Search found 36 matches

by grondinjm
2014.08.22 15:02
Forum: Ab Initio Shape Determination
Topic: DAMMIF - low Chi
Replies: 2
Views: 2422

DAMMIF - low Chi

This topic has been brought up before but the thread was old, so I thought I'd reanimate it. I am getting chi values of about 0.3 in DAMMIF for two separate samples. The fit and P(r) of the GNOM are good in both cases. I have read previously that the error estimates (I assume in GNOM) are too high, ...
by grondinjm
2014.08.20 22:25
Forum: Ab Initio Shape Determination
Topic: Chi-sqaured too low
Replies: 4
Views: 4124

Re: Chi-sqaured too low

I am having the same issue. Data is from CHESS G1 beamline and to my knowledge the beamline operator did not change the error estimates (or at least didn't tell me about it).

How do we go about manually changing the error estimates?
by grondinjm
2014.07.28 20:48
Forum: Mixtures and Flexible Systems
Topic: sequence mess up after generating random pool
Replies: 7
Views: 4640

Re: sequence mess up after generating random pool

The problem is that alignment and colouring by domain is near impossible if the sequences are all jumbled. If you just want to show the whole thing in one colour with no alignment then there's no issue. The solution to the problem seems to be a simple renumbering python script. Protein now looks nor...
by grondinjm
2014.07.28 20:35
Forum: Rigid Body Modelling
Topic: BUNCH - forcing domains apart
Replies: 4
Views: 3493

Re: BUNCH - forcing domains apart

1. Conveniently, I collected on SWING at SOLEIL! Also, I think we have found a solution to the problem. To follow up on the test I did with my friend, we figured out that there is something strange going on with the prebunch.pdb I was using. Using the same .pdbs to create .alm in the same manner wit...
by grondinjm
2014.07.27 03:19
Forum: Rigid Body Modelling
Topic: BUNCH - forcing domains apart
Replies: 4
Views: 3493

Re: BUNCH - forcing domains apart

1. Actually you might be able to help me with this since we aren't sure how to go about this: we used online HPLC-SAXS to collect this data on an instrument that uses water as a standard, so I am not sure how to calculate MW based on this. Emails to beamline operators have not been returned, and my ...
by grondinjm
2014.07.25 17:27
Forum: Rigid Body Modelling
Topic: BUNCH - forcing domains apart
Replies: 4
Views: 3493

BUNCH - forcing domains apart

Hello, BUNCH modelling of a 2-domain protein connected by a linker (13aa) is giving models in which the 2 domains are pushed together and the linker is shoved up inside one of the domains. How would I write the .cnd file such that a minimum distance is enforced between the domains? I'm not sure what...
by grondinjm
2014.07.24 20:28
Forum: Primary Data Processing
Topic: Questions about primary analysis
Replies: 1
Views: 2037

Questions about primary analysis

Hi all, A few questions regarding scaling, ALMERGE and data truncation: 1. I have been advised on this forum that prior to merging/extrapolating, ALMERGE assumes that the data is normalized to concentration aka. scaled. I have 2 samples in which I used different techniques: a) Dr. Kikhney helped me ...
by grondinjm
2014.06.20 17:18
Forum: Mixtures and Flexible Systems
Topic: sequence mess up after generating random pool
Replies: 7
Views: 4640

Re: sequence mess up after generating random pool

I'm also having this issue where the sequences are all jumbled. I realize this was uploaded a year ago, but the link to the script gives me a 404 error. The other issue is that regardless of the sequences being jumbled, I can't visualize the domains in 'cartoon' form in PyMOL - I get these disjointe...
by grondinjm
2014.06.20 16:37
Forum: Primary Data Processing
Topic: Extrapolating in ALMERGE
Replies: 4
Views: 2609

Re: Extrapolating in ALMERGE

- Extrapolation using only 2 curves in multiple combinations gives the same result.
- The Rg is exactly the same at all three concentrations (~42).
- Attached are the scaled curves.
by grondinjm
2014.06.19 20:47
Forum: Mixtures and Flexible Systems
Topic: "NaN" error in EOM + general question
Replies: 10
Views: 3445

Re: "NaN" error in EOM + general question

The raw data of sample and buffer match very well at high q.
by grondinjm
2014.06.19 19:31
Forum: Primary Data Processing
Topic: Extrapolating in ALMERGE
Replies: 4
Views: 2609

Extrapolating in ALMERGE

Hello! I have previously used ALMERGE's extrapolation tool on three curves, and the result was a curve which I have used successfully for BUNCH, EOM etc. Here I was using the three most concentrated curves from a series of five as previous merging attempts were giving poor curves using very dilute s...
by grondinjm
2014.06.05 00:25
Forum: Mixtures and Flexible Systems
Topic: "NaN" error in EOM + general question
Replies: 10
Views: 3445

Re: "NaN" error in EOM + general question

Sorry, I made a mistake. The buffer subtracted is from the online HPLC-SAXS run. We injected the sample and collected 100+ curves spanning the elution of the protein from the column. The buffer curve we choose to subtract comes prior to the void volume of the column, so the buffers should be the sam...
by grondinjm
2014.06.04 20:41
Forum: Mixtures and Flexible Systems
Topic: "NaN" error in EOM + general question
Replies: 10
Views: 3445

Re: "NaN" error in EOM + general question

1. As in my other post in the BUNCH forum, I can't get the extrapolation to work following the instructions given. I get an error that my concentrations cannot be read. Could you please provide an example of how to get almerge to extrapolate? Or explain the example in the manual a little further? 2....
by grondinjm
2014.06.04 17:39
Forum: Rigid Body Modelling
Topic: Problem getting good chi values in BUNCH
Replies: 12
Views: 6508

Re: Problem getting good chi values in BUNCH

Ok, that makes sense. I tried almerge but I'm not sure I did it properly. Here is how I ran it according to the manual and the results. I should note that concentration cannot be read from my headers. $ almerge conc10.dat conc5.dat conc25.dat conc175.dat conc125.dat Concentration Overlap File ? (ref...
by grondinjm
2014.06.04 17:08
Forum: Mixtures and Flexible Systems
Topic: "NaN" error in EOM + general question
Replies: 10
Views: 3445

Re: "NaN" error in EOM + general question

Attached are the PDB files of the two rigid bodies and the sequence of the full construct. Please delete once you are finished - thanks! I should point out that the cat.pdb represents a single domain (chain A) but there is some density missing (if you try to extract a sequence using a PDB-->Fasta co...