Search found 44 matches

by Yann
2013.02.12 12:21
Forum: ATSAS Package in General
Topic: ATSAS installation guide for the Mac
Replies: 22
Views: 13299

Re: ATSAS installation guide for the Mac

Hi guys, I have three questions: 1) I installed the new ATSAS for Mac (I am running on Lion). I opened Primus but couldn't perform any action. For example, when I try to average, primus says the file avrg001.dat does not exist! Same for when I try to merge. Also Guinier and p(r) analysis did not wor...
by Yann
2012.09.17 11:23
Forum: Mixtures and Flexible Systems
Topic: EOM - GaJoe Manual
Replies: 14
Views: 7890

Re: EOM - GaJoe Manual

Hi Giancarlo,

concerning this discussion. Does this imply that when you choose not to use constant subtraction during the fitting that the scaling factor is chosen to be 1 by default for all data points in the calculation of chi2?

Thanks,

Yann
by Yann
2012.09.14 15:53
Forum: Mixtures and Flexible Systems
Topic: EOM - GaJoe Manual
Replies: 14
Views: 7890

Re: EOM - GaJoe Manual

Hi Giancarlo,

thanks for the reply.

I calculated chi2 with and without the scaling factor and got quasi similar results. Guess I did a good job preparing my sample and buffer then... :-)

Cheers guys,

Yann
by Yann
2012.09.13 16:04
Forum: Mixtures and Flexible Systems
Topic: EOM - GaJoe Manual
Replies: 14
Views: 7890

Re: EOM - GaJoe Manual

Hi guys,

a quick question concerning the definition of the chi2 used in EOM.

Can anybody tell me what the exact function of that scaling factor is?

Second question: the chi value in the .fit file is the square of the defined chi2?

Thanks,

Yann
by Yann
2012.07.17 15:00
Forum: Mixtures and Flexible Systems
Topic: EOM - GaJoe Manual
Replies: 14
Views: 7890

Re: EOM - GaJoe Manual

Alright Giancarlo!

Thanks a bunch again

Is there any way to acknowledge this forum in a paper? I consider these to be valuable discussions...

Is there any way to 'officially' acknowledge you or do you guys prefer no acknowledgements? What is your (group) policy on this?

Cheers,

Yann
by Yann
2012.07.13 14:43
Forum: Mixtures and Flexible Systems
Topic: EOM - GaJoe Manual
Replies: 14
Views: 7890

Re: EOM - GaJoe Manual

Hi Giancarlo, thanks for your replies! They have been of great help. I'll go for the option without constant subtraction. Final question: why would you would to change the inputted experimental data by subtraction? Intuitively, it seems a bit dodgy to me to change the experimental data. But probably...
by Yann
2012.07.12 11:08
Forum: Mixtures and Flexible Systems
Topic: Custom Pool for EOM
Replies: 6
Views: 3192

Re: Custom Pool for EOM

Hi Alex, the problem I had was the following (read below). I tried renumbering, renaming, etc, but I still had the problem 'no file with such extension' when I tried to run onefile. I couldn't really find out what went wrong, so this is why we wrote the python scripts. Cheers, Yann Hi lads, has any ...
by Yann
2012.07.11 18:30
Forum: Mixtures and Flexible Systems
Topic: Custom Pool for EOM
Replies: 6
Views: 3192

Re: Custom Pool for EOM

Hi Alex,

the reason we wrote the scripts is because for some reason we couldn't get the onefile command to work properly.

Not trying to re-invent the wheel, just an in-house solution because we got stuck and couldn't figure out why ;-).

Cheers,

Yann
by Yann
2012.07.11 18:23
Forum: Mixtures and Flexible Systems
Topic: EOM - GaJoe Manual
Replies: 14
Views: 7890

Re: EOM - GaJoe Manual

Hi guys, small question on the best (and most correct) way of presenting the fit after an EOM run. My goal is to compare the outputs of gajoe runs starting with two different pools. I'll try to list my questions as clear as I can. 1) Question1: I first ran gajoe13 allowing constant subtraction (defa...
by Yann
2012.07.05 14:31
Forum: Mixtures and Flexible Systems
Topic: EOM - GaJoe Manual
Replies: 14
Views: 7890

Re: EOM - GaJoe Manual

Hi Giancarlo, thanks for your quick reply! As I am running on Mac, I am still using gajoe13 and ranch13... Another question with which you could maybe help me out. I was reading the initial EOM paper (Bernado et al JACS 2007) and was wondering how the 'test sets' were generated. I imagine the pool o...
by Yann
2012.07.05 10:26
Forum: Mixtures and Flexible Systems
Topic: EOM - GaJoe Manual
Replies: 14
Views: 7890

EOM - GaJoe Manual

Hi guys, maybe a bit of a naive question, but I'm hoping somebody can help me out. I was wondering if there is any literature on the effect of all of the different parameters you can play around with in GaJoe (number of generations, cross-overs, etc) on the final result? Second question, is there a ...
by Yann
2012.07.05 10:19
Forum: Mixtures and Flexible Systems
Topic: Custom Pool for EOM
Replies: 6
Views: 3192

Re: Custom Pool for EOM

Hi, I ran into a similar problem and we wrote a script to create the master intensity file (junxxx.int) and the size list file (Size_listxxx.txt). These scripts are python scripts should be run as follows python joinCrysolIntFiles.py '*00.int' test.int (test can be any name you like, I always use ju...
by Yann
2012.06.19 13:58
Forum: Mixtures and Flexible Systems
Topic: Modelling Dimers in Ranch
Replies: 11
Views: 8309

Re: Modelling Dimers in Ranch

Hi guys,

great news about the progress in EOM!

I don't mean to nag, but could anybody help me out with my previous question?

Thanks,

Yann
by Yann
2012.06.11 16:48
Forum: Mixtures and Flexible Systems
Topic: Modelling Dimers in Ranch
Replies: 11
Views: 8309

Re: Modelling Dimers in Ranch

Hi Dave, Thanks for the quick reply. This will come in handy for sure. Other than a construction of a pool of dimers I was mainly referring to the issue of ONEFILE keeping returning "No file with this extension" despite the fact that I am using the correct procedure of naming in the EOM manual. Any ...
by Yann
2012.06.11 16:11
Forum: Mixtures and Flexible Systems
Topic: Modelling Dimers in Ranch
Replies: 11
Views: 8309

Re: Modelling Dimers in Ranch

Hi lads, has any solution been found in the end? I am struggling with a similar problem. I have generated a pool of conformers using flexible meccano and get the following output files after running crysol: 0a_71_sccomp00.int until 999a_71_sccomp00.int. When I try to run 'one file' (I am running on ...