aware that most of these research papers and articles are at a very high reading level and it might take some digesting to get the understanding you need.

Re: Protein Modeling C

Posted: February 23rd, 2020, 2:37 pm
by eagerlearner102
I recommend using the addgene e book about CRISPR. Its more than 100 pages long, but I read the CRISPR information. I don't have enough time to read the methodology and experiments :(
By the ways, is the JMOL exploration on the regional using Jmol software (Java) or online Jmol? How big is the difference between the two softwares? For the exploration, are we going to go on the PDB website or only Jmol?

Re: Protein Modeling C

Posted: February 23rd, 2020, 4:14 pm
by CookiePie1
eagerlearner102 wrote:
February 23rd, 2020, 2:37 pm
I recommend using the addgene e book about CRISPR. Its more than 100 pages long, but I read the CRISPR information. I don't have enough time to read the methodology and experiments :(
By the ways, is the JMOL exploration on the regional using Jmol software (Java) or online Jmol? How big is the difference between the two softwares? For the exploration, are we going to go on the PDB website or only Jmol?
so, if your regional ES decides to use the cbm supplied tests and such, then it will be an online jmol, and you will be allowed to use the pdb website with the links disabled. (they are screenshots). the online jmol is probably the easiest UI and for many functions you just need to right click on the screen. The offline version is more flexible and you can do more with it, but the general premise is the same. You just need to know how to find things, especially the console.

Re: Protein Modeling C

Posted: February 24th, 2020, 4:47 pm
by Tejas
Could someone please explain how to download JMole, thanks!

Re: Protein Modeling C

Posted: February 24th, 2020, 7:11 pm
by CookiePie1
Tejas wrote:
February 24th, 2020, 4:47 pm
Could someone please explain how to download JMole, thanks!
Go to this link: https://sourceforge.net/projects/jmol/

download and extract the contents and you can delete everything except the jmol.jar file, which you can run to start using jmol.

Re: Protein Modeling C

Posted: February 25th, 2020, 6:52 am
by eagerlearner102
For the Jmol exploration, they won't expect us to use other PDB visualization programs that include ligand explorer, simple viewer, and protein workshop right?
I am currently reading a jmol manual that is quite comprehensive.

Re: Protein Modeling C

Posted: February 25th, 2020, 6:54 am
by CookiePie1
eagerlearner102 wrote:
February 25th, 2020, 6:52 am
For the Jmol exploration, they won't expect us to use other PDB visualization programs that include ligand explorer, simple viewer, and protein workshop right?
I am currently reading a jmol manual that is quite comprehensive.
well, again it depends on who's writing the test. I think it's pretty safe to assume that msoe written tests won't expect you to know that, but if someone else is writing the test they might hae questions that require that.

Re: Protein Modeling C

Posted: February 26th, 2020, 12:13 pm
by Tejas
Thanks Cookie!