From users at lists.sasview.org Thu May 7 14:47:59 2020 From: users at lists.sasview.org (Grayson Johnson via users) Date: Thu, 7 May 2020 14:47:59 -0400 Subject: [SasView Users] Treatment of Self-Assembled Structures Message-ID: Dear Users Forum, I’m new to the process of fitting SAXS data, and I am looking for guidance on what assumptions to make for my models. I have a set of small, probably spherical particles that assemble into micron length rectangular prism shaped structures. I have a known crystal structure from TEM images. Is it better to model the SAXS profile as a parallelepiped (and presumably miss out on the structure factor information that is present) or as spheres? If I do as spheres, is there a good way to use the crystal structure information to help the model along? When I perform a fit with spheres, I don’t seem to get the really low q behavior that I get with the parallelepiped. When I fit with the parallelepiped, the fit takes upwards of 30 minutes, and I haven’t quite been able to dial in on the parameters. The assemblies have a lot of variation in length, but not too much in width and height. Thanks for any help that you can provide, Grayson Johnson -------------- next part -------------- An HTML attachment was scrubbed... URL: From users at lists.sasview.org Fri May 8 10:59:14 2020 From: users at lists.sasview.org (Paul Butler via users) Date: Fri, 8 May 2020 10:59:14 -0400 Subject: [SasView Users] Treatment of Self-Assembled Structures In-Reply-To: References: Message-ID: Hi Grayson, I see you are not starting with an easy system to analyze by SAXS :-) The first question in any scattering analysis would be: “What information are you seeking?” Not having that here are some general thoughts that may be useful. Let me ignore for the moment that you expect your fibrils to be formed of spherical particles and focus on the large object for a minute as this is (I think) the easier one to deal with. As long as you are at low enough Q that the spheres are “too small to see” this should be a reasonable zeroth order approximation I think. For this a rectangular prism (or also the model called parallelepiped in SasView) would be appropriate. However, the length of microns is way beyond the length resolvable by SAXS so just fixing that parameter to something you feel is about right will be necessary (do not try to fit it! The data will not have enough information). This leaves the width and height to fit. The second caveat here will of course be the concentration. If they are concentrated enough (and at microns in length that doesn’t have to be much) then you should see an isotropic to nematic transition in your system? At this point things get harder. However one can estimate the cross section from the position of the peak and the known volume fraction (assuming it is in fact known) and try to fit the model to data at Q higher than the peak to get height and width. Of course the problem with that last bit is that you say your prism is formed of spheres and that you have a crystal structure? My first question would be: what do you mean by crystal structure? If the spheres are reasonably monodisperse and are packing into a close packed structure with the center to center distance being the diameter,D, of the sphere, then I would assume that at Q=2*PI/D there will be a sharp peak? If so the analysis above becomes difficult and one with which I have had little experience. I would need to see a data set to have any more ideas. In principle one can use the modulation of the bragg peak heights to infer something about the underlying form factor but in this case all the form factor information of interest is at lower Q and I would guess suppressed for at least some range of Q. That goes a bit beyond my experience but hope it helps. Maybe someone else has more experience with this? Cheers Paul On Thu, May 7, 2020 at 2:53 PM Grayson Johnson via users < users at lists.sasview.org> wrote: > Dear Users Forum, > > > > I’m new to the process of fitting SAXS data, and I am looking for guidance > on what assumptions to make for my models. I have a set of small, probably > spherical particles that assemble into micron length rectangular prism > shaped structures. I have a known crystal structure from TEM images. Is it > better to model the SAXS profile as a parallelepiped (and presumably miss > out on the structure factor information that is present) or as spheres? If > I do as spheres, is there a good way to use the crystal structure > information to help the model along? When I perform a fit with spheres, I > don’t seem to get the really low q behavior that I get with the > parallelepiped. When I fit with the parallelepiped, the fit takes upwards > of 30 minutes, and I haven’t quite been able to dial in on the parameters. > The assemblies have a lot of variation in length, but not too much in width > and height. > > > > > > Thanks for any help that you can provide, > > Grayson Johnson > _______________________________________________ > users mailing list > users at