<table cellspacing="0" cellpadding="0" border="0" ><tr><td valign="top" style="font: inherit;"><br><blockquote style="border-left: 2px solid rgb(16, 16, 255); margin-left: 5px; padding-left: 5px;"><div id="yiv1061018729"><table border="0" cellpadding="0" cellspacing="0"><tbody><tr><td style="font-family: inherit; font-style: inherit; font-variant: inherit; font-weight: inherit; font-size: inherit; line-height: inherit; font-size-adjust: inherit; font-stretch: inherit; -x-system-font: none;" valign="top"><font size="2">Version: 1.7<br> Release tag: 650<br> Platform: intel-linux-2.6-x86_64 linux<br> User: haytham</font><br><br>why phenix does not recognise ACT, PO4 Sn and Br (unusual residue) as you see in this part in the Log file.. (see below)<br><br>Chain: "C"<br> Number of atoms: 4<br> Number of conformers: 1<br> Conformer:
""<br> Number of residues, atoms: 1, 4<br> Unusual residues: {'ACT': 1}<br> Classifications: {'undetermined': 1}<br> Chain: "C"<br> Number of atoms: 4<br> Number of conformers: 1<br> Conformer: ""<br> Number of residues, atoms: 1,
4<br> Unusual residues: {'ACT': 1}<br> Classifications: {'undetermined': 1}<br> Chain: "E"<br> Number of atoms: 1<br> Number of conformers: 1<br> Conformer: ""<br> Number of residues, atoms: 1, 1<br> Unusual residues: {' SN': 1}<br> Classifications: {'undetermined': 1}<br> Chain: "E"<br> Number of atoms: 1<br> Number of conformers: 1<br> Conformer: ""<br> Number of residues, atoms: 1, 1<br>
Unusual residues: {' SN': 1}<br> Classifications: {'undetermined': 1}<br> Chain: "F"<br> Number of atoms: 1<br> Number of conformers: 1<br> Conformer: ""<br> Number of residues, atoms: 1, 1<br> Unusual residues: {' SN': 1}<br> Classifications: {'undetermined': 1}<br> Chain: "G"<br> Number of atoms: 5<br> Number of conformers: 1<br> Conformer: ""<br> Number of residues, atoms: 1, 5<br> Unusual residues: {'PO4':
1}<br> Classifications: {'undetermined': 1}<br> Chain: "G"<br> Number of atoms: 5<br> Number of conformers: 1<br> Conformer: ""<br> Number of residues, atoms: 1, 5<br> Unusual residues: {'PO4': 1}<br> Classifications: {'undetermined': 1}<br> Chain: "H"<br> Number of atoms: 1<br> Number of conformers: 1<br> Conformer: ""<br> Number of residues, atoms: 1, 1<br> Unusual residues: {' BR': 1}<br>
Classifications: {'undetermined': 1}<br> Residues with excluded nonbonded symmetry interactions: 2<br> residue:<br> pdb=" SN SN E 1 " occ=0.70<br> residue:<br> pdb=" SN SN E 2 " occ=0.20<br>---------------------------------------------------------<br>when i try to refine specially the Tin atom (not other, ACT,...) in coot after phenix.refine. coot display ((no restraints Found,...lablabla))<br><br>-----------------------------------------------------------<br><br><br>this is the PDB (what is the wrong with that)<br>HETATM 3552 O HOH S 361 11.670 -4.327 9.559 1.00 34.14 O <br>TER 3553 HOH S
361 <br>HETATM 3554 OXT ACT C 1 10.133 -3.417 7.937 1.00 20.00 O <br>HETATM 3555 C ACT C 1 9.911 -2.331 7.357 1.00 20.00 C <br>HETATM 3556 O ACT C 1 10.897 -1.607 7.183 1.00 20.00 O <br>HETATM 3557
CH3 ACT C 1 8.550 -1.912 6.905 1.00 20.00 C<br>TER 3558 ACT C 1<br>HETATM 3559 OXT ACT C 2 10.700 -2.628 9.985 1.00 20.00 O <br>HETATM 3560 C ACT C 2 10.962 -1.952 11.000 1.00 20.00 C <br>HETATM 3561 O ACT C 2 11.756 -2.461 11.809 1.00 20.00 O <br>HETATM 3562 CH3 ACT C 2 10.364 -0.601
11.240 1.00 20.00 C<br>TER 3563 ACT C 2<br>HETATM 3564 SN SN E 1 6.346 -4.396 -16.894 0.70 20.00 SN<br>TER 3565 SN E 1<br>HETATM 3566 SN SN E 2 6.492 -2.146 -14.779 0.20 20.00 SN<br>TER 3567 SN E 2<br>HETATM 3568 SN SN F 1 10.186 0.632 6.366 1.00 30.00 SN<br>TER
3569 SN F 1<br>HETATM 3570 P PO4 G 1 5.763 10.047 -3.974 1.00 30.00 P <br>HETATM 3571 O1 PO4 G 1 6.960 10.924 -4.190 1.00 30.00 O <br>HETATM 3572 O2 PO4 G 1 4.531 10.872 -4.101 1.00 30.00 O <br>HETATM 3573 O3 PO4 G 1 5.758 8.978 -5.017 1.00 30.00 O <br>HETATM 3574 O4 PO4 G
1 5.835 9.456 -2.607 1.00 30.00 O<br>TER 3575 PO4 G 1<br>HETATM 3576 P PO4 G 2 9.060 -4.976 -17.812 1.00 30.00 P <br>HETATM 3577 O1 PO4 G 2 10.418 -5.179 -18.415 1.00 30.00 O <br>HETATM 3578 O2 PO4 G 2 8.223 -4.116 -18.710 1.00 30.00 O <br>HETATM 3579 O3 PO4 G 2 8.412 -6.316 -17.597 1.00
30.00 O <br>HETATM 3580 O4 PO4 G 2 9.172 -4.280 -16.485 1.00 30.00 O<br>TER 3581 PO4 G 2<br>HETATM 3582 BR BR H 1 9.484 11.317 -29.959 1.00 20.00 BR<br>TER 3583 BR H 1<br>END<br></td></tr></tbody></table></div></blockquote></td></tr></table>