<!DOCTYPE html>
<html>
<head>
<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
</head>
<body>
<p>Hi Clemens,</p>
<p>thanks for your help.</p>
<p>crossec runs fine when used directly from the command line, but
is stuck when using refine... <br>
</p>
<p>However, disabling the check about form factor seems to be
working!</p>
<p>If I can help to identify the source of the problem, don't
hesitate to get in touch,</p>
<p>kind regards</p>
<p>laurent<br>
</p>
<pre wrap="" class="moz-quote-pre">
</pre>
<div class="moz-cite-prefix">Le 13/01/2025 à 10:44, Clemens Vonrhein
a écrit :<br>
</div>
<blockquote type="cite"
cite="mid:Z4TgkRfRadcwssjt@babinet.globalphasing.com">
<pre wrap="" class="moz-quote-pre">Hi Laurent,
On Wed, Jan 08, 2025 at 09:26:31AM +0100, Laurent Maveyraud via buster-discuss wrote:
</pre>
<blockquote type="cite">
<pre wrap="" class="moz-quote-pre">I just upgraded my MacBookPro to the latest M4 chip, and have problems while
running buster (snapshot 20240710) with CCP4 9.
It seems that it get stuck at crossec step at the first cycle : crossec
keeps running (I stopped it after 15 minutes....).
</pre>
</blockquote>
<pre wrap="" class="moz-quote-pre">
That suggests a problem with the CCP4 "crossec" program. Can you try
running e.g.
crossec <<e
ATOM S
NWAV 1 1.0
e
This should be VERY fast and return you something like
...
$TABLE:Wave length v F' and F"- S :
$GRAPHS:Lambda v F' and F" S :A:2,3,4: $$
Atom_type Lambda F' F" $$
Lambda F' F" $$
S 1.0000 0.1886 0.2439
...
</pre>
<blockquote type="cite">
<pre wrap="" class="moz-quote-pre">Are there any known problems with M4 / Sequoia ?
</pre>
</blockquote>
<pre wrap="" class="moz-quote-pre">
Not from our (Global Phasing software) side (yet) - but we have only
access to a M1 system running 15.1 (where the above command works
fine).
You can switch off the check about formfactors (which is the part that
runs CROSSEC) via the
AutomaticFormfactorCorrectionAnalyse=no
parameter (until there is a better understanding where the problem
comes from).
Does that help here?
Cheers
Clemens
</pre>
<blockquote type="cite">
<pre wrap="" class="moz-quote-pre">have a nice day,
laurent
this is the command I used :
refine -p ./refine_02/refine-coot-0.pdb -Gelly ./refine_02/occ.gelly -l
../../my.restraints.cif -m ./scale_01/staraniso_alldata-unique.mtz -WAT 3 -d
refine_03 -nthreads 6 > refine_03.log &
here are the last lines of the logfile :
################################ BIG cycle 1
#################################
ESC[1mNOTEESC[m : (controllable) refinement parameters = XYZ B OCC
running BUSTER (187.01405 - 1.48565 A) in refine_03/01-BUSTER/Cycle-1
[extra library /tmp/maveyrau-BUSTER/maveyrau-1736324017-refine__22844.elib]:
ESC[1mNOTEESC[m : created file for BABSLV by removing 165 atom(s)
</pre>
</blockquote>
</blockquote>
<div class="moz-signature">-- <br>
<div class="container"
style="background-color: white;max-width: 680px;position: relative;width: 100%;padding-top: 5px;padding-left: 7px;">
<div class="col-25-ipbs"
style="display: inline-block;vertical-align: top;margin: auto;width: 20%;">
<img class="logo-ipbs"
src="https://www.ipbs.fr/others/ipbs2020.png"
alt="logo-ipbs" style="padding-right: 10px;width: 90%;"> </div>
<div class="col-75-ipbs"
style="width: 79%;display: inline-block;vertical-align: top;padding-top: 5px;">
<!-- Nom à modifier ci-dessous -->
<h1 class="nom-ipbs"
style="font-family:Arial,sans-serif;font-weight: 600;color: #22376D;font-size: 16px;margin: 0;line-height: 20px;padding-top: 3px;">Laurent
Maveyraud</h1>
<!-- Rôle à modifier ci-dessous -->
<h2 class="role-ipbs"
style="font-family:Arial,sans-serif;font-weight: 600;color: #2CAFE6;font-size: 14px;margin: 0;line-height: 20px;padding-top: 3px;">Professor
of Biophysics | University of Toulouse </h2>
<!-- Description à modifier ci-dessous -->
<p class="description-ipbs"
style="font-family:Arial,sans-serif;font-weight: 600;color: #2CAFE6;font-size: 14px;margin: 0;line-height: 20px;padding-top: 3px;">Doctoral
School Biology - Health - Biotechnologies</p>
<!-- Liens à modifier ci-dessous -->
<div class="liens-ipbs"
style="border-left: 3px solid #2CAFE6;padding-left: 10px;padding-top: 3px;display: inline-block;">
<p class="tel-ipbs"
style="font-family:Arial,sans-serif;font-weight: 700;color: #22376D;font-size: 12px;line-height:18px;margin: 0px;"><img