lists.sasview.org > http://lists.sasview.org/cgi-bin/mailman/listinfo/users > -------------- next part -------------- An HTML attachment was scrubbed... URL: From users at lists.sasview.org Fri May 8 10:59:14 2020 From: users at lists.sasview.org (Paul Butler via users) Date: Fri, 8 May 2020 10:59:14 -0400 Subject: [SasView Users] Treatment of Self-Assembled Structures In-Reply-To: References: Message-ID: Hi Grayson, I see you are not starting with an easy system to analyze by SAXS :-) The first question in any scattering analysis would be: “What information are you seeking?” Not having that here are some general thoughts that may be useful. Let me ignore for the moment that you expect your fibrils to be formed of spherical particles and focus on the large object for a minute as this is (I think) the easier one to deal with. As long as you are at low enough Q that the spheres are “too small to see” this should be a reasonable zeroth order approximation I think. For this a rectangular prism (or also the model called parallelepiped in SasView) would be appropriate. However, the length of microns is way beyond the length resolvable by SAXS so just fixing that parameter to something you feel is about right will be necessary (do not try to fit it! The data will not have enough information). This leaves the width and height to fit. The second caveat here will of course be the concentration. If they are concentrated enough (and at microns in length that doesn’t have to be much) then you should see an isotropic to nematic transition in your system? At this point things get harder. However one can estimate the cross section from the position of the peak and the known volume fraction (assuming it is in fact known) and try to fit the model to data at Q higher than the peak to get height and width. Of course the problem with that last bit is that you say your prism is formed of spheres and that you have a crystal structure? My first question would be: what do you mean by crystal structure? If the spheres are reasonably monodisperse and are packing into a close packed structure with the center to center distance being the diameter,D, of the sphere, then I would assume that at Q=2*PI/D there will be a sharp peak? If so the analysis above becomes difficult and one with which I have had little experience. I would need to see a data set to have any more ideas. In principle one can use the modulation of the bragg peak heights to infer something about the underlying form factor but in this case all the form factor information of interest is at lower Q and I would guess suppressed for at least some range of Q. That goes a bit beyond my experience but hope it helps. Maybe someone else has more experience with this? Cheers Paul On Thu, May 7, 2020 at 2:53 PM Grayson Johnson via users < users at lists.sasview.org> wrote: > Dear Users Forum, > > > > I’m new to the process of fitting SAXS data, and I am looking for guidance > on what assumptions to make for my models. I have a set of small, probably > spherical particles that assemble into micron length rectangular prism > shaped structures. I have a known crystal structure from TEM images. Is it > better to model the SAXS profile as a parallelepiped (and presumably miss > out on the structure factor information that is present) or as spheres? If > I do as spheres, is there a good way to use the crystal structure > information to help the model along? When I perform a fit with spheres, I > don’t seem to get the really low q behavior that I get with the > parallelepiped. When I fit with the parallelepiped, the fit takes upwards > of 30 minutes, and I haven’t quite been able to dial in on the parameters. > The assemblies have a lot of variation in length, but not too much in width > and height. > > > > > > Thanks for any help that you can provide, > > Grayson Johnson > _______________________________________________ > users mailing list > users at lists.sasview.org > http://lists.sasview.org/cgi-bin/mailman/listinfo/users > -------------- next part -------------- An HTML attachment was scrubbed... URL: From users at lists.sasview.org Thu May 28 08:56:03 2020 From: users at lists.sasview.org (Stephen King - UKRI STFC via users) Date: Thu, 28 May 2020 12:56:03 +0000 Subject: [SasView Users] SasView-5.0.2 and 4.2.2 Own Model on MaxOS In-Reply-To: References: Message-ID: <308f03cb243941ee8fc5f8303767717b@stfc.ac.uk> Dear Sebastian, Beatrice, Thank you for contacting us. Please could you resend the two attachments in a zip file. Mail clients are blocking plain source code attachments these days for security reasons. Thank you. Kind regards, Steve King On behalf of the Developers From: Sebastian Lages Sent: 28 May 2020 13:37 To: users at sasview.org Cc: Beatrice Swensson Subject: SasView-5.0.2 and 4.2.2 Own Model on MaxOS Dear SasViewers, we wrote our own model, see attached files. It's based on in-build models and runs perfectly fine on my LinuxMint 18. The files live in "/home/sebastian/SasView/sasmodels/models/". Just like it said in the description