Search found 6 matches

by jcopps
2013.01.15 21:30
Forum: Rigid Body Modelling
Topic: Coral P2 Symmetry contacts
Replies: 15
Views: 16728

Re: Coral P2 Symmetry contacts

As a followup question, I've noticed that CORAL does not seem to correctly identify separate chains from my conditions file, which is written in the format I specified in my previous post. I'm dealing with a two chain system with P2 symmetry (so four chains total), and I'm trying to specify contacts...
by jcopps
2013.01.15 05:06
Forum: Rigid Body Modelling
Topic: Coral P2 Symmetry contacts
Replies: 15
Views: 16728

Re: Coral P2 Symmetry contacts

How does one specify contacts between P2 symmetry mates in CORAL? If I have a dimer and I want to create a contact of 2A between corresponding residues (let's say Leu1), do I write:

dist 2
1 1 1 1 1 1

or does the symmetry mate become its own chain, thus:

dist 2
1 1 1 2 1 1

Thank you
by jcopps
2009.04.06 19:42
Forum: Rigid Body Modelling
Topic: Bunch and protein protein interaction
Replies: 4
Views: 5733

Hello, I'm reading my question again now, and I don't think I described the situation accurately. My tetramer is something like the following: B-A-A-B, where A and B are distinct polypeptide chains. What I have in terms of crystal structures: 1) the N-terminus of both the A monomers in one crystal s...
by jcopps
2009.02.20 01:56
Forum: Rigid Body Modelling
Topic: Bunch and protein protein interaction
Replies: 4
Views: 5733

Rigid modeling w/ multiple peptide chains, missing structure

I have a related question. I have SAXS data for a tetrameric structure (formed by two heterodimers), and known crystal structure for one of the monomers, with partial known structure for the other monomer. Which program do I use to fit the SAXS data to these structures? I was suggested to use BUNCH,...
by jcopps
2009.01.14 21:10
Forum: Ab Initio Shape Determination
Topic: "Independent" parts of protein in GASBOR models
Replies: 1
Views: 2772

"Independent" parts of protein in GASBOR models

Hello, I am attempting to model in GASBOR a heterodimer complex (630 residues) which forms into a tetramer (2 heterodimers, 1260 residues) in solution. I am not sure which residues need to be specified as the "independent part of the particle" as mentioned in the GASBOR manual. Do I specify 630 resi...
by jcopps
2008.12.31 02:13
Forum: Working with Models
Topic: Can't get DAMAVER automated mode to work on Linux
Replies: 1
Views: 3252

Can't get DAMAVER automated mode to work on Linux

Hello, My apologies for a rudimentary question. I am attempting to use DAMAVER to average 10 DAMMIN models of a ~150 kD protein complex. However, while the individual programs seem to operate correctly, I cannot run "automated" mode. Running ./damaver.l86 /a simply causes the following to be printed...