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<font class="Apple-style-span" face="Tahoma" size="2">Dear All,</font><div style="font-family: Tahoma; font-size: 10pt; "><br></div><div style="font-family: Tahoma; font-size: 10pt; ">I am new to Phenix. I have a structure 2.74 A structure with R/freeR 22.7/27.9%. But the molprobity score is 50th percentile.</div><div><font class="Apple-style-span" face="Tahoma" size="2">If I fix the outliers they wouldn't go away and molprobity score remains same or get worst. </font></div><div><font class="Apple-style-span" face="Tahoma" size="2">This structure was solved by molecular replacement using a bacterial protein with 38% identity.</font></div><div><font class="Apple-style-span" face="Tahoma" size="2">I am wondering if there is an model bias? I have not identified particular region in model for bias.</font></div><div><font class="Apple-style-span" face="Tahoma" size="2"><br></font></div><div><font class="Apple-style-span" face="Tahoma" size="2">My questions are: Am I right in thinking if there is model bias based on above info?</font></div><div><font class="Apple-style-span" face="Tahoma" size="2">I added my .pdb and .mtz and do SA-composit omit map. This is running from morning and I have feeling that I will get results after thanksgiving. Is this the correct way of doing a omit map for the purpose I mentioned? </font></div><div><font class="Apple-style-span" face="Tahoma" size="2">I saw lot of discussions on omit map but couldn't grasp everything and I am sure same questions might have been asked before.</font></div><div><font class="Apple-style-span" face="Tahoma" size="2">I have couple of classical papers next to me but I need help. </font><span class="Apple-style-span" style="font-family: Tahoma; font-size: 10pt; ">I would appreciate if you could help me out either suggesting me how and what to do or pointing to previous thread over the this BB.</span></div><div><font class="Apple-style-span" face="Tahoma" size="2"><br></font></div><div><font class="Apple-style-span" face="Tahoma" size="2">Happy Thanksgiving..</font></div><div><font class="Apple-style-span" face="Tahoma" size="2"><br></font></div><div><font class="Apple-style-span" face="Tahoma" size="2">Rajesh</font></div><div><font class="Apple-style-span" face="Tahoma" size="2"><br></font><br><div style="font-family: Tahoma; font-size: 10pt; "><hr id="stopSpelling">Date: Tue, 22 Nov 2011 10:50:53 -0500<br>From: hdutta10@gmail.com<br>To: phenixbb@phenix-online.org<br>Subject: [phenixbb] measuring angle<br><br>Hi,<br><br>Could you please tell me how I can measure angle between two helices. Can COOT or PYMOL measure this? <br>I have another question.<br><br>In PDBSET, I can use CHAIN command in shell script to write a pdb file with a desired chain ID. What is the command<br>
in shell script to write a pdb file with a desired SEGID? As for example:-<br><br>pdbset xyzin start.pdb xyzout end.pdb <<eof >& pdbset.log<br>ROTATE [INVERT] [MATRIX] values<br>CHAIN A<br>end<br>eof <br><br>
This will change the chain ID to A after rotation. But, I also like to give a segid in the end coordinate.<br><br>Thank you in advance and have a nice THANKS GIVING WEEKEND<br><br>Hena<br>
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