<html><head><meta http-equiv="Content-Type" content="text/html; charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class="">Using single-precision for XPLOR output fixed the problem<br class=""><div><br class=""><blockquote type="cite" class=""><br class="Apple-interchange-newline"><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px;" class=""><span style="font-family: -webkit-system-font, Helvetica Neue, Helvetica, sans-serif; color:rgba(0, 0, 0, 1.0);" class=""><b class="">From: </b></span><span style="font-family: -webkit-system-font, Helvetica Neue, Helvetica, sans-serif;" class="">ISHWOR POUDYAL</span></div></blockquote><blockquote type="cite" class=""><div class=""><div class=""><div style="font-family:verdana, helvetica, sans-serif;font-size:10px;" class=""><div style="font-family:verdana, helvetica, sans-serif;font-size:10px;" class=""><div class=""><div class="">Hello Tom,</div></div><div class=""><br class=""></div><div class="">Many thanks! I changed the double precision to single-precision and it works.</div><div class=""><br class=""></div><div class="">Ishwor</div>
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On Monday, August 13, 2018, 12:09:15 PM CDT, Tom Goddard <<a href="mailto:goddard@sonic.net" class="">goddard@sonic.net</a>> wrote:
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<div class=""><div id="yiv0371423699" class=""><div class="">HI Ishwor,<div class="yiv0371423699"><br clear="none" class="yiv0371423699"></div><div class="yiv0371423699"> The XPLOR format requires lines where the first 12 columns holds the first number, the second 12 columns holds the second number, … 12 columns per number. The example lines you provide do not use 12 columns per number. The software that wrote that file is not writing it in the correct format. My guess is that software fails because of the 3 digit exponents (e.g "E-166”) — probably the writing software only fails to follow the 12 columns per number rule when you have 3-digit exponents. In single-precision (32-bit floats) you would never get 3 digit exponents and perhaps the error is that the writing program was converted from single precision to double precision.</div><div class="yiv0371423699"><br clear="none" class="yiv0371423699"></div><div class="yiv0371423699"><span class="yiv0371423699Apple-tab-span" style="white-space:pre;"> </span>Tom</div><div class="yiv0371423699"><br clear="none" class="yiv0371423699"><div class=""><br clear="none" class="yiv0371423699"><blockquote class="yiv0371423699" type="cite"><div class="yiv0371423699yqt0606334630" id="yiv0371423699yqt76195"><div class="yiv0371423699">On Aug 12, 2018, at 7:51 PM, ISHWOR POUDYAL <<a rel="nofollow" shape="rect" class="yiv0371423699" ymailto="mailto:ishwor_p_19@yahoo.com" target="_blank" href="mailto:ishwor_p_19@yahoo.com">ishwor_p_19@yahoo.com</a>> wrote:</div><br clear="none" class="yiv0371423699Apple-interchange-newline"><div class="yiv0371423699"><div class="yiv0371423699"><div class="yiv0371423699" style="font-family:verdana, helvetica, sans-serif;font-size:10px;"><div class="yiv0371423699">Hello All,</div><div class="yiv0371423699"><br clear="none" class="yiv0371423699"></div><div class="yiv0371423699">I try to convert electron density obtained from iterative phasing in *.xplor file format to view in the chimera. Something went wrong which I could not figure out. The generated density reads as follows for the first few lines. </div><div class="yiv0371423699"><br clear="none" class="yiv0371423699"></div><div class="yiv0371423699">##########################################################</div><div class="yiv0371423699"><span class="yiv0371423699"></span><p class="yiv0371423699ydpc5675b8dp1"><span class="yiv0371423699ydpc5675b8ds1"><span class="yiv0371423699ydpc5675b8dApple-converted-space"> </span><i class="yiv0371423699">241<span class="yiv0371423699ydpc5675b8dApple-converted-space"> </span>-120 <span class="yiv0371423699ydpc5675b8dApple-converted-space"> </span>120 <span class="yiv0371423699ydpc5675b8dApple-converted-space"> </span>241<span class="yiv0371423699ydpc5675b8dApple-converted-space"> </span>-120 <span class="yiv0371423699ydpc5675b8dApple-converted-space"> </span>120 <span class="yiv0371423699ydpc5675b8dApple-converted-space"> </span>241<span class="yiv0371423699ydpc5675b8dApple-converted-space"> </span>-120 <span class="yiv0371423699ydpc5675b8dApple-converted-space"> </span>120</i></span></p><p class="yiv0371423699ydpc5675b8dp1"><span class="yiv0371423699ydpc5675b8ds1"><i class="yiv0371423699"><span class="yiv0371423699ydpc5675b8dApple-converted-space"> </span>3.26000E+02 3.26000E+02 3.26000E+02 9.00000E+01 9.00000E+01 9.00000E+01</i></span></p><p class="yiv0371423699ydpc5675b8dp1"><span class="yiv0371423699ydpc5675b8ds1"><i class="yiv0371423699">ZYX</i></span></p><p class="yiv0371423699ydpc5675b8dp1"><span class="yiv0371423699ydpc5675b8ds1"><i class="yiv0371423699"><span class="yiv0371423699ydpc5675b8dApple-converted-space"> </span>0</i></span></p><p class="yiv0371423699ydpc5675b8dp1"><span class="yiv0371423699ydpc5675b8ds1"><i class="yiv0371423699"><span class="yiv0371423699ydpc5675b8dApple-converted-space"> </span>2.21928E-166 0.00000E+00 1.59337E-167 0.00000E+00 1.14399E-168 0.00000E+00</i></span></p><p class="yiv0371423699ydpc5675b8dp1"><span class="yiv0371423699ydpc5675b8ds1"><i class="yiv0371423699"><span class="yiv0371423699ydpc5675b8dApple-converted-space"> </span>8.21346E-170 0.00000E+00 5.89700E-171 0.00000E+00 4.23386E-172 0.00000E+00</i></span></p>#############################################################</div><div class="yiv0371423699"><br clear="none" class="yiv0371423699"></div><div class="yiv0371423699">While I try to view the electron density in chimera it says</div><div class="yiv0371423699">"SyntaxError:Bad number format in line <span class="yiv0371423699"><i class="yiv0371423699" style="font-family:verdana, helvetica, sans-serif;font-size:10px;"><span class="yiv0371423699ydpc5675b8dApple-converted-space"> </span>2.21928E-166 0.00000E+00 1.59337E-167 0.00000E+00 1.14399E-168 0.00000E+00</i></span>"</div><div class="yiv0371423699"><br clear="none" class="yiv0371423699"></div><div class="yiv0371423699">WOuld you please help me out</div><div class="yiv0371423699"><br clear="none" class="yiv0371423699"></div><div class="yiv0371423699">Many thanks</div><div class="yiv0371423699" style="font-family:verdana, helvetica, sans-serif;font-size:10px;"></div></div></div>_______________________________________________<br clear="none" class="yiv0371423699">Chimera-users mailing list: <a rel="nofollow" shape="rect" class="yiv0371423699" ymailto="mailto:Chimera-users@cgl.ucsf.edu" target="_blank" href="mailto:Chimera-users@cgl.ucsf.edu">Chimera-users@cgl.ucsf.edu</a><br clear="none" class="yiv0371423699">Manage subscription: <a rel="nofollow" shape="rect" class="yiv0371423699" target="_blank" href="http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users">http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users</a><br clear="none" class="yiv0371423699"></div></div></blockquote></div><br clear="none" class="yiv0371423699"></div></div></div></div>
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