<html>
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8">
</head>
<body text="#000000" bgcolor="#FFFFFF">
<p><br>
</p>
<p>Yes, that's what it does. If you look at
tst_nanoBragg_minimal.py you will see some code for running it.
Currently, I have the call to "sfall" commented out for testing
purposes, but you can uncomment it to make structure factors from
a PDB as shown.</p>
<p> Twinning is fairly straightforward. You can cheat by
"pre-twinning" the data (square the Fs, re-index, weighted sum,
then square root). However, what I generally do for twinning is
generate two diffraction images with different crystal
orientations and then add them together. My plan is to set this
up so you do the image manipulations as flex arrays. This would
also allow background to be done separately. Then you would use
"noisify" to add the final noise and generate the image files
using the new dxtbx output functions. Working on getting those
"pythonized" today. In the meantime, it should be a simple matter
to generate noiseless test images.</p>
<p>Or, if you're in a hurry, I can probably tell you how to do
something using the standalone code. Like this twinning example:</p>
<p><a class="moz-txt-link-freetext" href="http://bl831.als.lbl.gov/~jamesh/challenge/twin/">http://bl831.als.lbl.gov/~jamesh/challenge/twin/</a><br>
</p>
<p>Does that help?</p>
<p>-James<br>
</p>
<br>
<div class="moz-cite-prefix">On 6/5/2017 4:14 AM, R.D. Oeffner
wrote:<br>
</div>
<blockquote type="cite"
cite="mid:2d7a4b576264307c7cb421ad3ecd4417@cam.ac.uk">
<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>
<p> </p>
<p> </p>
<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/%7Ejamesh/mlfsom/"
moz-do-not-send="true">http://bl831.als.lbl.gov/~jamesh/mlfsom/</a><br>
<a class="moz-txt-link-freetext"
href="http://bl831.als.lbl.gov/%7Ejamesh/nanoBragg/"
moz-do-not-send="true">http://bl831.als.lbl.gov/~jamesh/nanoBragg/</a><br>
<a class="moz-txt-link-freetext"
href="http://bl831.als.lbl.gov/%7Ejamesh/nearBragg/"
moz-do-not-send="true">http://bl831.als.lbl.gov/~jamesh/nearBragg/</a><br>
<a class="moz-txt-link-freetext"
href="http://bl831.als.lbl.gov/%7Ejamesh/nonBragg/"
moz-do-not-send="true">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"
moz-do-not-send="true">markus.gerstel@diamond.ac.uk</a>
wrote:</div>
<blockquote type="cite" style="padding-left:5px;
border-left:#1010ff 2px solid; margin-left:5px"><!-- meta ignored -->
<div class="WordSection1">
<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>
<p class="MsoNormal"><span style="font-size: 11.0pt;
font-family: 'Calibri',sans-serif; color: #1f497d;
mso-fareast-language: EN-US;"><!-- 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;">Sorry, outsider
perspective here. I don't know what simtbx does or is
supposed to do.<!-- 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;"><!-- 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;">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>
<p class="MsoNormal"><span style="font-size: 11.0pt;
font-family: 'Calibri',sans-serif; color: #1f497d;
mso-fareast-language: EN-US;"><!-- 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;">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>
<p class="MsoNormal"><span style="font-size: 11.0pt;
font-family: 'Calibri',sans-serif; color: #1f497d;
mso-fareast-language: EN-US;"><!-- 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;">-Markus<!-- 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;"><!-- o ignored --> </span></p>
<p class="MsoNormal"><a name="_MailEndCompose"
moz-do-not-send="true"></a><span style="font-size:
11.0pt; font-family: 'Calibri',sans-serif; color:
#1f497d; mso-fareast-language: EN-US;"><!-- o ignored --> </span></p>
<span style="mso-bookmark: _MailEndCompose;"></span>
<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"
moz-do-not-send="true">cctbxbb-bounces@phenix-online.org</a>
[<a class="moz-txt-link-freetext"
href="mailto:cctbxbb-bounces@phenix-online.org"
moz-do-not-send="true">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"
moz-do-not-send="true"><cctbxbb@phenix-online.org></a><br>
<strong>Subject:</strong> Re: [cctbxbb] simtbx<!-- o ignored --></span></p>
<p class="MsoNormal"><!-- o ignored --> </p>
<div>
<p class="MsoNormal">Markus,<!-- o ignored --></p>
<div>
<p class="MsoNormal"><!-- o ignored --> </p>
</div>
<div>
<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>
</div>
<div>
<p class="MsoNormal"><!-- o ignored --> </p>
</div>
<div>
<p class="MsoNormal">Nick<!-- o ignored --></p>
</div>
</div>
<div>
<p class="MsoNormal"><br clear="all">
<!-- o ignored --></p>
<div>
<div>
<div>
<div>
<div>
<div>
<div>
<div>
<p class="MsoNormal">Nicholas K. Sauter,
Ph. D.<br>
Senior Scientist, Molecular Biophysics
& Integrated Bioimaging Division<!-- o ignored --></p>
<div>
<p class="MsoNormal">Lawrence Berkeley
National Laboratory<br>
1 Cyclotron Rd., Bldg. 33R0345<br>
Berkeley, CA 94720<br>
(510) 486-5713<!-- o ignored --></p>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
<p class="MsoNormal"><!-- o ignored --> </p>
<div>
<p class="MsoNormal">On Wed, May 3, 2017 at 7:49 AM,
<<a href="mailto:markus.gerstel@diamond.ac.uk"
