Hello all, I have been having very weird problems refining a structure with several ligands. The weirdest problem is that if I try to run ligand fit giving just the name of the ligands, no problem - it finds the ligands (FAD and MTE). I save the pdb with all the ligands in and phenix.refine complains that MTE is not recognised, I have to run ready-set. I do it. Run phenix.refine again, and now it complains with the following: Number of atoms with unknown nonbonded energy type symbols: 116 "HETATM18439 C1' MTE A3003 .*. C " "HETATM18441 C2' MTE A3003 .*. C " "HETATM18443 C3' MTE A3003 .*. C " "HETATM18444 O3' MTE A3003 .*. O " "HETATM18474 N9A FAD A3005 .*. N " "HETATM18475 C8A FAD A3005 .*. C " "HETATM18476 N7A FAD A3005 .*. N " "HETATM18477 C5A FAD A3005 .*. C " "HETATM18478 C6A FAD A3005 .*. C " "HETATM18480 N1A FAD A3005 .*. N " ... (remaining 106 not shown) Any help will be greatly appreciated. Jose José Trincão, PhD CQFB@FCT-UNL 2829-516 Caparica, Portugal "It's very hard to make predictions... especially about the future" - Niels Bohr
Hi Jose,
Could you send me (off-list) the fragment from your PDB file with the
two ligands?
Could you also let me know the phenix version number of your installation?
Ralf
On Tue, Jul 5, 2011 at 5:53 AM, José Trincão
Hello all, I have been having very weird problems refining a structure with several ligands. The weirdest problem is that if I try to run ligand fit giving just the name of the ligands, no problem - it finds the ligands (FAD and MTE). I save the pdb with all the ligands in and phenix.refine complains that MTE is not recognised, I have to run ready-set. I do it. Run phenix.refine again, and now it complains with the following: Number of atoms with unknown nonbonded energy type symbols: 116 "HETATM18439 C1' MTE A3003 .*. C " "HETATM18441 C2' MTE A3003 .*. C " "HETATM18443 C3' MTE A3003 .*. C " "HETATM18444 O3' MTE A3003 .*. O " "HETATM18474 N9A FAD A3005 .*. N " "HETATM18475 C8A FAD A3005 .*. C " "HETATM18476 N7A FAD A3005 .*. N " "HETATM18477 C5A FAD A3005 .*. C " "HETATM18478 C6A FAD A3005 .*. C " "HETATM18480 N1A FAD A3005 .*. N " ... (remaining 106 not shown)
Any help will be greatly appreciated.
Jose
José Trincão, PhD CQFB@FCT-UNL 2829-516 Caparica, Portugal
"It's very hard to make predictions... especially about the future" - Niels Bohr
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Hello, Would anyone know an easy way of imposing disulphide bridges during the initial rosetta building step of phenix.mr_rosetta? One thing I have tried is putting SSBOND information in the header of the input model + renaming the relevant cysteines to CYD. At the start of the rosetta rebuilding, the CYD residues were indeed read with connections as given in the header. But then it went on reverting what I think are the less "geometrically proper" bridges to CYS and subsequently re-connected them wrongly. The resulting models are completely messed up. Any help would be greatly appreciated, Elena Details: This is my input script #!/bin/sh # #Running mr_rosetta with a model that is already place in the unit cell # setenv PHENIX_ROSETTA_PATH /rosetta/321 set ROSETTA_BIN = /rosetta/321/rosetta_source/bin phenix.mr_rosetta \ seq_file= Seq.dat \ data= rosettatest.mtz \ search_models= rosettatest.pdb \ already_placed=True \ fragment_files = aat000_03_05.200_v1_3.gz \ fragment_files = aat000_09_05.200_v1_3.gz \ rescore_mr.relax=False \ rosetta_models=20 \ ncs_copies=1 \ space_group=r32 \ use_all_plausible_sg=False \ nproc=3 Excerpt of rebuild.log: ...(first it reads in the header info) core.conformation.Conformation: Connecting residues: 48 ( CYD ) and 166 ( CYD ) at atoms SG and SG core.conformation.Conformation: with mututal distances: 3.8087 and 0.733173 core.conformation.Conformation: Connecting residues: 83 ( CYD ) and 93 ( CYD ) at atoms SG and SG core.conformation.Conformation: with mututal distances: 3.09896 and 3.52089 core.conformation.Conformation: Connecting residues: 179 ( CYD ) and 222 ( CYD ) at atoms SG and SG core.conformation.Conformation: with mututal distances: 1.70468 and 1.16652 core.conformation.Conformation: Connecting residues: 208 ( CYD ) and 235 ( CYD ) at atoms SG and SG core.conformation.Conformation: with mututal distances: 2.49179 and 3.53666 core.conformation.Conformation: Connecting residues: 237 ( CYD ) and 248 ( CYD ) at atoms SG and SG core.conformation.Conformation: with mututal distances: 3.73229 and 5.15675 core.conformation.Conformation: Connecting residues: 251 ( CYD ) and 265 ( CYD ) at atoms SG and SG core.conformation.Conformation: with mututal distances: 3.38617 and 3.74316 core.conformation.Conformation: Connecting residues: 268 ( CYD ) and 282 ( CYD ) at atoms SG and SG core.conformation.Conformation: with mututal distances: 2.6711 and 2.63 core.conformation.Conformation: Connecting residues: 284 ( CYD ) and 300 ( CYD ) at atoms SG and SG core.conformation.Conformation: with mututal distances: 0.617564 and 2.38221 core.conformation.Conformation: Connecting residues: 341 ( CYD ) and 355 ( CYD ) at atoms SG and SG core.conformation.Conformation: with mututal distances: 4.70923 and 2.94228 core.conformation.Conformation: Connecting residues: 344 ( CYD ) and 352 ( CYD ) at atoms SG and SG core.conformation.Conformation: with mututal distances: 1.53246 and 3.97459 ...