for writing own models. However, on MacOS we cannot make it work. Not with SasView-4.2.2, not with SasView-5.0.2. Every time we choose the model from the FitPage's drop down menu, we get an error message. And there's more. The model "flexible_cylinder" stopped working as well. It stopped completely. Interestingly with the same error message we got for our own model. Only a fresh installation of SasView is able to correct this behaviour, restarting the software is not enough. How can we correct this? Best regards, Sebastian Materials Physics Department of Physics Chalmers University of Technology SE-412 96 Göteborg Sweden Homepage Liebi Group This email and any attachments are intended solely for the use of the named recipients. If you are not the intended recipient you must not use, disclose, copy or distribute this email or any of its attachments and should notify the sender immediately and delete this email from your system. UK Research and Innovation (UKRI) has taken every reasonable precaution to minimise risk of this email or any attachments containing viruses or malware but the recipient should carry out its own virus and malware checks before opening the attachments. UKRI does not accept any liability for any losses or damages which the recipient may sustain due to presence of any viruses. Opinions, conclusions or other information in this message and attachments that are not related directly to UKRI business are solely those of the author and do not represent the views of UKRI. -------------- next part -------------- An HTML attachment was scrubbed... URL: From users at lists.sasview.org Thu May 28 09:12:28 2020 From: users at lists.sasview.org (Stephen King - UKRI STFC via users) Date: Thu, 28 May 2020 13:12:28 +0000 Subject: [SasView Users] SasView-5.0.2 and 4.2.2 Own Model on MaxOS In-Reply-To: <64e7df87f43c4392909b2b50520098de@chalmers.se> References: , <308f03cb243941ee8fc5f8303767717b@stfc.ac.uk> <64e7df87f43c4392909b2b50520098de@chalmers.se> Message-ID: <6f025c63abfc46179dc0888c3ccc6630@stfc.ac.uk> Thanks. We'll take a look. From: Sebastian Lages Sent: 28 May 2020 14:01 To: King, Stephen (STFC,RAL,ISIS) ; users at sasview.org Cc: Beatrice Swensson Subject: Re: SasView-5.0.2 and 4.2.2 Own Model on MaxOS Dear Stephen, this is a quick reply! Thanks a lot! I feel obliged to return the favour of a quick answer and here it is. Please find the source code attached in a zip-file. Best regards from Sweden, Sebastian Materials Physics Department of Physics Chalmers University of Technology SE-412 96 Göteborg Sweden Homepage Liebi Group ________________________________ From: Stephen King - UKRI STFC > Sent: Thursday, May 28, 2020 2:56:03 PM To: Sebastian Lages; users at sasview.org Cc: Beatrice Swensson Subject: RE: SasView-5.0.2 and 4.2.2 Own Model on MaxOS Dear Sebastian, Beatrice, Thank you for contacting us. Please could you resend the two attachments in a zip file. Mail clients are blocking plain source code attachments these days for security reasons. Thank you. Kind regards, Steve King On behalf of the Developers From: Sebastian Lages > Sent: 28 May 2020 13:37 To: users at sasview.org Cc: Beatrice Swensson > Subject: SasView-5.0.2 and 4.2.2 Own Model on MaxOS Dear SasViewers, we wrote our own model, see attached files. It's based on in-build models and runs perfectly fine on my LinuxMint 18. The files live in "/home/sebastian/SasView/sasmodels/models/". Just like it said in the description for writing own models. However, on MacOS we cannot make it work. Not with SasView-4.2.2, not with SasView-5.0.2. Every time we choose the model from the FitPage's drop down menu, we get an error message. And there's more. The model "flexible_cylinder" stopped working as well. It stopped completely. Interestingly with the same error message we got for our own model. Only a fresh installation of SasView is able to correct this behaviour, restarting the software is not enough. How can we correct this? Best regards, Sebastian Materials Physics Department of Physics Chalmers University of Technology SE-412 96 Göteborg Sweden Homepage Liebi Group This email and any attachments are intended solely for the use of the named recipients. If you are not the intended recipient you must not use, disclose, copy or distribute this email or any of its attachments and should notify the sender immediately and delete this email from your system. UK Research and Innovation (UKRI) has taken every reasonable precaution to minimise risk of this email or any attachments containing viruses or malware but the recipient should carry out its own virus and malware checks before opening the attachments. UKRI does not accept any liability for any losses or damages which the recipient may sustain due to presence of any viruses. Opinions, conclusions or other information in this message and attachments that are not related directly to UKRI business are solely those of the author and do not represent the views of UKRI. -------------- next part -------------- An HTML attachment was scrubbed... URL: