Search found 7 matches

by tmulhern
2010.04.29 08:28
Forum: Mixtures and Flexible Systems
Topic: svdplot
Replies: 1
Views: 2619

svdplot

Hi guys, I can get svdplot to run and analyse four curves indicating two species are present, but I don't seem to get any output other than the text in the command window and the associated plot. Are there output files with those curves? Also, I am not sure how to interpret those curves. Does svdplo...
by tmulhern
2008.12.01 00:58
Forum: Working with Models
Topic: SANS I(s) prediction for prot-duet protein complex
Replies: 1
Views: 3059

SANS I(s) prediction for prot-duet protein complex

Hi, I want to use CRYSON to predict the I(s) profiles for a protein complex where one component is deuterated. Reading the paper it seeems CRYSON calculates scattering lengths based only on exchange of hydrophillic side chain NHn, OH and SH groups and backbone NH groups. E.g How do I incorporate inf...
by tmulhern
2008.11.28 00:06
Forum: Mixtures and Flexible Systems
Topic: adding a structure to the pool
Replies: 3
Views: 4730

adding a structure to the pool

Hi, I am looking a protein that where the two domains that can become dislocated. I believe the SAXS profile represents folded protein plus a small fraction of dislocated protein. I generated a pool with the two domains in random orientations, and the gajaoe output agrees with my intial hypothesis, ...
by tmulhern
2008.11.27 23:56
Forum: Mixtures and Flexible Systems
Topic: loop modeling in EOM
Replies: 1
Views: 2777

loop modeling in EOM

Hi,

Want to model a long felxible loop in EOM. Is there a direct way of doing it, or do I need to define the two parts of the PDB as separate domains and then fix their positions? I couldn't see how to fix positions in EOM.

Terry
by tmulhern
2007.11.26 00:44
Forum: Mixtures and Flexible Systems
Topic: contacts in BUNCH
Replies: 6
Views: 6793

Problem solved!

It was a syntax problem after all. :D I was unaware the th 1st and 4th numbers were chain identifiers and not subunit identifiers. I have it working now. By the way, the tutorial contacts.cnd file for the gst-dhfr should be changed accordingly to 1 and 1, as that is a single chain multidomain exampl...
by tmulhern
2007.11.23 02:15
Forum: Mixtures and Flexible Systems
Topic: contacts in BUNCH
Replies: 6
Views: 6793

BUNCH contacts

This is the error message when attempting the GST-DHRF tutorial - E -- worng format of conditions file 1 77 77 2 86 86 ---------------------------------- Here is the contents of the condition file dist 7.0 1 77 77 2 86 86 dist 7.0 1 69 69 2 97 97 This is unchanged from the files distributed. I get t...
by tmulhern
2007.11.21 08:14
Forum: Mixtures and Flexible Systems
Topic: contacts in BUNCH
Replies: 6
Views: 6793

contacts in BUNCH

I am using the windows version of BUNCH 8.0 and it won't read my .cnd file. So, I tried the tutorial gst-dhfr and it also would not read the associated .cnd file. Is it just me or is this a bug?