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<p>Dear James,</p>
<p>I'm curious about simtbx. Does it allow me to supply a set of atomic coordinates in an ASU and then spit out corresponding diffraction images? I suppose it can't generate twinned data sets.</p>
<p>Many thanks,</p>
<p>Rob</p>
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<p>On 03/05/2017 16:28, James Holton wrote:</p>
<blockquote type="cite" style="padding-left:5px; border-left:#1010ff 2px solid; margin-left:5px"><!-- html ignored --><!-- head ignored --><!-- meta ignored --><br /> "simtbx" is the name we are giving to my diffraction image simulation codes. You may or may not of heard of their standalone versions as MLFSOM, fastBragg (now nanoBragg), nonBragg and nearBragg. Nick and I thought the capability of creating absolutely realistic diffraction data from a completely independent code base would be an excellent way to generate test data for cctbx, dials, phenix, and even third-party packages. There is also the idea of fitting a simulation directly to diffraction images, which I have had some success doing independently, but we hope this will work better under cctbx. Until recently, all this was standalone c code, with home pages here:<br /><br /><a class="moz-txt-link-freetext" href="http://bl831.als.lbl.gov/~jamesh/mlfsom/">http://bl831.als.lbl.gov/~jamesh/mlfsom/</a><br /><a class="moz-txt-link-freetext" href="http://bl831.als.lbl.gov/~jamesh/nanoBragg/">http://bl831.als.lbl.gov/~jamesh/nanoBragg/</a><br /><a class="moz-txt-link-freetext" href="http://bl831.als.lbl.gov/~jamesh/nearBragg/">http://bl831.als.lbl.gov/~jamesh/nearBragg/</a><br /><a class="moz-txt-link-freetext" href="http://bl831.als.lbl.gov/~jamesh/nonBragg/">http://bl831.als.lbl.gov/~jamesh/nonBragg/</a><br /><br /> I have spent the bulk of my time for three months trying to wire these codes into the boost/Python framework of cctbx. I put docstrings into every single one of my objects, but since I am new to Python I don't know where people look for documentation.<br /><br /> Again, sorry this broke everything. It's been in there since February and I was surprised to find that a new developer here couldn't access it. This is why I've been asking so many questions about tests I should perform before checking things in, but apparently it was all for naught.<br /><br /> -James<br /><br />
<div class="moz-cite-prefix">On 5/3/2017 7:57 AM, Pavel Afonine wrote:</div>
<blockquote type="cite" style="padding-left:5px; border-left:#1010ff 2px solid; margin-left:5px">Same questions here as Markus asked.. What is simtbx? First time hear about it. How cctbx can benefit from it?<br /> Pavel<br /><br />
<div class="moz-cite-prefix">On 5/3/17 07:53, <a class="moz-txt-link-abbreviated" href="mailto:markus.gerstel@diamond.ac.uk">markus.gerstel@diamond.ac.uk</a> wrote:</div>
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<p class="MsoNormal"><span style="font-size: 11.0pt; font-family: 'Calibri',sans-serif; color: #1f497d; mso-fareast-language: EN-US;">Hi Nick,<!-- o ignored --></span></p>
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<p class="MsoNormal"><span style="font-size: 11.0pt; font-family: 'Calibri',sans-serif; color: #1f497d; mso-fareast-language: EN-US;">Sorry, outsider perspective here. I don't know what simtbx does or is supposed to do.<!-- o ignored --></span></p>
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<p class="MsoNormal"><span style="font-size: 11.0pt; font-family: 'Calibri',sans-serif; color: #1f497d; mso-fareast-language: EN-US;">What is the benefit of having code in a repository that, according to your earlier mail, is explicitly not used in the project?<!-- o ignored --></span></p>
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<p class="MsoNormal"><span style="font-size: 11.0pt; font-family: 'Calibri',sans-serif; color: #1f497d; mso-fareast-language: EN-US;">Or more bluntly: We (and ccp4) distribute dials and, as part of it, the cctbx_project repository.<!-- o ignored --></span></p>
<p class="MsoNormal"><span style="font-size: 11.0pt; font-family: 'Calibri',sans-serif; color: #1f497d; mso-fareast-language: EN-US;">Why should we ship dead code?<!-- o ignored --></span></p>
