Search found 15 matches

by jmarie
2018.11.12 11:50
Forum: Mixtures and Flexible Systems
Topic: EOM of dimer with missing loops
Replies: 1
Views: 3098

Re: EOM of dimer with missing loops

Hi
Did you see this post
viewtopic.php?f=10&t=3822&hilit=eom+dimer+of+dimers

It might help you
Cheers
JM
by jmarie
2018.11.07 13:53
Forum: Mixtures and Flexible Systems
Topic: EOM alpha Helices swapping
Replies: 0
Views: 6274

EOM alpha Helices swapping

I obtained pretty good SAXS data on a monomeric protein which contains 6 a-helices bundle . The crystal structure of this monomeric form is known but doesn’t fit with my SAXS data using Crysol. It is certainly due to a very high flexibility of my protein. From the N-term to the C-term there are 6 a-...
by jmarie
2017.10.20 11:06
Forum: Mixtures and Flexible Systems
Topic: EOM - Using two models with internal P2 symmetry
Replies: 12
Views: 7226

Re: EOM - Using two models with internal P2 symmetry

Dear All I got a similar problem of two models with internal P2. But this time with a relatively long IDR at the Nter. from the picture you can see the organisation of my protein: eom-dim.png 1- Nter linker (50aa), 2- first dimer interface with the pdb. 3- then another linker (110 aa) 4- finally the...
by jmarie
2016.09.08 11:10
Forum: Rigid Body Modelling
Topic: Transform Ca chain (from eom or coral) to a full atoms chain
Replies: 6
Views: 6583

Re: Transform Ca chain (from eom or coral) to a full atoms c

Thanks Alex

I thought there will be a easiest way.
I have plenty files to convert, so it's better if try first by myself.
If I fail I will come back to you.
Thanks again
by jmarie
2016.09.06 12:51
Forum: Rigid Body Modelling
Topic: Transform Ca chain (from eom or coral) to a full atoms chain
Replies: 6
Views: 6583

Re: Transform Ca chain (from eom or coral) to a full atoms c

Dear Alex
do you think it will be possible for me to try it.
Thanks in advance
JM
by jmarie
2016.09.05 17:15
Forum: Rigid Body Modelling
Topic: Transform Ca chain (from eom or coral) to a full atoms chain
Replies: 6
Views: 6583

Transform Ca chain (from eom or coral) to a full atoms chain

Dear all,
Do you know a way to change the CA obtain from EOM or Coral to a real backbone (with peptide bonds) and then to applied the sequence (to get the side chains).
The goal is to obtain a full atom model.
Thanks in advance
JM
by jmarie
2016.01.08 10:50
Forum: Primary Data Processing
Topic: different concentration superposition
Replies: 7
Views: 3723

Re: different concentration superposition

Hi
Can we know on which synchrotron you did you experiment.
Thx
JM
by jmarie
2015.05.18 17:01
Forum: Mixtures and Flexible Systems
Topic: GAJOE - version 2.1 - (r4556) ERROR
Replies: 3
Views: 2183

GAJOE - version 2.1 - (r4556) ERROR

Dear all When I run the new version of GAJOE 2.1 using old Ranch 2.0 ensemble I get at the end of the selection this error message: "At line 1119 of file /home/atsas/svn/2.6.0/atsas/eom/ranch_application.f90 (unit = 11, file = './2H.log') Fortran runtime error: Bad value during integer read" :? :? :...
by jmarie
2013.07.31 15:44
Forum: Primary Data Processing
Topic: Buffer and protein subtraction
Replies: 1
Views: 3329

Buffer and protein subtraction

Hi At large concentration (20 mg/ml) of my protein (6.5Kda) I notice a strong deviation form the buffer at high q (see picture1). However around 3.5 nm the signals are parallels as you can see on the close (picture2) up where I scaled both curves. I'm pretty sure that the buffer is corresponding to ...
by jmarie
2013.06.11 16:48
Forum: Working with Models
Topic: Crysol with and without fitting
Replies: 1
Views: 2638

Crysol with and without fitting

Hi I've just compared the curves from Crysol (last version 2.8.2) with and without fitting with an experimental curve. I was a bit surprised that the shape of two curves are different roughly below the Guinier zone. After that point the two forms factors are clearly different... Is that normal and w...
by jmarie
2012.02.28 13:39
Forum: Ab Initio Shape Determination
Topic: MONSA - average jobs
Replies: 9
Views: 8304

Monsaver

Hi
I just want to know if there is an "official" alternative to Monsaver, in order to average Monsa results. thanks in advance
Jean-Marie
by jmarie
2011.11.04 19:02
Forum: Rigid Body Modelling
Topic: Coral choice of scatering curves
Replies: 1
Views: 2192

Coral choice of scatering curves

Hello everyone I must admit I didn’t understand well: How coral knows which scattering curves use? For instance I have an interaction between A and B A is form by A1 and A2 The individual structure of A1 and A2 are known separately The structure of B is known The complex AB is not known as well as a...
by jmarie
2010.06.30 09:22
Forum: Rigid Body Modelling
Topic: Merge and Maths
Replies: 1
Views: 2309

Merge and Maths

Hi
Easy question (for teaching purposed)

What is behind the merge button of primus ?

More precisely I'm looking for the maths behind this function of Primus. Does anyone knows how merge works in details. And if there are other approaches to perform this step?
Thanks in advance

JM :?:
by jmarie
2010.05.31 14:00
Forum: Ab Initio Shape Determination
Topic: Monsa symmetry of one partner
Replies: 2
Views: 3612

Monsa symmetry of one partner

Hi I'm trying to characterize an interaction between two proteins by SAXS. I ve the scattering curves for each partner, and for the complex (curve A, curve B and a curve for AB). "A" as no symmetry, "B" is a disulphide bridge homo trimmer with a P3 symmetry. Is there away in MONSA to notify that B i...
by jmarie
2009.01.12 11:50
Forum: Rigid Body Modelling
Topic: homodimer with 2domains per monomer
Replies: 2
Views: 3971

homodimer with 2domains per monomer

Hi My problem is : I have a homodimer and the SAXS data of it. Each monomer is made by two domains. I have the structure of each individual domain. However I have no indication of the structure of the monomer, not even of the linker in between the monomers. My question is it possible to reconstruct ...