Search found 5 matches

by nassos
2018.05.08 12:26
Forum: SAXS & SANS Software
Topic: Running Dammin from Scatter
Replies: 2
Views: 10545

Re: Running Dammin from Scatter

Hi a2west,

You can run dammin multiple times, with a for loop inside the terminal. If you check the dammif manual you can see the syntax for bash:

$ for i in `seq 1 10` ; do dammif --prefix=lyz-$i --mode=slow lyz.out; done

https://www.embl-hamburg.de/biosaxs/manuals/dammif.html

Best regards
nassos
by nassos
2018.04.11 15:34
Forum: Working with Models
Topic: Trouble in data collection or analysis
Replies: 2
Views: 4748

Re: Trouble in data collection or analysis

Hi, If your dataset is good then you need to consider if your protein adopts a different conformation in solution than the crystal structure of the homologue. Also did you collect SEC-SAXS data? Maybe you can consider running DAMMIN for 10-20 times and average the output models so you will have a be...
by nassos
2018.02.19 16:44
Forum: Ab Initio Shape Determination
Topic: MONSA_running protocol
Replies: 1
Views: 4963

Re: MONSA_running protocol

Hi Susana, How many datasets do you have? Ideally you should have the protein alone the DNA alone and the complex. You can also get some information if you have just the protein alone and the protein bound with DNA. If you have the 3 datasets then you have 2 phases. Phase 1 protein without DNA Phase...
by nassos
2017.12.15 10:59
Forum: Primary Data Processing
Topic: Plot ready for publication- SOFTWARE?
Replies: 3
Views: 5046

Re: Plot ready for publication- SOFTWARE?

I have not tried but it seems good software for generating plots. Maybe its a good idea to give it a try. I always save the plots as pdf and change fonts, colors etc in illustrator without having any problem in quality.

Nassos
by nassos
2017.12.14 18:08
Forum: Primary Data Processing
Topic: Plot ready for publication- SOFTWARE?
Replies: 3
Views: 5046

Re: Plot ready for publication- SOFTWARE?

Hi Giulia,

You can save the plots as a pdf file, if you choose the print option in PRIMUS and then import the pdf in Adobe illustrator for further changes.

Nassos