Try elbow.builder and phenix.refine in the phenix package. It will make your life much easier.
Jae Hyun wrote: > Dear all, > > I have a decavanadate anion in my structure, and want to refine it. For > that, I got parameter and topology files from HIC-Up website, and used in > CNS. But, it gave the error message as follows: > > Program version= 1.1 File version= 1.1 > Torsion Topology> > Torsion Topology> fix group ( &atom_rigid ) > SELRPN: 0 atoms have been selected out of 4464 > Torsion Topology> > Torsion Topology> end > Torsion Dynamics> nstep=0 > Torsion Dynamics> cmremove=true > Torsion Dynamics> end > -------------------------- Torsion Topology > ----------------------------------- > ERROR: A group has too many joints. > Please increase MAXJNT and re-run. > > %TORSION:TOPOLOGY error encountered: Fatal Topology Error > (CNS is in mode: SET ABORT=NORMal END) > ***************************************************** > ABORT mode will terminate program execution. > ***************************************************** > Program will stop immediately. > > > And, I also tried to generate CIF files of the decavanadate so that I can > use REFMAC. But, it gives other error message like this: > > > WARNING : DVT : observed angle value will used > chem_type : OH1 -V -O 99.322 (O26 -V9 -O8 > WARNING : DVT : observed angle value will used > chem_type : O2 -V -O 79.829 (O4 -V9 -O8 > WARNING : DVT : observed angle value will used > chem_type : O2 -V -O 152.442 (O27 -V9 -O8 > WARNING : DVT : observed angle value will used > chem_type : O2 -V -OH1 99.366 (O23 -V10 -O28 > WARNING : DVT : observed angle value will used > chem_type : O2 -V -O2 78.183 (O23 -V10 -O18 > WARNING : DVT : observed angle value will used > chem_type : O2 -V -O2 154.744 (O23 -V10 -O15 > WARNING : DVT : observed angle value will used > chem_type : O2 -V -O2 75.004 (O23 -V10 -O27 > WARNING : DVT : observed angle value will used > chem_type : O2 -V -O 75.164 (O23 -V10 -O2 > WARNING : DVT : observed angle value will used > chem_type : O2 -V -O2 99.544 (O18 -V10 -O15 > WARNING : DVT : observed angle value will used > chem_type : O2 -V -O2 147.025 (O18 -V10 -O27 > WARNING : DVT : observed angle value will used > chem_type : O2 -V -O2 96.632 (O15 -V10 -O27 > WARNING : DVT : observed angle value will used > chem_type : O2 -V -O 79.049 (O18 -V10 -O2 > WARNING : DVT : observed angle value will used > chem_type : O2 -V -O 79.699 (O15 -V10 -O2 > WARNING : DVT : observed angle value will used > chem_type : O2 -V -O 75.832 (O27 -V10 -O2 > WARNING : DVT : observed angle value will used > chem_type : OH1 -V -O2 102.115 (O28 -V10 -O18 > WARNING : DVT : observed angle value will used > chem_type : OH1 -V -O2 105.654 (O28 -V10 -O15 > WARNING : DVT : observed angle value will used > chem_type : OH1 -V -O2 100.876 (O28 -V10 -O27 > WARNING : DVT : observed angle value will used > chem_type : OH1 -V -O 174.132 (O28 -V10 -O2 > WARNING: there is not metal chirality for:V10 > WARNING: there is not metal chirality for:V1 > WARNING: there is not metal chirality for:V9 > WARNING: there is not metal chirality for:V7 > WARNING: there is not metal chirality for:V6 > WARNING: there is not metal chirality for:V8 > WARNING: there is not metal chirality for:V5 > WARNING: there is not metal chirality for:V2 > WARNING: there is not metal chirality for:V4 > WARNING: there is not metal chirality for:V3 > * Plotfile: /tmp/refmac5_temp1.20489_new_DVT.ps > -------------------------------- > --- title of input coord file --- > > PDB_code:xxxx > PDB_name:---- > PDB_date:XX-XXX-XX > -------------------------------- > ... and more ... > Number of chains : 4 > Total number of monomers : 624 > Number of atoms : 4430 > Number of missing atoms : 71 > Number of rebuilt atoms : 0 > Number of unknown atoms : 0 > Number of deleted atoms : 0 > > Number of bonds restraints : 4389 > Number of angles restraints : 6074 > Number of torsions restraints : 3037 > Number of chiralities : 638 > Number of planar groups : 763 > I am writing new library: > /ccp4/P > > Important, Important, Important!!!!! > > Your coordinate file has a ligand which has either minimum or no > description > in the library > A new ligand description has been added to /ccp4/PROJECT_6_lib.cif > Picture of the new ligand can be viewed using postscript file. See above > Check description in this file and, if satisfied, use it as the input > library > Otherwise either edit bond orders manually or use CCP4i Sketcher to view > and > edit the ligand > and create a library entry by running libcheck > It is strongly recommended that dictionary entry should be checked > carefully before using it > If you are happy with the library description then use the keyword (MAKE > CHECK NONE) > I.e. do not check correctness of the coordinates > ===> Error: New ligand has been encountered. Stopping now > <B><FONT COLOR="#FF0000"><!--SUMMARY_BEGIN--> > Refmac_5.2.0019: New ligand has been encountered. Stopping now > Times: User: 7.7s System: 0.2s Elapsed: 0:08 > </pre> > </html> > <!--SUMMARY_END--></FONT></B> > > > I need your kind advice to solve this problem. Thank you in adveance. >
