Search found 696 matches

by Alex
2020.05.27 17:29
Forum: Mixtures and flexible systems
Topic: linker residue representation
Replies: 1
Views: 621

Re: linker residue representation

I am doing eom analysis on a two-domain structure with a linker in between. I entered both the sequence file and the pdb files for both the domains. The problem is that the output pdb file with the linker only displayed as the central carbon atom (i.e. only one atom per residue) which prevents prop...
by Alex
2020.03.10 21:46
Forum: Mixtures and flexible systems
Topic: maximum number of curves in the random pool
Replies: 4
Views: 595

Re: maximum number of curves in the random pool

Great! Thanks! i get back with some feedback at some point.
by Alex
2020.02.26 20:19
Forum: Mixtures and flexible systems
Topic: maximum number of curves in the random pool
Replies: 4
Views: 595

Re: maximum number of curves in the random pool

hey Hayds!
better long time than never :)
anyway, thanks for the reply! i don't use RANCH for generating the models, and the number of models can be very very big.
Could you please check the size of the array in GAJOE?
thanks in advance
Alex
by Alex
2020.02.11 14:43
Forum: Mixtures and flexible systems
Topic: maximum number of curves in the random pool
Replies: 4
Views: 595

maximum number of curves in the random pool

what is the maximum size of the random pool that GAJOE can work with?
I have a really large external pool and wonder to which extend i can extend it?
Alex
by Alex
2020.02.11 14:38
Forum: Mixtures and flexible systems
Topic: Discrepance between EOM and Crysol model dimentions
Replies: 2
Views: 4216

Re: Discrepance between EOM and Crysol model dimentions

So, I used Crysol to simulate the scattering of the models generated by the EOM software and noticed a discrepancy between the values of Rg and Dmax obtained using the two softwares. just note that EOM uses CRYSOL in a non-fitting mode. if you use CRYSOL in fitting mode with '--keep' the results ma...
by Alex
2017.09.25 16:56
Forum: Mixtures and flexible systems
Topic: Gajoe -p command line options
Replies: 1
Views: 1896

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: 6907

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: 6907

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: 4277

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: 4277

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: 10481

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: 5842

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: 1484

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: 4737

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: 4737

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...