src="https://www.ipbs.fr/others/j7k4.png"
style="width: 10px;margin-right: 5px;"><span
style="font-family:Arial,sans-serif;font-weight: 700;color: #22376D;font-size: 12px;line-height:18px;margin: 0px;text-decoration: none !important;">+33
5 61 17 54 35 | +33 6 46 04 21 11 |</span> <a
href="mailto:laurent.maveyraud@ipbs.fr"
style="text-decoration: none;font-family:Arial,sans-serif;font-weight: 700;color: #22376D;font-size: 12px;line-height:18px;">Laurent.Maveyraud@ipbs.fr</a></p>
<p class="adresse-ipbs"
style="font-family:Arial,sans-serif;font-weight: 700;color: #22376D;font-size: 12px;line-height:18px;margin: 0px;"><img
src="https://www.ipbs.fr/others/eabv.png"
style="width: 10px;margin-right: 5px;"><span
style="font-family:Arial,sans-serif;font-weight: 700;color: #22376D;font-size: 12px;line-height:18px;margin: 0px;text-decoration: none !important;">UMR5089
| CNRS - UT3 | 205 Route de Narbonne BP 64182 - 31077
Toulouse Cedex 4</span></p>
<div class="reseaux-sociaux-ipbs">
<p class="site-ipbs"
style="font-family:Arial,sans-serif;font-weight: 700;color: #22376D;font-size:12px;line-height:18px;margin: 0px;display: inline-block;"><img
src="https://www.ipbs.fr/others/3st5.png"
style="width: 10px;margin-right: 5px;"><a
href="https://www.ipbs.fr"
style="text-decoration: none;font-family:Arial,sans-serif;font-weight: 700;color: #22376D;font-size: 12px;line-height:18px;">ipbs.fr</a></p>
<p class="twitter-ipbs"
style="font-family:Arial,sans-serif;font-weight: 700;color: #22376D;font-size: 12px;line-height:18px;margin: 0px;display: inline-block;"><img
src="https://www.ipbs.fr/others/z411.png"
style="width: 10px;margin-right: 5px;"><a
href="https://twitter.com/IpbsToulouse"
style="text-decoration: none;font-family:Arial,sans-serif;font-weight: 700;color: #22376D;font-size: 12px;line-height:18px;">@IpbsToulouse
</a></p>
<p class="facebook-ipbs"
style="font-family:Arial,sans-serif;font-weight: 700;color: #22376D;font-size: 12px;line-height:18px;margin: 0px;display: inline-block;"><img
src="https://www.ipbs.fr/others/34qf.png"
style="height: 10px;margin-right: 5px;"><a
href="https://www.facebook.com/IPBS.CNRS/"
style="text-decoration: none;font-family:Arial,sans-serif;font-weight: 700;color: #22376D;font-size: 12px;line-height:18px;">ipbs.cnrs</a></p>
<img src="https://www.ipbs.fr/others/3st5.png"
style="width: 10px;margin-right: 5px;"><a
href="https://www.ipbs.fr/structural-biophysics"
style="text-decoration: none;font-family:Arial,sans-serif;font-weight: 700;color: #22376D;font-size: 12px;line-height:18px;">our
group</a> <img
src="https://orcid.org/sites/default/files/images/orcid_16x16.png"
style="width: 10px;margin-right: 5px;"><a
href="https://orcid.org/0000-0003-4610-8319"
style="text-decoration: none;font-family:Arial,sans-serif;font-weight: 700;color: #22376D;font-size: 12px;line-height:18px;"
l.maveyraud="" <="" a=""><img
src="https://www.ipbs.fr/others/linke.png"
style="height: 10px;margin-right: 5px;"></a><a
href="https://www.linkedin.com/in/laurent-maveyraud-8b394a5/"
style="text-decoration: none;font-family:Arial,sans-serif;font-weight: 700;color: #22376D;font-size: 12px;line-height:18px;"
l.="" maveyraud="" <="" a="">
<p></p>
</a></div>
<a
href="https://www.linkedin.com/in/laurent-maveyraud-8b394a5/"
style="text-decoration: none;font-family:Arial,sans-serif;font-weight: 700;color: #22376D;font-size: 12px;line-height:18px;"
l.="" maveyraud="" <="" a=""> </a></div>
<a
href="https://www.linkedin.com/in/laurent-maveyraud-8b394a5/"
style="text-decoration: none;font-family:Arial,sans-serif;font-weight: 700;color: #22376D;font-size: 12px;line-height:18px;"
l.="" maveyraud="" <="" a=""> </a></div>
<a href="https://www.linkedin.com/in/laurent-maveyraud-8b394a5/"
style="text-decoration: none;font-family:Arial,sans-serif;font-weight: 700;color: #22376D;font-size: 12px;line-height:18px;"
l.="" maveyraud="" <="" a="">
</a></div>
<a href="https://www.linkedin.com/in/laurent-maveyraud-8b394a5/"
style="text-decoration: none;font-family:Arial,sans-serif;font-weight: 700;color: #22376D;font-size: 12px;line-height:18px;"
l.="" maveyraud="" <="" a="">
<p></p>
<style>
@media screen and (max-width: 600px) {
.nom-ipbs {
font-size: 12px !important;
}
.role-ipbs {
font-size: 10px !important;
}
}
</style></a></div>
</body>
</html>