SAXS

Small Angle X-ray Scattering Initiative for Europe :: Forum
It is currently 2014.07.31 23:36

All times are UTC + 1 hour [ DST ]




Post new topic Reply to topic  [ 8 posts ] 
Author Message
 Post subject: Primus > Porod
PostPosted: 2008.10.13 18:16 
Offline
Member
User avatar

Joined: 2008.10.13 17:54
Posts: 5
Location: Reykjavík, Iceland
Hello everyone,

I'm trying to estimate the volume of my particle using the Porod button in Primus. I don't understand how to choose nBeg and nEnd (first and last data point). The manual says: For proper evaluation it is necessary to select the appropriate range of the s-axis (to set values for N1 and N2 data points that will be taken ), so that the product (smax*R) doesn't exceed 1.5. (it is better to use the values N1 and N2 from "Guinier" analysis).
But the Guinier region is just a short part of the data, it doesn't even look like a Porod plot!

Kind regards,
Guðrún


Top
 Profile  
 
 Post subject: N min and N max
PostPosted: 2008.11.04 10:04 
Offline
Member

Joined: 2007.08.20 17:55
Posts: 10
Location: University of Copenhagen
From what I have learnt (thanks Maxim) you should chose N1 from the Guinier (as for all other subsequent data analysis) and N2 can then be interactively chosen while watching your Porod plot, such that you have (close to) linearity at higher angles in the plot. Also watch that your choice is in a reasonably 'stable' area, i.e. that the calculated values to not vary significantly in the region. Play with it a bit. Good luck.


Top
 Profile  
 
 Post subject:
PostPosted: 2009.10.19 14:15 
Offline
Member

Joined: 2007.11.28 01:45
Posts: 10
Location: Montpellier
Thanks for this answer.
I want to calcul the error bar for the porod volume calculated by the porod function on primus.
What is the better way to do this.

thanks


Top
 Profile  
 
 Post subject: Porod volume error bars
PostPosted: 2009.10.19 20:02 
Offline
Administrator
User avatar

Joined: 2007.08.03 18:55
Posts: 435
Location: EMBL Hamburg, Germany
I would use just 10% error bars. The proper way would be to observe changes of Vp when changing smax in Primus but the outcome will not be too different from 10%.
You may read the Glatter & Kratky book for theory on Porod plot; see "General theory", page 28 equation 33.


Top
 Profile  
 
 Post subject:
PostPosted: 2009.10.20 11:45 
Offline
Member

Joined: 2007.11.28 01:45
Posts: 10
Location: Montpellier
Thanks for this quick answer.
I done porod analysis on data from DNA /protein complex. I obtain a Vp around 1200 nm^3 for an Rg around 4.2 nm.
I think my Vp is overestimated maybe it's due to the DNA.
I joine my data and some picture.

thans


Attachments:
File comment: porod plot image
porod.JPG
porod.JPG [ 145.85 KiB | Viewed 5976 times ]
File comment: SAXS data
mcut2.dat [53.7 KiB]
Downloaded 186 times
Top
 Profile  
 
 Post subject:
PostPosted: 2009.10.28 11:33 
Offline
Member

Joined: 2007.11.28 01:45
Posts: 10
Location: Montpellier
Nobody would have an answer to this question.

I compared rg and Vp for a protein and my DNA proteine/complex

protein Rg:4 nm and Vp: 100 nm^3

protein Rg:4.2 nm and Vp: 1200 nm^3

I put below the result from damin calculations on this same data and i obtain a V= 229 nm^3

REMARK Project description: mgnom.out /sy P1 /mo K /lo Mdamz
REMARK j: 309 T: 0.359E-07 Suc: 1 Eva: 8720890 CPU: 0.605E+04 SqF: 0.0086
REMARK Rf: 0.00262 Los:0.0223 Dis:0.0000 Per: 0.4342 Sca: 0.139E-07
REMARK Computation mode ................................ : Keep
REMARK Number of particle atoms ........................ : 1125
REMARK Number of graphs ................................ : 1
REMARK Anisometry penalty .............................. : 0.0
REMARK Point symmetry group ............................ : P1
REMARK DAM packing radius .............................. : 3.300
REMARK Average volume per atom ......................... : 203.4
REMARK Total excluded DAM volume ....................... : 2.289e+5
REMARK Particle center: -4.3296 -3.0565 0.8421
Radius of gyration ..................................... : 42.38
Maximum diameter ....................................... : 129.7

I don't understand why i can found this various results

thanks for help


Top
 Profile  
 
 Post subject:
PostPosted: 2009.10.30 12:43 
Offline
Active member

Joined: 2007.08.15 16:30
Posts: 23
Location: LNBio - CNPEM/ABTLuS, Brazil
Hi everyone,

I think that the question here is understanding the theory of the Porod volume. In order to calculate the Porod volume, the intensity curve need to have a q^4-decay (Porod's Law), otherwise, a constant value is subtracted from the intensity to force this decay (e.g., I(q)~A/q^4 + B), and you should determine this B. This procedures is well described in Glatter & Kratky book). Anyway, the PRIMUS automatically subtract this constant. However, the q^4-decay only appears in the SAXS intensity curve from compact and non-flexible protein. It's well know that DNA may have some flexibility, which can overestimated you porod volume (there are other reason). So, the DNA of your complex can change this exponential decay. PRIMUS plots a q^4I(q) vs. q graph, so you must have a plateau at the end of your curve is it respects the Porod's law or after the constant subraction. Be careful with the last point that you take into account when you do it. The right way in PRIMUS is to selected only N1 from the Guinier region, but not the N2. You did wrong in your figure. The N2, like Bente said, should be interactively selected, but you need to see that plateau in the q^4I(q) vs. q plot. The Vp that I did with your data is ~230nm^3 +/- 10nm^3, using a reasonable region of your curve.
That's it.


Top
 Profile  
 
 Post subject:
PostPosted: 2009.10.30 15:33 
Offline
Member

Joined: 2007.11.28 01:45
Posts: 10
Location: Montpellier
Thank you so much for your answer


Top
 Profile  
 
Display posts from previous:  Sort by  
Post new topic Reply to topic  [ 8 posts ] 

All times are UTC + 1 hour [ DST ]


Who is online

Users browsing this forum: No registered users and 0 guests


You cannot post new topics in this forum
You cannot reply to topics in this forum
You cannot edit your posts in this forum
You cannot delete your posts in this forum
You cannot post attachments in this forum

Search for:
Jump to:  
cron
Powered by phpBB® Forum Software © phpBB Group