[Date Prev][Date Next][Thread Prev][Thread Next][Date Index][Thread Index]
Reply to: [list | sender only]
Re: [Imgcif-l] Direct beam vector / direction
- To: Graeme.Winter@Diamond.ac.uk, The Crystallographic Binary File and its imgCIF application to image data <imgcif-l@iucr.org>
- Subject: Re: [Imgcif-l] Direct beam vector / direction
- From: "Herbert J. Bernstein" <yaya@bernstein-plus-sons.com>
- Date: Thu, 23 Jun 2011 08:53:23 -0400 (EDT)
- In-Reply-To: <13999B6FC038EB44B067771E3CFBD09108C78D@EXCHMBX03.fed.cclrc.ac.uk>
- References: <13999B6FC038EB44B067771E3CFBD09108B71C@EXCHMBX03.fed.cclrc.ac.uk><alpine.BSF.2.00.1106230708140.78984@epsilon.pair.com><13999B6FC038EB44B067771E3CFBD09108C78D@EXCHMBX03.fed.cclrc.ac.uk>
Please bear with me: 1. First, the source vector only exists if you have put it in the header in the first place, and what you would have almost always put there is [0,0,1] because the axis system is defined in terms of the principal axis of the goniometer and the vector from sample to to source (which I would think of as the opposite of the beam vector). 2. The "almost always" comes up for 2 reasons: 2.1. You may have designed your experiment to cant or offert the goniometer relative to the beam; and/or 2.2. After you set up your experiment, you found that things were not quite where you intended them to be, and despite your original intention to have the beam at right angles to the principal axis of the goniometer, it as actually canted at some measurable angle or has some measurable offset. In those two cases, source certainly should be something other than [0,0,1], but it won't get into your CBF header unless somebody puts it there. What did you have in mind for a way in which something other than [0,0,1] is getting into the header? Regards, Herbert ===================================================== Herbert J. Bernstein, Professor of Computer Science Dowling College, Kramer Science Center, KSC 121 Idle Hour Blvd, Oakdale, NY, 11769 +1-631-244-3035 yaya@dowling.edu ===================================================== On Thu, 23 Jun 2011, Graeme.Winter@Diamond.ac.uk wrote: > Dear Herbert, > > Thanks for the confirmation - the approach I have taken is therefore to fetch it out as follows (using pycbf) > > # find the direct beam vector - takes a few steps > cbf_handle.find_category('axis') > > # find record with equipment = source > cbf_handle.find_column('equipment') > cbf_handle.find_row('source') > > # then get the vector and offset from this > > beam_direction = [] > > for j in range(3): > cbf_handle.find_column('vector[%d]' % (j + 1)) > beam_direction.append(cbf_handle.get_doublevalue()) > > Is this the most efficient way to extract the values? It would make sense that there should be a way to extract the whole vector in one go but I could not see it (certainly not in the pycbf api) > > I am slightly worried about efficiency as the first step in xia2 processing is to inspect every single image header, which for 1000 + (or even 10k) image headers could be considerable... not that these parameters will change from one frame to the next. > > Many thanks, > > Graeme > > -----Original Message----- > From: imgcif-l-bounces@iucr.org [mailto:imgcif-l-bounces@iucr.org] On Behalf Of Herbert J. Bernstein > Sent: 23 June 2011 12:09 > To: The Crystallographic Binary File and its imgCIF application to image data > Subject: Re: [Imgcif-l] Direct beam vector / direction > > Yes -- that all sounds right. -- Herbert > > ===================================================== > Herbert J. Bernstein, Professor of Computer Science > Dowling College, Kramer Science Center, KSC 121 > Idle Hour Blvd, Oakdale, NY, 11769 > > +1-631-244-3035 > yaya@dowling.edu > ===================================================== > > On Thu, 23 Jun 2011, Graeme.Winter@Diamond.ac.uk wrote: > >> Hi Folks, >> >> So, I am looking very closely into the cif side of imgCIF now and have started to wonder about how / where we record the direct beam vector. Specifically: >> >> - the rotation axis is canonically 1, 0, 0 >> - the component of the vector from sample to source PERPENDICULAR to the primary rotation axis is 0, 0, 1 >> >> In the example CIF headers in the big book (Tables G) there is a >> >> SOURCE general source . 