Search found 86 matches

by ckerr
2016.09.20 18:35
Forum: Ab Initio Shape Determination
Topic: multiple runs DAMMIN batch mode
Replies: 3
Views: 4282

Re: multiple runs DAMMIN batch mode

There's no way to do this from within DAMMIN. Instead, use some external program to call DAMMIN repeatedly.

e.g. on a bash terminal (Linux / Mac)

for ((N=0; N<10; N++))
do
dammin --lo=job$N [other dammin options]
done
by ckerr
2016.09.20 09:41
Forum: Mixtures and Flexible Systems
Topic: Average Rg in OLIGOMER
Replies: 1
Views: 1182

Re: Average Rg in OLIGOMER

It is calculated using the Rg values of the components The formula is: sum_i ( X(i) Rg(i)^2 I0(i) ) / sum_i ( X(i) I0(i) ) X(i) is the number concentration (e.g. mmol) of component i Rg(i) is its radius of gyration (computed from the form factor) I0 is the forward scattering (i.e. the value of the f...
by ckerr
2016.08.16 08:28
Forum: Mixtures and Flexible Systems
Topic: ffmaker crash
Replies: 1
Views: 1044

Re: ffmaker crash

Try running it from the command line (in windows: cmd.exe) - then the window won't close immediately and you will be able to see the error message.
by ckerr
2016.08.15 08:01
Forum: Primary Data Processing
Topic: Explanation of scattering curves - Help
Replies: 1
Views: 4353

Re: Explanation of scattering curves - Help

Do you mean the high Q region (0.2-0.35 inverse Angstrom)? It looks to me as if there is a slight error in the buffer subtraction - this will of course be more noticeable at the lower concentrations, so that the intensity does not fall off with concentration the way you would expect.
by ckerr
2016.07.20 13:24
Forum: Rigid Body Modelling
Topic: pre-bunch: no gap between the domains
Replies: 2
Views: 3483

Re: pre-bunch: no gap between the domains

pre_bunch uses its own PDB parser which only reads the alpha carbons, and then only when the 'CA' is in columns 14-15 (i.e. atom name is " CA "). Your PDB files have 'CA' in columns 15-16 (i.e. atom name is " CA"). See the PDB format specifications here: http://www.wwpdb.org/documentation/file-forma...
by ckerr
2016.07.19 08:37
Forum: Working with Models
Topic: CRYSOL prediction error
Replies: 2
Views: 3605

Re: CRYSOL prediction error

If the structure has voids, deep pockets, or extended unfolded chains, the prediction from crysol 2 will have systematic errors because of the way it calculates excluded volume (everything between the origin and the furthest atom in any given direction is considered to be excluded). Crysol 3 (the pr...
by ckerr
2016.07.19 08:31
Forum: Rigid Body Modelling
Topic: pre-bunch: no gap between the domains
Replies: 2
Views: 3483

Re: pre-bunch: no gap between the domains

My guess is that it is being too enthusiastic about aligning the sequences, thus putting them directly next to one another.

If you send me the PDB and sequence files at ckerr@embl-hamburg.de then I can take a look.
by ckerr
2016.07.14 17:11
Forum: Working with Models
Topic: CRYSON Bug in Batch Mode?
Replies: 3
Views: 3837

Re: CRYSON Bug in Batch Mode?

Thanks for reporting this, the bug has been fixed and the fix will be included in the next version of ATSAS
by ckerr
2016.07.04 10:53
Forum: Working with Models
Topic: Problem with upload Damaver program
Replies: 1
Views: 3167

Re: Problem with upload Damaver program

damaver only runs on the command line.
by ckerr
2016.07.04 10:51
Forum: Mixtures and Flexible Systems
Topic: What is the content of EOM's Size_listXXX.txt output file?
Replies: 1
Views: 1414

Re: What is the content of EOM's Size_listXXX.txt output fil

The EOM manual says in Size_listXXX.txt there would be the respective Rg and Dmax values. But I find four values in there, actually. Are those Rg, Dmax, Ca-Ca-distance and excluded volume (in this order)? How are those values calculated? Are they computed from the actual atomic positions in the pdb...
by ckerr
2016.06.17 08:39
Forum: ATSAS Package in General
Topic: Still Can't Install on OSX El Capitan version 10.11.4
Replies: 4
Views: 5271

Re: Still Can't Install on OSX El Capitan version 10.11.4

After opening the .tar.gz file you should get a folder called either 'ATSAS' or 'ATSAS-2.7.2'. This folder needs to be moved to the 'Applications' folder and renamed to 'ATSAS' You might need root access (sudo) to do this There are instructions here: http://www.embl-hamburg.de/biosaxs/manuals/instal...
by ckerr
2016.06.08 15:41
Forum: ATSAS Package in General
Topic: DAMMIF software
Replies: 2
Views: 4643

Re: DAMMIF software

Try C:\ATSAS or C:\ATSAS\bin
by ckerr
2016.06.08 09:15
Forum: ATSAS Package in General
Topic: Still Can't Install on OSX El Capitan version 10.11.4
Replies: 4
Views: 5271

Re: Still Can't Install on OSX El Capitan version 10.11.4

You need to unpack the downloaded package in /Applications/ATSAS (currently the files are in /Users/USER/Downloads)
by ckerr
2016.06.08 09:13
Forum: Ab Initio Shape Determination
Topic: Shape determination of porous nanostructures
Replies: 1
Views: 3798

Re: Shape determination of porous nanostructures

By "I only have the published plot" - do you mean the data that is plotted or the image file of the plot itself? If you only have the image file then there's not much you can do, short of hacking together some kind of computer vision program to extract the data back out from the plot.
by ckerr
2016.06.08 09:08
Forum: Working with Models
Topic: Different I(0) for Models of Same Protein
Replies: 2
Views: 4067

Re: Different I(0) for Models of Same Protein

The I0 in vacuum (3rd column in the .int file) is proportional to the number of electrons in the molecule - this should be the same for all models of a given polypeptide. However, the overall scattering also takes into account the scattering from the displaced solvent and the higher-density solvent ...