Search found 101 matches

by Hayds
2015.01.20 16:59
Forum: Mixtures and Flexible Systems
Topic: Gajoe on external pool error
Replies: 9
Views: 3562

Re: Gajoe on external pool error

Ah I see,

so you can run it successfully on a subset of this pool? Does GAJOE crash on a particular PDB file?

Haydyn
by Hayds
2015.01.20 14:25
Forum: Mixtures and Flexible Systems
Topic: Gajoe on external pool error
Replies: 9
Views: 3562

Re: Gajoe on external pool error

Hi Tiago,

could you please PM me the intensities file for your pool and the data (I will keep it confidential) and I will try and reproduce the error.

Cheers,

Haydyn
by Hayds
2014.11.12 17:07
Forum: ATSAS Package in General
Topic: ATSAS release 2.6.0
Replies: 0
Views: 6561

ATSAS release 2.6.0

Dear Small-Angle Scatterers, this message is to announce the new ATSAS release 2.6.0 The features of this release include: New Programs ============ * ambimeter: evaluates the ambiguity measure of the given scattering profile * dam2dam: regrids a dummy atom model onto another * datclass: classify sc...
by Hayds
2014.02.05 14:27
Forum: ATSAS Package in General
Topic: ATSAS release 2.5.2
Replies: 2
Views: 3428

ATSAS release 2.5.2

Dear Small-Angle Scatterers, this message is to announce a new update to ATSAS release 2.5. The features of this release include: Changes ATSAS-2.5.2 =================== Changes in programs ------------------- * almerge: minor fixes * autorg: works on data with outliers (very high intensity points),...
by Hayds
2013.03.23 07:30
Forum: Ab Initio Shape Determination
Topic: flexible tail in DAMMIF
Replies: 1
Views: 1789

Re: flexible tail in DAMMIF

Hi sevny,

are the P(r) functions different? Do you see a significant increase in Dmax for your larger construct?

Cheers,

Haydyn
by Hayds
2013.03.23 06:58
Forum: SAXS & SANS Software
Topic: Calculation of intensity errors in Background subtraction
Replies: 2
Views: 6499

Re: Calculation of intensity errors in Background subtractio

Hi HLee,

i think you also need to divide by n, where n is the number of "files".

eg. Err = SQRT( (Int_1)^2 + (In_2)^2))/n

(with n=2 here).

I think that is what's typically done. Does that make sense to any stats wizz's out there?

Cheers,

Haydyn
by Hayds
2012.06.04 04:38
Forum: Ab Initio Shape Determination
Topic: Conversion of FLM and SLD files to PDB
Replies: 2
Views: 2305

Re: Conversion of FLM and SLD files to PDB

Yep, I was thinking the same thing, but am still unsure how to get em2dam to do what I want in this case. I think I need to understand how to use the multipole coefficients to generate something three-dimensional (ie. the SLD file), and then I might be getting somewhere.

Thanks old guy, \m/

h
by Hayds
2012.06.01 14:55
Forum: Ab Initio Shape Determination
Topic: Conversion of FLM and SLD files to PDB
Replies: 2
Views: 2305

Conversion of FLM and SLD files to PDB

Hi gang,

has anyone worked out the best way to convert .flm and .sld files from SASHA/MASSHA to PDB files? I would like to compare some of the "old-school" models with some new ones for a workshop.

Thanks for any insights!

Haydyn
by Hayds
2012.02.21 08:30
Forum: SAXS & SANS Software
Topic: Pair distance distribution vs electron density distribution
Replies: 1
Views: 4997

wsDens

Hi Caner, the ATSAS package does not have any tools for you to do this, however, Jan Skov Pedersen has an approach in a program called wsDens which will generate a radial-density distribution from the output of WIFT (and in principle GNOM, but I have found that to be tricky). These packages form par...
by Hayds
2011.12.22 14:55
Forum: Ab Initio Shape Determination
Topic: MONSA online MONSA offline - Connectivity comparison
Replies: 9
Views: 5122

Cheers Al,

you rock!

:D

h
by Hayds
2011.12.22 03:01
Forum: Ab Initio Shape Determination
Topic: MONSA online MONSA offline - Connectivity comparison
Replies: 9
Views: 5122

Sorry James, Maxim is right. I was confused by this line in the manual: -- Line 4 Connectivity indicators of phases (free format) (if jConn.NE. 0, phase is interconnected) REQUIRED) -- Which of course means that if the CONNECTED flag is NOT set to 0, the phase will be disconnected (ie. if set to 1, ...
by Hayds
2011.12.21 01:04
Forum: Ab Initio Shape Determination
Topic: MONSA online MONSA offline - Connectivity comparison
Replies: 9
Views: 5122

Hmmm. Ok, I'll see if the master can set us straight. This is indeed confusing.

h
by Hayds
2011.12.20 00:26
Forum: Ab Initio Shape Determination
Topic: MONSA online MONSA offline - Connectivity comparison
Replies: 9
Views: 5122

No worries James!

As for the symmetry definition, I'm not sure. To be honest I haven't needed that option yet :)

Maybe Maxim will set us straight?

h
by Hayds
2011.12.19 06:42
Forum: Ab Initio Shape Determination
Topic: quick monsa question
Replies: 7
Views: 6758

Hi ankitgpta,

one of the problems usually is not having a comment or blank line in the data files. MONSA is very picky about this. The rest of the set-up should be the same I think between the online and stand alone versions.

Cheers,

Haydyn
by Hayds
2011.12.19 03:11
Forum: Ab Initio Shape Determination
Topic: MONSA online MONSA offline - Connectivity comparison
Replies: 9
Views: 5122

Hi James, in the MONSA manual http://www.embl-hamburg.de/biosaxs/manual_monsa.html you can define the "connected-ness" on line 4 of the master file: eg. Master file for PROT 55.0 21 0.0 0.0 -1.0 -1.0 0.0 0.0 0 1 0.0 0.0 'prot1_500pts.con' -1 'prot2_500pts.con' -1 This specifies that phase 2 (volume ...