moz-do-not-send="true">markus.gerstel@diamond.ac.uk</a>>
wrote:<!-- o ignored --></p>
<blockquote style="border: none; margin-left: 4.8pt;
margin-right: 0cm;">
<div>
<div>
<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"
moz-do-not-send="true">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"
moz-do-not-send="true">
https://github.com/cctbx/cctbx_project/tree/master/simtbx</a>
</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;">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>
<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;">NB: This issue is
independent of resolving the
dials-dependency issue.</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;">-Markus</span><!-- o ignored --></p>
<p class="MsoNormal" style="mso-margin-top-alt:
auto; mso-margin-bottom-alt: auto;"><a
name="m_-2651995399140751371__MailEndCompose"
moz-do-not-send="true"></a><span
style="color: #1f497d;"> </span><!-- o ignored --></p>
<div>
<div style="border: none; padding: 3.0pt 0cm
0cm 0cm;">
<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"
moz-do-not-send="true">cctbxbb-bounces@phenix-online.org</a>
[mailto:<a
href="mailto:cctbxbb-bounces@phenix-online.org"
moz-do-not-send="true">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"
moz-do-not-send="true">Graeme.Winter@Diamond.ac.uk</a>>;
<a
href="mailto:cctbxbb@phenix-online.org"
moz-do-not-send="true">cctbxbb@phenix-online.org</a><br>
<strong>Subject:</strong> Re: [cctbxbb]
simtbx</span><!-- o ignored --></p>
</div>
</div>
<div>
<div>
<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>
<div>
<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"
moz-do-not-send="true">Graeme.Winter@Diamond.ac.uk</a>
wrote:<!-- o ignored --></p>
</div>
<blockquote style="margin-top: 5.0pt;
margin-bottom: 5.0pt;">
<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>
<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;">I thought
simtbx was a separate repo?<!-- 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;">Cheerio
Graeme<!-- o ignored --></p>
<p> <!-- o ignored --></p>
<p>-- <!-- o ignored --></p>
<p>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.<br>
Any opinions expressed within this
e-mail are those of the individual and
not necessarily of Diamond Light Source
Ltd. <br>
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.<br>
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<br>
<!-- o ignored --></p>
</blockquote>
<p class="MsoNormal"
style="mso-margin-top-alt: auto;
mso-margin-bottom-alt: auto;"> <!-- o ignored --></p>
</div>
</div>
</div>
<div>
<div>
<p> <!-- o ignored --></p>
<p>-- <!-- o ignored --></p>
<p>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.<br>
Any opinions expressed within this e-mail
are those of the individual and not
necessarily of Diamond Light Source Ltd. <br>
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.<br>
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<br>
<!-- o ignored --></p>
</div>
</div>
</div>
<p class="MsoNormal" style="margin-bottom: 12.0pt;"><br>
_______________________________________________<br>
cctbxbb mailing list<br>
<a href="mailto:cctbxbb@phenix-online.org"
moz-do-not-send="true">cctbxbb@phenix-online.org</a><br>
<a
href="http://phenix-online.org/mailman/listinfo/cctbxbb"
moz-do-not-send="true">http://phenix-online.org/mailman/listinfo/cctbxbb</a><!-- o ignored --></p>
</blockquote>
</div>
<p class="MsoNormal"><!-- o ignored --> </p>
</div>
</div>
<br>
<fieldset class="mimeAttachmentHeader"></fieldset>
<br>
<pre>_______________________________________________
cctbxbb mailing list
<a class="moz-txt-link-abbreviated" href="mailto:cctbxbb@phenix-online.org" moz-do-not-send="true">cctbxbb@phenix-online.org</a>
<a class="moz-txt-link-freetext" href="http://phenix-online.org/mailman/listinfo/cctbxbb" moz-do-not-send="true">http://phenix-online.org/mailman/listinfo/cctbxbb</a>
</pre>
</blockquote>
<br>
<br>
<fieldset class="mimeAttachmentHeader"></fieldset>
<br>
<pre>_______________________________________________
cctbxbb mailing list
<a class="moz-txt-link-abbreviated" href="mailto:cctbxbb@phenix-online.org" moz-do-not-send="true">cctbxbb@phenix-online.org</a>
<a class="moz-txt-link-freetext" href="http://phenix-online.org/mailman/listinfo/cctbxbb" moz-do-not-send="true">http://phenix-online.org/mailman/listinfo/cctbxbb</a>
</pre>
</blockquote>
<br>
<!-- html ignored --><br>
<pre>_______________________________________________
cctbxbb mailing list
<a href="mailto:cctbxbb@phenix-online.org" moz-do-not-send="true">cctbxbb@phenix-online.org</a>
<a href="http://phenix-online.org/mailman/listinfo/cctbxbb" moz-do-not-send="true">http://phenix-online.org/mailman/listinfo/cctbxbb</a>
</pre>
</blockquote>
<p> </p>
<br>
<fieldset class="mimeAttachmentHeader"></fieldset>
<br>
<pre wrap="">_______________________________________________
cctbxbb mailing list
<a class="moz-txt-link-abbreviated" href="mailto:cctbxbb@phenix-online.org">cctbxbb@phenix-online.org</a>
<a class="moz-txt-link-freetext" href="http://phenix-online.org/mailman/listinfo/cctbxbb">http://phenix-online.org/mailman/listinfo/cctbxbb</a>
</pre>
</blockquote>
<br>
</body>
</html>