0 0 1 . . . >> >> record which I assume would be the place (small values for 0 0 assumed, near unity for 1 when we add in "real" values) however there does not appear to be a mechanism in cbflib to extract this easily, in the same way that there is for the rotation axes and detector orientation. >> >> Before I start to code up a mechanism to fetch this out I thought I should check my assumptions first! >> >> Is this right? >> >> Many thanks in advance, >> >> Graeme >> >> Dr. Graeme Winter >> Senior Software Scientist >> Diamond Light Source >> >> +44 1235 778091 (work) >> +44 7786 662784 (work mobile) >> >> >> >> >> >> -- >> >> This e-mail and any attachments may contain confidential, copyright and or privileged material, and are for the use of the intended addressee only. If you are not the intended addressee or an authorised recipient of the addressee please notify us of receipt by returning the e-mail and do not use, copy, retain, distribute or disclose the information in or attached to the e-mail. >> >> Any opinions expressed within this e-mail are those of the individual and not necessarily of Diamond Light Source Ltd. >> >> Diamond Light Source Ltd. cannot guarantee that this e-mail or any attachments are free from viruses and we cannot accept liability for any damage which you may sustain as a result of software viruses which may be transmitted in or with the message. >> >> Diamond Light Source Limited (company no. 4375679). Registered in England and Wales with its registered office at Diamond House, Harwell Science and Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom >> >> >> >> >> >> >> >> >> >> _______________________________________________ >> imgcif-l mailing list >> imgcif-l@iucr.org >> http://scripts.iucr.org/mailman/listinfo/imgcif-l >> > _______________________________________________ > imgcif-l mailing list > imgcif-l@iucr.org > http://scripts.iucr.org/mailman/listinfo/imgcif-l > > -- > This e-mail and any attachments may contain confidential, copyright and or privileged material, and are for the use of the intended addressee only. If you are not the intended addressee or an authorised recipient of the addressee please notify us of receipt by returning the e-mail and do not use, copy, retain, distribute or disclose the information in or attached to the e-mail. > Any opinions expressed within this e-mail are those of the individual and not necessarily of Diamond Light Source Ltd. > Diamond Light Source Ltd. cannot guarantee that this e-mail or any attachments are free from viruses and we cannot accept liability for any damage which you may sustain as a result of software viruses which may be transmitted in or with the message. > Diamond Light Source Limited (company no. 4375679). Registered in England and Wales with its registered office at Diamond House, Harwell Science and Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom > > > > > _______________________________________________ > imgcif-l mailing list > imgcif-l@iucr.org > http://scripts.iucr.org/mailman/listinfo/imgcif-l > _______________________________________________ imgcif-l mailing list imgcif-l@iucr.org http://scripts.iucr.org/mailman/listinfo/imgcif-l
Reply to: [list | sender only]
- Follow-Ups:
- Re: [Imgcif-l] Direct beam vector / direction (Graeme.Winter)
- References:
- [Imgcif-l] Direct beam vector / direction (Graeme.Winter)
- Re: [Imgcif-l] Direct beam vector / direction (Herbert J. Bernstein)
- Re: [Imgcif-l] Direct beam vector / direction (Graeme.Winter)
- Prev by Date: Re: [Imgcif-l] Direct beam vector / direction
- Next by Date: Re: [Imgcif-l] Direct beam vector / direction
- Prev by thread: Re: [Imgcif-l] Direct beam vector / direction
- Next by thread: Re: [Imgcif-l] Direct beam vector / direction
- Index(es):