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<p class="MsoNormal"><span style="font-size: 11.0pt; font-family: 'Calibri',sans-serif; color: #1f497d; mso-fareast-language: EN-US;">-Markus<!-- o ignored --></span></p>
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<p class="MsoNormal"><strong><span style="font-size: 11.0pt; font-family: 'Calibri',sans-serif;">From:</span></strong><span style="font-size: 11.0pt; font-family: 'Calibri',sans-serif;"> <a class="moz-txt-link-abbreviated" href="mailto:cctbxbb-bounces@phenix-online.org">cctbxbb-bounces@phenix-online.org</a> [<a class="moz-txt-link-freetext" href="mailto:cctbxbb-bounces@phenix-online.org">mailto:cctbxbb-bounces@phenix-online.org</a>] <strong>On Behalf Of </strong>Nicholas Sauter<br /><strong>Sent:</strong> 03 May 2017 15:52<br /><strong>To:</strong> cctbx mailing list <a class="moz-txt-link-rfc2396E" href="mailto:cctbxbb@phenix-online.org"><cctbxbb@phenix-online.org></a><br /><strong>Subject:</strong> Re: [cctbxbb] simtbx<!-- o ignored --></span></p>
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<p class="MsoNormal">Markus,<!-- o ignored --></p>
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<p class="MsoNormal">We want option c. simtbx should be in the cctbx_project directory. No separate git repository. We need to double check we've gotten all the files in cctbx_project, then remove them from the separate repo. James, could you look into this?<!-- o ignored --></p>
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<p class="MsoNormal">Nick<!-- o ignored --></p>
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<p class="MsoNormal">Nicholas K. Sauter, Ph. D.<br /> Senior Scientist, Molecular Biophysics & Integrated Bioimaging Division<!-- o ignored --></p>
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<p class="MsoNormal">Lawrence Berkeley National Laboratory<br /> 1 Cyclotron Rd., Bldg. 33R0345<br /> Berkeley, CA 94720<br /> (510) 486-5713<!-- o ignored --></p>
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<p class="MsoNormal">On Wed, May 3, 2017 at 7:49 AM, <<a href="mailto:markus.gerstel@diamond.ac.uk">markus.gerstel@diamond.ac.uk</a>> wrote:<!-- o ignored --></p>
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<p class="MsoNormal" style="mso-margin-top-alt: auto; mso-margin-bottom-alt: auto;"><span style="color: #1f497d;">Hi James,</span><!-- o ignored --></p>
<p class="MsoNormal" style="mso-margin-top-alt: auto; mso-margin-bottom-alt: auto;"><span style="color: #1f497d;"> </span><!-- o ignored --></p>
<p class="MsoNormal" style="mso-margin-top-alt: auto; mso-margin-bottom-alt: auto;"><span style="color: #1f497d;">It looks that you now have two separate places where simtbx code is kept. One is in the simtbx repository, where you fixed the sign earlier, and the other one is in the cctbx repository, where you just now fixed it again.</span><!-- o ignored --></p>
<p class="MsoNormal" style="mso-margin-top-alt: auto; mso-margin-bottom-alt: auto;"><span style="color: #1f497d;">Simtbx repo: <a href="https://github.com/dials/simtbx">https://github.com/dials/simtbx</a></span><!-- o ignored --></p>
<p class="MsoNormal" style="mso-margin-top-alt: auto; mso-margin-bottom-alt: auto;"><span style="color: #1f497d;">Simtbx folder in cctbx repo: <a href="https://github.com/cctbx/cctbx_project/tree/master/simtbx"> https://github.com/cctbx/cctbx_project/tree/master/simtbx</a> </span><!-- o ignored --></p>
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<p class="MsoNormal" style="mso-margin-top-alt: auto; mso-margin-bottom-alt: auto;"><span style="color: #1f497d;">I guess suppose there are three options here:</span><!-- o ignored --></p>
<p class="m-2651995399140751371msolistparagraph"><span style="color: #1f497d;">a.</span><span style="font-size: 7.0pt; color: #1f497d;"> </span><span style="color: #1f497d;">move simtbx into the module directory, add simtbx to the bootstrap script so it is initialised correctly.</span><!-- o ignored --></p>
<p class="m-2651995399140751371msolistparagraph"><span style="color: #1f497d;">b.</span><span style="font-size: 7.0pt; color: #1f497d;"> </span><span style="color: #1f497d;">leave simtbx inside the cctbx_project directory and repository, but as its own git repository (using git submodule)</span><!-- o ignored --></p>
