Search found 44 matches

by Yann
2018.08.05 21:32
Forum: Ab Initio Shape Determination
Topic: DAMMIN_error_starting_guess_PDB
Replies: 3
Views: 6285

Re: DAMMIN_error_starting_guess_PDB

Hi all, I have a similar question. I am currently working on a protein that forms an octamer in solution (we have native MS, SEC-MALLS, DLS, analytical SEC, and SAXS to support this). I am no working on getting an ab initio shape. I ran DAMMIF multiple times to generate about 20 ab initio models in ...
by Yann
2016.10.05 15:53
Forum: Primary Data Processing
Topic: ALMERGE question
Replies: 2
Views: 3975

Re: ALMERGE question

Found it for those interested. The concentration must be on line 25 of the dat file (before the data) and must be given in as 'Concentration: 0.1' if the sample has a concentration of 0.1 mg/ml.

ALMERGE will now find the concentration in the file header.

Cheers,

Yann
by Yann
2016.10.05 11:28
Forum: Primary Data Processing
Topic: ALMERGE question
Replies: 2
Views: 3975

ALMERGE question

Hi, I am trying to use ALMERGE for a zero concentration extrapolation. I fail to produce any output, because ALMERGE has trouble reading the concentration from my .dat files. Does the concentration have to be entered in the .dat file in a specific way or on a specific line for ALMERGE to find it? Al...
by Yann
2014.11.28 17:10
Forum: ATSAS Package in General
Topic: ATSAS 2.6.0 fail in Mac OSX
Replies: 2
Views: 2470

ATSAS 2.6.0 fail in Mac OSX

Hi guys, I just installed the new ATSAS, but it does not seem to be working. For instance, when I try to run crysol, I get dyld: Library not loaded: /Applications/ATSAS/lib/libsaxsdocument.1.dylib Referenced from: /Applications/ATSAS_v2p6/bin/crysol Reason: image not found Trace/BPT trap: 5 Also, do...
by Yann
2014.03.06 23:30
Forum: Primary Data Processing
Topic: Influence of iron-heme on scattering data?
Replies: 8
Views: 4609

Re: Influence of iron-heme on scattering data?

Hi Alex,

I did that and always get around 34kDa - 35kDa which are the expected molecular masses for monomers.

Maybe some aspecific oligomerization in the case of the holo protein.

Thanks again,

Yann
by Yann
2014.03.06 20:46
Forum: Primary Data Processing
Topic: Influence of iron-heme on scattering data?
Replies: 8
Views: 4609

Re: Influence of iron-heme on scattering data?

Ah ok, that simple :). Didn't know I could zoom. Nope, the apo form does not seem to do that. We do know that the holo can only interact with its partner when it has the iron-heme. When it is apo, it does not bind its partner. Maybe there is some self-self interaction once the protein becomes holo, ...
by Yann
2014.03.06 18:36
Forum: Primary Data Processing
Topic: Influence of iron-heme on scattering data?
Replies: 8
Views: 4609

Re: Influence of iron-heme on scattering data?

Hi Alex, no, the data was collected at the ESRF in Grenoble in batch mode. Well, what could then explain the 'aggregation' is that the iron-heme does decrease the solubility of the protein, so we probably have the formation of some higher-order oligomers as you suggest. Maybe a bit of a naive questi...
by Yann
2014.03.06 13:59
Forum: Primary Data Processing
Topic: Influence of iron-heme on scattering data?
Replies: 8
Views: 4609

Re: Influence of iron-heme on scattering data?

Hi Alex, wasn't really trying to 'blame' PRIMUS here. Maybe I formulated my concern the wrong way, mea culpa. From your post I conclude that the tail I see in the p(r) function for Holo is real then? We do have a concern that the iron-heme might 'leak' out from the protein as the iron-heme is NOT co...
by Yann
2014.03.06 11:55
Forum: Primary Data Processing
Topic: Influence of iron-heme on scattering data?
Replies: 8
Views: 4609

Influence of iron-heme on scattering data?

Hi all, I am working with the holo and apo form of a cytochrome c peroxidase. The MM of the apo form is 34.4 kDa. The presence of the iron-heme in the protein increases the MM to 35.1 kDa. Both data sets were collected in batch mode. There were some small concentration-dependent effects, but after t...
by Yann
2013.09.17 12:30
Forum: Rigid Body Modelling
Topic: SASREF combined with BUNCH or CORAL
Replies: 17
Views: 11458

Re: SASREF combined with BUNCH or CORAL

Hi Alex,

just post my pdb here or send you a mail with my pdb file?

Thanks a bunch!

Yann

PS: Guess you'll also need my experimental data
by Yann
2013.09.17 12:12
Forum: Rigid Body Modelling
Topic: SASREF combined with BUNCH or CORAL
Replies: 17
Views: 11458

Re: SASREF combined with BUNCH or CORAL

Hi Alex, big indeed! AllosMod indeed uses MODELLER and I used FOXS with the default settings (uses hydration layer to improve fit). I tried to use CORAL, but it always stopped with the error message 'STOP cannot build C-terminal'. Don't know what went wrong there... The data set was recorded at the ...
by Yann
2013.09.17 11:29
Forum: Rigid Body Modelling
Topic: SASREF combined with BUNCH or CORAL
Replies: 17
Views: 11458

Re: SASREF combined with BUNCH or CORAL

Hi Alex, thanks for your quick reply. Yes, I'll explain my problem. I have a crystal structure of a complex comprising 16 subunits: it is hexadecamer built up of 8 heterodimers. All of them have affinity tags, which are not visible in the structure, but are there. One partner has an N-terminal FLAG-...
by Yann
2013.09.17 09:02
Forum: Rigid Body Modelling
Topic: SASREF combined with BUNCH or CORAL
Replies: 17
Views: 11458

Re:

Hi guys, I was wondering if there is already any software available for NMA-assisted refinement of structures against SAXS data. At the moment we are trying to model overall changes which occur upon complex formation using NMA and SAXS. Although, it is probably the easiest possible scenario - modeli...
by Yann
2013.02.12 18:50
Forum: ATSAS Package in General
Topic: ATSAS installation guide for the Mac
Replies: 22
Views: 12896

Re: ATSAS installation guide for the Mac

Hi Daniel,

now it works: the path was indeed empty!

Thanks for all your help ;),

Yann
by Yann
2013.02.12 18:31
Forum: ATSAS Package in General
Topic: ATSAS installation guide for the Mac
Replies: 22
Views: 12896

Re: ATSAS installation guide for the Mac

Hi Daniel,

I downloaded the new package. I can open Primus now, but whatever I try to do, I get the following message (see picture).

Thanks for your help,

Yann