Search found 691 matches

by Alex
2017.09.25 16:56
Forum: Mixtures and Flexible Systems
Topic: Gajoe -p command line options
Replies: 1
Views: 1462

Re: Gajoe -p command line options

perhaps try to put all your answers in the text file and run, like: $> gajoe -p < myanswers.txt
by Alex
2017.05.12 18:50
Forum: Rigid Body Modelling
Topic: which alm for bunch ?
Replies: 4
Views: 4786

Re: which alm for bunch ?

the problem is that it is not that flexible... it's best to check dKratky plot preferably with reference folded/unfolded proteins. Or have some additional evidence from CD spectra, for example. Based on result, you can judge about level and regions of flexibility. To me it sounded like that you hav...
by Alex
2017.05.12 15:42
Forum: Rigid Body Modelling
Topic: which alm for bunch ?
Replies: 4
Views: 4786

Re: which alm for bunch ?

you should take the original structure with n-term and c-term removed.

If it is that flexible (as you can see from comparative dimensionless Kratky plot), you better use EOM and let it output PDB files. This you
will get a large random pool with variable conformation of flexible parts.

HTH, Alex
by Alex
2017.05.11 18:12
Forum: Mixtures and Flexible Systems
Topic: EOM not writing fit file
Replies: 11
Views: 2806

Re: EOM not writing fit file

normally, i don't use EOM suite as a single program. Typically, i would run RANCH to generate random pool and then GAJOE to do a selection. GAJOE should generate GA0*/ directory with *.fit file. Why don't you just try to run GAJOE now? Although it should work like you wrote as well. I think it would...
by Alex
2017.05.11 15:34
Forum: Mixtures and Flexible Systems
Topic: EOM not writing fit file
Replies: 11
Views: 2806

Re: EOM not writing fit file

RANCH will never output *.fit file. GAJOE should always output *.fit file. So you should be more specific when you encounter the problem.
Alex
by Alex
2017.05.08 17:53
Forum: Primary Data Processing
Topic: Zero extrapolation using Primus qw
Replies: 3
Views: 8438

Re: Zero extrapolation using Primus

One has to analyze each set separately and try to decompose it in terms of fraction of oligomer species.
by Alex
2017.04.25 11:55
Forum: Primary Data Processing
Topic: Normalizing P(r)
Replies: 2
Views: 4105

Re: Normalizing P(r)

typically, you have to normalize P(R) function to unity by dividing by max value of P(R) function. This way you
can compare different P(R) functions.
by Alex
2017.04.06 12:38
Forum: Mixtures and Flexible Systems
Topic: Oligomer maximum number of curves in form factor file?
Replies: 1
Views: 1097

Re: Oligomer maximum number of curves in form factor file?

i think Oligomer is meant for limited number of conformations, assuming your system is not that flexible. If your system is flexible, i believe you should use EOM. Perhaps, one can play with number of curves per ensemble setting it to a very high number (i have not tried more that 50-100 though). HT...
by Alex
2017.04.03 17:38
Forum: Mixtures and Flexible Systems
Topic: Attempting to Use EOM with Ig Fragments
Replies: 7
Views: 3761

Re: Attempting to Use EOM with Ig Fragments

Please, do update this thread with your successful "recipe".
by Alex
2017.03.31 11:39
Forum: Mixtures and Flexible Systems
Topic: Attempting to Use EOM with Ig Fragments
Replies: 7
Views: 3761

Re: Attempting to Use EOM with Ig Fragments

Hi Kento 1)Should I treat this structure as homo-dimer? If I treat this structure as dimer, it needs to input P2 symmetry. you can try doing that, but then you need to align Fab domain dimer to Z-axis (using alpraxin program), then also specify, the contact conditions (which i think also should be p...
by Alex
2017.03.26 17:50
Forum: SAXS & SANS Software
Topic: datasw - tool to analyse HPLC-SAXS data
Replies: 2
Views: 9951

Re: datasw - tool to analyse HPLC-SAXS data

Dear All,

Update of DATASW is now available:
https://sourceforge.net/projects/datasw ... tasw-v1.2/

Changes since DATASW v1.1 include following:
* compatible with latest ATSAS 2.8.0
* a number of fixes and improvements
* DATASW now depends on GNUPLOT/QT

Thank you for using DATASW!
Alex
by Alex
2017.03.22 11:00
Forum: Primary Data Processing
Topic: datclass: parse error (only on Ubuntu 14.04)
Replies: 2
Views: 4349

Re: datclass: parse error (only on Ubuntu 14.04)

Hi Daniel
yeah, you are right - i started with installation using *tar.gz and had ATSAS variables
set in my bashrc, whereas then i switched to synaptic manager installation without reverting changes
in my bashrc.

thanks, Alex
by Alex
2017.03.21 22:45
Forum: Primary Data Processing
Topic: datclass: parse error (only on Ubuntu 14.04)
Replies: 2
Views: 4349

datclass: parse error (only on Ubuntu 14.04)

I installed ATSAS 2.8.0 using synaptic package manager on ubuntu 14.04. when using 'datclass' i get the following error: $ /usr/bin/datclass --rg=2.96 --i0=88.2 bsa_00583.out : parse error $ /usr/bin/datclass --rg=2.96 --i0=88.2 bsa_00583.dat : parse error and ..:) /usr/bin/datclass : parse error Ot...
by Alex
2017.03.13 16:25
Forum: Primary Data Processing
Topic: How can I determine the data's Dmax with the ATSAS(2.8)?
Replies: 2
Views: 4122

Re: How can I determine the data's Dmax with the ATSAS(2.8)?

How can I determine the data's Dmax accurately with the ATSAS(2.8)? In which gnom has no interactive mode to view the p(r) function variation while I changing the value of Dmax. Is not there an interactive mode for determining Dmax in Primus? Is the Dmax value important for the beads model building...
by Alex
2017.03.08 14:50
Forum: Working with Models
Topic: CRYSOL:deal with the missing part in the pdb file?
Replies: 2
Views: 4124

Re: CRYSOL:deal with the missing part in the pdb file?

and how can i add the missing part to the structural model to make it complete?
use BUNCH and/or CORAL.