<p class="m-2651995399140751371msolistparagraph"><span style="color: #1f497d;">c.</span><span style="font-size: 7.0pt; color: #1f497d;"> </span><span style="color: #1f497d;">leave simtbx inside the cctbx_project directory, delete the separate git repository</span><!-- o ignored --></p>
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<p class="MsoNormal" style="mso-margin-top-alt: auto; mso-margin-bottom-alt: auto;"><span style="color: #1f497d;">NB: This issue is independent of resolving the dials-dependency issue.</span><!-- o ignored --></p>
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<p class="MsoNormal" style="mso-margin-top-alt: auto; mso-margin-bottom-alt: auto;"><span style="color: #1f497d;">-Markus</span><!-- o ignored --></p>
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<p class="MsoNormal" style="mso-margin-top-alt: auto; mso-margin-bottom-alt: auto;"><strong><span>From:</span></strong><span> <a href="mailto:cctbxbb-bounces@phenix-online.org">cctbxbb-bounces@phenix-online.org</a> [mailto:<a href="mailto:cctbxbb-bounces@phenix-online.org">cctbxbb-bounces@phenix-online.org</a>] <strong>On Behalf Of </strong>James Holton<br /><strong>Sent:</strong> 03 May 2017 15:40<br /><strong>To:</strong> Winter, Graeme (DLSLtd,RAL,LSCI) <<a href="mailto:Graeme.Winter@Diamond.ac.uk">Graeme.Winter@Diamond.ac.uk</a>>; <a href="mailto:cctbxbb@phenix-online.org">cctbxbb@phenix-online.org</a><br /><strong>Subject:</strong> Re: [cctbxbb] simtbx</span><!-- o ignored --></p>
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<p class="MsoNormal" style="mso-margin-top-alt: auto; mso-margin-bottom-alt: auto;"> <!-- o ignored --></p>
<p class="MsoNormal" style="mso-margin-top-alt: auto; margin-bottom: 12.0pt;"><br /> Yesterday, Aaron and I were trying to set things up so that simtbx would be available to people who aren't James Holton. It's been checked in and working for over a month now, and only a few days ago I discovered that a fresh "bootstrap" has a broken simtbx, despite my "git status" telling me all my files are up to date. I asked Aaron and Nick for help with this.<br /><br /> I thought what we did was make cctbx.xfel depends on simtbx, since fitting simulations to stills is the whole reason for porting my stuff into python. <br /><br /> I set up simtbx with a constructor that takes a dxtbx detector as input, but does that make it depend on dials? I did not expect that.<br /><br /> Sorry, didn't mean to break anything! Would much appreciate any help on this. <br /><br /> -James<!-- o ignored --></p>
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<p class="MsoNormal" style="mso-margin-top-alt: auto; mso-margin-bottom-alt: auto;">On 5/3/2017 1:41 AM, <a href="mailto:Graeme.Winter@Diamond.ac.uk">Graeme.Winter@Diamond.ac.uk</a> wrote:<!-- o ignored --></p>
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<p class="MsoNormal" style="mso-margin-top-alt: auto; mso-margin-bottom-alt: auto;">Hi Folks<!-- o ignored --></p>
<p class="MsoNormal" style="mso-margin-top-alt: auto; mso-margin-bottom-alt: auto;"> <!-- o ignored --></p>
<p class="MsoNormal" style="mso-margin-top-alt: auto; mso-margin-bottom-alt: auto;">We have noticed that simtbx, part of the core cctbx now, depends on dials<!-- o ignored --></p>
<p class="MsoNormal" style="mso-margin-top-alt: auto; mso-margin-bottom-alt: auto;"> <!-- o ignored --></p>
<p class="MsoNormal" style="mso-margin-top-alt: auto; mso-margin-bottom-alt: auto;">This means if you do not have a dials build your cctbx will be broken<!-- o ignored --></p>
<p class="MsoNormal" style="mso-margin-top-alt: auto; mso-margin-bottom-alt: auto;"> <!-- o ignored --></p>
<p class="MsoNormal" style="mso-margin-top-alt: auto; mso-margin-bottom-alt: auto;">This is probably not the way we want things?<!-- o ignored --></p>
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<p class="MsoNormal" style="mso-margin-top-alt: auto; mso-margin-bottom-alt: auto;">I thought simtbx was a separate repo?<!-- o ignored --></p>
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<p class="MsoNormal" style="mso-margin-top-alt: auto; mso-margin-bottom-alt: auto;">Cheerio Graeme<!-- o ignored --></p>
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<p>-- <!-- o ignored --></p>
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