Tagged questions

Generate inter-proton distance restraints from an X-ray structure

1 1 4k
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Hello, Does anyone know of any program that can generate inter-proton distance restraints from an X-ray structure? I w...
Posted: Wenjin Wu 61 / Updated: Josef Chmelik 1 May 07 '13 at 05:33

cs23d vs. cs-rosetta

2 1 6k
answers votes views
Does anybody have any thoughts on this ? I dont really know which is better, CS23D or CS-ROSETTA. Clearly they are ide...
Posted: j 131 / Updated: Thomas Garner 81 Jan 19 '11 at 08:05

How to keep XPLOR structure calculation from exploding?

1 0 4k
answers votes views
Trying to calculate a structure using sa.inp script and the energy in the cooling loop increases instead of going down. ...
Updated: Evgeny Fadeev 5771 Nov 02 '10 at 11:57

How to assign (perturbed) resonances when structure is known?

1 0 5k
answers votes views
I had two problems like this one recently: have protein (in solution) of known general structure resonance assignments...
Posted: Evgeny Fadeev 5771 / Updated: Aleksandr Yakimov 11 Apr 25 '10 at 01:17

Is there a tool to manage NOE and other restraint lists for the structure calculations?

1 0 5k
answers votes views
Hello, I'm currently working on solving a peptide NMR solution structure using NIH-XPLOR. I find myself a lot starting ...
Posted: Evgeny Fadeev 5771 / Updated: Ilango 171 Apr 02 '10 at 05:45

Software to model a 9-mer peptide that binds divalent metals and may oligomerize?

1 1 11624
answers votes views
I'm gearing up for a project in which we're looking at the structure of a short peptide that should fold upon binding di...
Posted: jkurutz 131 / Updated: Evgeny Fadeev 5771 Mar 18 '10 at 09:32

How do you use PyMol to visualize structure bundles and related MR data?

0 0 7k
answers votes views
Hello, are you using pymol to analyze NMR structures? (I've been mostly using Molmol before). Have you learned any PyMo...
Updated: Evgeny Fadeev 5771 Mar 02 '10 at 12:29

Are there alternatives to MOLMOL for visualization of NMR structure ensemebles?

2 0 5k
answers votes views
Hi folks, I've been using Molmol, but found significant issues when working with a non-standard structure. For example...
Updated: Evgeny Fadeev 5771 Mar 02 '10 at 08:05

How would you compare solving NMR structure of a smaller peptide vs that of globular protein?

2 0 19390
answers votes views
By smaller peptide I mean somewhere around 15-20 aminoacids, having a cycle or two that constrain the geometry. Also - ...
Posted: Evgeny Fadeev 5771 / Updated: SankarampadiAravamudhan 91 Mar 17 '11 at 01:01

What are the biggest differences in solving NMR structures of DNA or RNA vs. proteins?

2 1 13255
answers votes views
I've only solved NMR structure of globular proteins (actually in a complex with a short stretch of DNA), but never a str...
Posted: Evgeny Fadeev 5771 / Updated: Justin Frank 1 Jun 27 '16 at 19:27

How do you find incorrectly assigned NOE restraints?

3 1 7k
answers votes views
So you've analyzed your NOE data sets and have 1000+ assigned restraints, with probably inevitable errors. Going through...
Updated: Evgeny Fadeev 5771 Mar 02 '10 at 09:09

How to display NMR structure of molecule with non-standard residues?

1 0 11779
answers votes views
... solving a structure of a cyclic peptide with Ornithine residue, where Orn side-chain participates in an amide bond. ...
Updated: Evgeny Fadeev 5771 Feb 02 '10 at 08:59

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