<html><body><div style="color:#000; background-color:#fff; font-family:HelveticaNeue, Helvetica Neue, Helvetica, Arial, Lucida Grande, sans-serif;font-size:10pt">hi,<br>we have no chains defined<br>that column is empty for all atoms<br><div><br><span></span></div><div style="color: rgb(0, 0, 0); font-size: 13.3333px; font-family: HelveticaNeue,Helvetica Neue,Helvetica,Arial,Lucida Grande,sans-serif; background-color: transparent; font-style: normal;"><span>thanks</span></div><div style="color: rgb(0, 0, 0); font-size: 13.3333px; font-family: HelveticaNeue,Helvetica Neue,Helvetica,Arial,Lucida Grande,sans-serif; background-color: transparent; font-style: normal;"><span>jpd<br></span></div><div><br></div> <div style="font-family: HelveticaNeue, Helvetica Neue, Helvetica, Arial, Lucida Grande, sans-serif; font-size: 10pt;"> <div style="font-family: HelveticaNeue, Helvetica Neue, Helvetica, Arial, Lucida Grande, sans-serif; font-size: 12pt;"> <div
dir="ltr"> <hr size="1"> <font face="Arial" size="2"> <b><span style="font-weight:bold;">From:</span></b> Pavel Afonine <pafonine@lbl.gov><br> <b><span style="font-weight: bold;">To:</span></b> phenixbb@phenix-online.org <br> <b><span style="font-weight: bold;">Sent:</span></b> Thursday, December 19, 2013 4:39 PM<br> <b><span style="font-weight: bold;">Subject:</span></b> Re: [phenixbb] Reduce NQH<br> </font> </div> <div class="y_msg_container"><br><div id="yiv9671819609"><div>
Hello,<br clear="none">
<br clear="none">
do you have two-letter chain IDs in PDB file?<br clear="none">
<br clear="none">
Pavel<br clear="none">
<br clear="none">
<div class="yiv9671819609yqt5228101572" id="yiv9671819609yqt28379"><div class="yiv9671819609moz-cite-prefix">On 12/19/13, 4:33 PM, jp d wrote:<br clear="none">
</div>
<blockquote type="cite">
<div style="color:#000;background-color:#fff;font-family:HelveticaNeue, Helvetica Neue, Helvetica, Arial, Lucida Grande, sans-serif;font-size:8pt;">
<div><span style="font-size:10px;">hi,<br clear="none">
we were going through the logs recently and see something
odd during Reduce N/Q/H analysis<br clear="none">
the log file looks like this:<br clear="none">
================================== NQH flips
==================================<br clear="none">
r_work=0.3047 r_free=0.3518<br clear="none">
Analyzing N/Q/H residues for possible flip corrections...<br clear="none">
segID AL01 renamed chain A for Reduce N/Q/H analysis<br clear="none">
segID AL02 renamed chain B for Reduce N/Q/H analysis<br clear="none">
...<br clear="none">
segID AL29 renamed chain Y for Reduce N/Q/H analysis<br clear="none">
segID AL30 renamed chain Z for Reduce N/Q/H analysis<br clear="none">
segID AL32 renamed chain a for Reduce N/Q/H analysis<br clear="none">
segID AL33 renamed chain a for Reduce N/Q/H analysis<br clear="none">
segID AL34 renamed chain b for Reduce N/Q/H analysis<br clear="none">
segID AL35 renamed chain b for Reduce N/Q/H analysis<br clear="none">
...</span></div>
<div style="color:rgb(0, 0, 0);font-size:10px;font-family:HelveticaNeue, Helvetica Neue, Helvetica, Arial, Lucida Grande, sans-serif;background-color:transparent;font-style:normal;"><span style="font-size:10px;">segID BL28 renamed
chain z for Reduce N/Q/H analysis<br clear="none">
segID BL31 renamed chain z for Reduce N/Q/H analysis<br clear="none">
</span><span style="font-size:10px;">segID BL13 renamed chain
AA for Reduce N/Q/H analysis<br clear="none">
segID BL29 renamed chain AB for Reduce N/Q/H analysis<br clear="none">
...<br clear="none">
</span></div>
<div style="color:rgb(0, 0, 0);font-size:10px;font-family:HelveticaNeue, Helvetica Neue, Helvetica, Arial, Lucida Grande, sans-serif;background-color:transparent;font-style:normal;"><br clear="none">
</div>
<div style="color:rgb(0, 0, 0);font-size:10px;font-family:HelveticaNeue, Helvetica Neue, Helvetica, Arial, Lucida Grande, sans-serif;background-color:transparent;font-style:normal;">we noticed that <span style="font-size:10px;">the
lower case chain letters start to duplicate themselves and
are not unique to each segid.<br clear="none">
when it starts the two letter chain, everything seems unique
again.<br clear="none">
forgive me if that is expected, it just seems kind of
strange<br clear="none">
</span></div>
<div style="color:rgb(0, 0, 0);font-size:10px;font-family:HelveticaNeue, Helvetica Neue, Helvetica, Arial, Lucida Grande, sans-serif;background-color:transparent;font-style:normal;"><span style="font-size:10px;"><br clear="none">
</span></div>
<div style="color:rgb(0, 0, 0);font-size:10px;font-family:HelveticaNeue, Helvetica Neue, Helvetica, Arial, Lucida Grande, sans-serif;background-color:transparent;font-style:normal;"><span style="font-size:10px;">this was seen in
mutlple log files and we are using version<br clear="none">
Version: 1.8.4<br clear="none">
Release tag: 1496<br clear="none">
if you need our files or more details, let me know</span></div>
<div style="color:rgb(0, 0, 0);font-size:10px;font-family:HelveticaNeue, Helvetica Neue, Helvetica, Arial, Lucida Grande, sans-serif;background-color:transparent;font-style:normal;"><br clear="none">
<span style="font-size:10px;"></span></div>
<div style="color:rgb(0, 0, 0);font-size:10px;font-family:HelveticaNeue, Helvetica Neue, Helvetica, Arial, Lucida Grande, sans-serif;background-color:transparent;font-style:normal;"><span style="font-size:10px;">thanks</span></div>
<div style="color:rgb(0, 0, 0);font-size:10px;font-family:HelveticaNeue, Helvetica Neue, Helvetica, Arial, Lucida Grande, sans-serif;background-color:transparent;font-style:normal;"><span style="font-size:10px;">jpd<br clear="none">
</span></div>
</div>
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</pre>
</blockquote></div>
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