Search found 101 matches

by Hayds
2010.09.27 09:48
Forum: Rigid Body Modelling
Topic: Modelling a chimeric structure into SAXS envelope
Replies: 1
Views: 2601

Hi mtmurakami, first thing to try is to extract the sequence from the PDB file you have created and see if this matches the sequence you are using for input in BUNCH. A quick sequence alignment will show if there are some missing residues or "mutations". Occasionally with user projects I find that a...
by Hayds
2010.09.10 17:32
Forum: Mixtures and Flexible Systems
Topic: GAJOE terminates prematurely
Replies: 2
Views: 2742

Oh, also. If you have the distribution of EOM that includes example files, try from a fresh directory and run through this and see if the error still occurs.

h
by Hayds
2010.09.10 17:30
Forum: Mixtures and Flexible Systems
Topic: GAJOE terminates prematurely
Replies: 2
Views: 2742

Hi Alex,

so the generations are complete up until 50? Then the error message appears?

Which version of EOM (ranch/gajoe) are you using and on what OS?

I have not seen this behavior so I think I will need as much info as you can give.

Cheers,

Haydyn
by Hayds
2010.08.24 16:58
Forum: Rigid Body Modelling
Topic: BUNCH wont converge
Replies: 13
Views: 6828

Hi Tom, You could take a representative "compact" model from the EOM pool and a representative "extended" model from the EOM pool and run OLIGOMER. Maybe you can further support a 2-state conformational equilibrium this way? In the previous post is the BUNCH model fit shown that from the BUNCH progr...
by Hayds
2010.08.24 13:09
Forum: Rigid Body Modelling
Topic: BUNCH wont converge
Replies: 13
Views: 6828

Hi Tom, looking at the Rg profile it would appear that your protein is almost as flexible as the random pool, indicating a large degree of intra-molecular flexibility. I think you can trust this interpretation as by eye the fit of the EOM ensemble to the SAXS data looks very good. By eye does CRYSOL...
by Hayds
2010.06.30 07:52
Forum: Mixtures and Flexible Systems
Topic: EOM on LINUX error
Replies: 4
Views: 3078

No problem Alexandra, hope EOM gives you some good results - make sure that there is no chance of higher oligomers present though by a thorough primary analysis first :)

Best,

Haydyn
by Hayds
2010.06.29 17:25
Forum: Mixtures and Flexible Systems
Topic: EOM on LINUX error
Replies: 4
Views: 3078

Hi Alexandra,

I can't replicate this result with some test data. Could you please send me the data and input files (PM me), and also let me know which version of ranch/gajoe you use.

I'll see what I can do.

Best,

Haydyn
by Hayds
2009.12.12 21:20
Forum: Mixtures and Flexible Systems
Topic: SYMMETRY IN EOM
Replies: 2
Views: 3212

Hi Stefan, sorry to leave you hanging on an answer for so long. I am looking into this now. There is no symmetry enabled version of EOM at present. I will try and be pro-active about this in the group, of course it is a question of manpower and time (and my Fortran is terrible, so if I decide to do ...
by Hayds
2009.12.07 13:55
Forum: Mixtures and Flexible Systems
Topic: on generation of pdbs by GAJOE
Replies: 2
Views: 2754

Hi Ellen,

just to get some more information on the problem. Are any of the produced files empty? Other than the GA001.log file is there text in the other files?

Haydyn
by Hayds
2009.10.16 13:39
Forum: Primary Data Processing
Topic: Proportion of scattering data to use for GNOM
Replies: 2
Views: 3737

Hi Cougar, typically I would start with the Guinier region, ie. cut all points closer to the beam-stop than the first guinier point (obtained manually or using AutoRg). Also cut the points at higher angles where the curve gets noisy and is featureless. From there you start playing with the indirect ...
by Hayds
2008.11.30 21:29
Forum: Rigid Body Modelling
Topic: globsymm contacts
Replies: 1
Views: 2682

globsymm contacts

Hi gang, what exactly is the string I need to enter (from the input pdb file) to define a contact in Globsymm? At the prompt for the first atom of the pair do I enter an actual string: eg. CA THR A (directly from the PDB file) Or, if this is the first CA in the file maybe just: eg. 1 I'm pretty sure...