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<p>Hello Joseph, </p>
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<p>Sorry for late reply, your email was not in my inbox.</p>
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I just changed my setting so that email to phenixbb@phenix-online.org will come to my inbox directly.</p>
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<p>Thank you for sharing your input file. I just ran your input pdb file, it appears that "<span style="font-family: Calibri, Helvetica, sans-serif, Helvetica, EmojiFont, "Apple Color Emoji", "Segoe UI Emoji", NotoColorEmoji, "Segoe UI Symbol", "Android Emoji", EmojiSymbols; font-size: 16px;">SO4,
"CD" are not in amber03 forcefield.</span></p>
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<p><span>I just added my comments like this</span></p>
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<div><span style="font-size: 9pt;"><b>Solution if these residue/atoms are important:</b> Fix wrong names of atoms/residues. Running real_space_refine via phenix GUI will show which atoms need to be removed/fixed</span></div>
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<div><span style="font-size: 9pt;">If gromacs amber03 force field doesn't have parameters for these residue/atoms, you may need to add parameters.</span></div>
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<div><span style="font-size: 9pt;">It is rather a sad fact that most MD simulation force fields</span><span style="font-size: 9pt;"> do not support all kinds of rare residue/atoms.</span></div>
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<div><span style="font-size: 9pt;">cryo_fit2 is under development to address this issue using phenix.eLBOW</span></div>
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<div><span style="font-size: 9pt;"> </span></div>
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<div><span style="font-size: 9pt;"><b>Solution if these residue/atoms are not important: </b></span></div>
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<div><span style="font-size: 9pt;">Remove</span><span style="font-size: 9pt;"> these \"wrong\" atoms/residues from user's input pdb file. Run</span><span style="font-size: 9pt;"> cryo_fit again</span></div>
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<div><b>Solution if your user's pdb file is big: </b></div>
<div><span style="font-size: 9pt;">Probably cryo_fit will change conformation just minimally, I would extract out these \"wrong\" atoms/residues from user's input pdb file, then add these extracted lines to cryo_fitted file</span></div>
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<div><span style="font-size: 12pt;">If you do</span></div>
<div><span style="font-size: 12pt;">git pull</span></div>
<div><span style="font-size: 12pt;">at your <phenix>/modules/cryo_fit </span></div>
<div><span style="font-size: 12pt;">and run again, you will see results at least to the final stage (that I can't run because of lack of map).</span></div>
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<div>best regards,</div>
<div>Doonam</div>
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<div id="divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" style="font-size:11pt" color="#000000"><b>From:</b> Finney, Joseph (NIH/NCI) [C] <joseph.finney@nih.gov><br>
<b>Sent:</b> Monday, April 8, 2019 9:09:23 AM<br>
<b>To:</b> Kim, Doo Nam<br>
<b>Cc:</b> bugs-from-web@phenix-online.org; phenixbb@phenix-online.org; Esser, Lothar (NCI)<br>
<b>Subject:</b> CryoFit run failure</font>
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<p class="MsoNormal">Hey Doonam,<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">As I said before I figured I would have some additional questions. The new version of phenix (1.15-3459-000) fixed my issues last week with the tutorial dataset. However, I am having trouble with our own testing dataset. As before we are
testing in GUI version first. I am using the same run conditions for both the tutorial set and out testing set.<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">I am attaching the log of the tutorial set as well as the log of our testing set and the test PDB. The density map is too large for email.<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="p1"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif">The major error I see is �</span><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:windowtext">Step 1 didn't run successfully� from the ferrtest run. Looking at
the tutorial PDB, it seems as though the header, the terminations, and the nonstandard atoms have been removed prior to use. I tried this and got a different error: �pdb file cleaning is not done, exit now�<o:p></o:p></span></p>
<p class="p1"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:windowtext"><o:p> </o:p></span></p>
<p class="p1"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:windowtext">Do you have any recommendations on how to succeed?<o:p></o:p></span></p>
<p class="p1"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:windowtext"><o:p> </o:p></span></p>
<p class="MsoNormal">Thanks in advance!<o:p></o:p></p>
<p class="MsoNormal"><b><span style="color:black">Joseph Finney [Contractor]</span></b><span style="font-size:12.0pt;color:black"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:12.0pt;color:black">Software Developer<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:black">National Cryo-EM Facility</span><span style="font-size:12.0pt;color:black"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:black">Cancer Research Technology Program</span><span style="font-size:12.0pt;color:black"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:black">Frederick National Laboratory for Cancer Research</span><span style="font-size:12.0pt;color:black"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:black">Leidos Biomedical Research Inc.</span><span style="font-size:12.0pt;color:black"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:black">PO Box B Frederick, MD 21702</span><span style="font-size:12.0pt;color:black"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:black">Tel: (301) 228-4313</span><span style="font-size:12.0pt;color:black"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:black">Cell: (615) 512-2053</span><span style="font-size:12.0pt;color:black"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:black"><a href="mailto:Joseph.finney@nih.gov"><span style="color:#954F72">Joseph.finney@nih.gov</span></a></span><span style="font-size:12.0pt;color:black"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:black"> </span><span style="font-size:12.0pt;color:black"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:black"> </span><span style="font-size:12.0pt;color:black"><o:p></o:p></span></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="p1"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:windowtext"><o:p> </o:p></span></p>
<p class="p1"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:windowtext"><o:p> </o:p></span></p>
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