(now it goes through the given list and rejects some) core.conformation.Conformation: Found disulfide between residues 48 166 core.conformation.Conformation: current variant for 48 CYD core.conformation.Conformation: current variant for 166 CYD core.conformation.Conformation: current variant for 48 CYD core.conformation.Conformation: current variant for 166 CYD core.conformation.Conformation: Found disulfide between residues 83 93 core.conformation.Conformation: current variant for 83 CYD core.conformation.Conformation: current variant for 93 CYD core.conformation.Conformation: current variant for 83 CYD core.conformation.Conformation: current variant for 93 CYD core.conformation.Conformation: Found disulfide between residues 179 222 core.conformation.Conformation: current variant for 179 CYD core.conformation.Conformation: current variant for 222 CYD core.conformation.Conformation: current variant for 179 CYD core.conformation.Conformation: current variant for 222 CYD core.conformation.Conformation: Found disulfide between residues 208 235 core.conformation.Conformation: current variant for 208 CYD core.conformation.Conformation: current variant for 235 CYD core.conformation.Conformation: current variant for 208 CYD core.conformation.Conformation: current variant for 235 CYD ...(next one is rejected) core.conformation.Conformation: Reverting out-of-date disulfide CYD to CYS at resid 237 core.conformation.Conformation: Reverting out-of-date disulfide CYD to CYS at resid 248 core.conformation.Conformation: Found disulfide between residues 251 265 core.conformation.Conformation: current variant for 251 CYD core.conformation.Conformation: current variant for 265 CYD core.conformation.Conformation: current variant for 251 CYD core.conformation.Conformation: current variant for 265 CYD core.conformation.Conformation: Found disulfide between residues 268 282 core.conformation.Conformation: current variant for 268 CYD core.conformation.Conformation: current variant for 282 CYD core.conformation.Conformation: current variant for 268 CYD core.conformation.Conformation: current variant for 282 CYD core.conformation.Conformation: Found disulfide between residues 284 300 core.conformation.Conformation: current variant for 284 CYD core.conformation.Conformation: current variant for 300 CYD core.conformation.Conformation: current variant for 284 CYD core.conformation.Conformation: current variant for 300 CYD core.conformation.Conformation: Reverting out-of-date disulfide CYD to CYS at resid 341 core.conformation.Conformation: Reverting out-of-date disulfide CYD to CYS at resid 344 core.conformation.Conformation: Reverting out-of-date disulfide CYD to CYS at resid 352 core.conformation.Conformation: Reverting out-of-date disulfide CYD to CYS at resid 355 ...(now it starts re-connecting, but in the wrong way) core.conformation.Conformation: Found disulfide between residues 48 222 core.conformation.Conformation: current variant for 48 CYS core.conformation.Conformation: current variant for 222 CYS core.conformation.Conformation: current variant for 48 CYD core.conformation.Conformation: current variant for 222 CYD core.conformation.Conformation: Found disulfide between residues 83 352 core.conformation.Conformation: current variant for 83 CYS core.conformation.Conformation: current variant for 352 CYS core.conformation.Conformation: current variant for 83 CYD core.conformation.Conformation: current variant for 352 CYD core.conformation.Conformation: Found disulfide between residues 93 251 core.conformation.Conformation: current variant for 93 CYS core.conformation.Conformation: current variant for 251 CYS core.conformation.Conformation: current variant for 93 CYD core.conformation.Conformation: current variant for 251 CYD core.conformation.Conformation: Found disulfide between residues 166 282 core.conformation.Conformation: current variant for 166 CYS core.conformation.Conformation: current variant for 282 CYS core.conformation.Conformation: current variant for 166 CYD core.conformation.Conformation: current variant for 282 CYD core.conformation.Conformation: Found disulfide between residues 179 237 core.conformation.Conformation: current variant for 179 CYS core.conformation.Conformation: current variant for 237 CYS core.conformation.Conformation: current variant for 179 CYD core.conformation.Conformation: current variant for 237 CYD core.conformation.Conformation: Found disulfide between residues 265 344 core.conformation.Conformation: current variant for 265 CYS core.conformation.Conformation: current variant for 344 CYS core.conformation.Conformation: current variant for 265 CYD core.conformation.Conformation: current variant for 344 CYD core.conformation.Conformation: Found disulfide between residues 268 284 core.conformation.Conformation: current variant for 268 CYS core.conformation.Conformation: current variant for 284 CYS core.conformation.Conformation: current variant for 268 CYD core.conformation.Conformation: current variant for 284 CYD ...
participants (3)
-
Elena Seiradake -
José Trincão -
Ralf Grosse-Kunstleve