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<div>Hi guys,<br>
Sorry for the detailed questions from a beginner! I am starting a modeling/refinement work for a set of cryo-EM data.<br>
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<div>Data basic information: phage data (looks like a ball with P1 space group), map size ~870 MB, resolution ~6 A, two X-ray structures for model building<br>
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General strategies: I select COOT for the model building; using phenix.real_sapce_refine for the real space refinement with secondary structure restrain and REFMAC for the reciprocal space refinement.<br>
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<div>Few questions are listed here.<br>
1. The map was too bigger to open it in COOT. The phenix.map_to_structure_factors was used to obtaine ~120 MB sized MTZ file (still a little big for my computer). I manually build up the whole ball-shaped phage with the rigid body fit in COOT (from two X-ray
structures to 120 chains). My first question will be: In this case, should I crop the map in Chimera or other software and only focus on a small asymmetric unit to do the model building and the followed refinement.<br>
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2. I would like to do a real space refinement after the model building. <br>
Input files: <br>
A pdb file I just built up from COOT<br>
A original MAP file<br>
A transfered MTZ file<br>
Two restraint files from two X-ray structures by ProSMART (TXT formart)<br>
The refinement parameters I would like to select in GUI interface:<br>
minimization_global, rigid_body, local_grid_search, adp<br>
Use secondary structure restraints<br>
Reference model restraints: use starting model as reference, main chain, side chain, fix outliers, secondary structure only<br>
Rotamer restraints<br>
Ramachandran restraints<br>
Show per residue<br>
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My second set of questions: Should I select the MAP file (~870 MB) or the MTZ file (~120 MB)? Is that necessary to add the two restraint files from ProSMART if I use the starting model as reference? Is the refinement parameters selected properly?<br>
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3. I gave a try by phenix.real_space_refine. An first error showed up:<br>
Number of atoms with unknown nonbonded energy type symbols: 6840<br>
"ATOM 184 HG1 SER 1 12 .*. H "<br>
"ATOM 458 HG1 SER 1 30 .*. H "<br>
"ATOM 699 HG1 SER 1 45 .*. H "<br>
"ATOM 720 HG1 SER 1 47 .*. H "<br>
"ATOM 762 HG1 SER 1 50 .*. H "<br>
"ATOM 1241 HG1 SER 1 81 .*. H "<br>
"ATOM 1465 HG1 SER 1 95 .*. H "<br>
"ATOM 1747 HG1 SER 1 113 .*. H "<br>
"ATOM 1758 HG1 SER 1 114 .*. H "<br>
"ATOM 2173 HG1 SER 1 141 .*. H "<br>
... (remaining 6830 not shown)</div>
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<div>I tried phenix.ready_set to fix this problem according to a previous discussion but it gave me another error: ENDMDL record missing at end of input.<br>
Thus my third question will be how to fix the first error?<br>
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Thank you for patience! I would really appreciate your help!</div>
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<div>Bing<br>
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