Thanks Damian, but I have been using my library file for refmac refinement and it works fine. And I can't find the line "Unrecognized atom type", but presumably, if it works in refmac refinement, why not in Arp/wArp?
Yes Gerrit, the "[" and "]" should not be there.....so auto_solvent.sh can recognize my mtz fp, etc. BUT I did check the box 'input a user-defined library file' in GUI and the command 'extralibrary' in the script, and again, it fails to read my library file or the one refmac just created, but obviously the extralibrary command works fine? Here is the log: Working directory /home/mchu/ArpwARP/l1/ArpwARP_070109/solvent/ Job ID is set to 20090108_114504 X-ray data file /home/mchu/ArpwARP/l1/ArpwARP_070109/solvent//L1.mtz Protein file /home/mchu/ArpwARP/l1/ArpwARP_070109/solvent//L1.pdb Extralibrary file /home/mchu/ArpwARP/l1/ArpwARP_070109/solvent//refmac5_temp1.10491_lib.cif TLS input file /home/mchu/ArpwARP/l1/ArpwARP_070109/solvent//L1_TLS.tls Creating directory /home/mchu/ArpwARP/l1/ArpwARP_070109/solvent/20090108_114504 Output solvent file /home/mchu/ArpwARP/l1/ArpwARP_070109/solvent/20090108_114504/L1_solvent.pdb mtz labels taken: F_New SIGF_New FreeR_flag Parameter file /home/mchu/ArpwARP/l1/ArpwARP_070109/solvent/20090108_114504/arp_warp_solvent.par Job launched in /home/mchu/ArpwARP/l1/ArpwARP_070109/solvent/20090108_114504 The log file is /home/mchu/ArpwARP/l1/ArpwARP_070109/solvent/20090108_114504/L1_warp_solvent_details.log But ERROR: 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 /tmp/mchu/refmac5_temp1.11125_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 I really have no idea what is the problem? Any suggestion would be greatly appreciated! Kind regards, Matt 2009/1/8 Damian Ekiert <dceki...@scripps.edu> Matt, I had a similar sounding problem once, but it may or may the problem in your case. Do you have any ligands or glycans on your protein that you just added in? I was working on a protein with glycosylations and hadn't yet removed the oxygens from my sugars that would be lost after condensation (e.g., the oxygen that would be lost as water when the first residue was attached to Asn). My suggestion would be to look a little bit higher up in the log file and see if you see any lines saying something like "Unrecognized atom type". I think when there is a discrepancy between the residue name and the names of the atoms in the residue, you can have this problem. Hope that helps. Best, Damian Ekiert 2009/1/8 Gerrit Langer <ger...@embl-hamburg.de> > Dear Matt, > > have you tried the 'input a user-defined library file' check box under > 'refmac parameters' in the gui? Else try the keyword 'extralibrary' when > using the 'auto_solvent.sh' script from the command line. Both options > define a string 'LIB_IN mylib.cif' that is passed on to refmac. > > When using the auto_solvent.sh script, please omit the '[' and ']' > characters. Type e.g.: auto_solvent.sh datafile L1.mtz protein L1.pdb fp > F_New sigfp SIGF_New extralibrary refmac5_templ.03957_lib.cif > > I hope this will help. > Regards, > Gerrit. > > > Matthew Chu wrote: > > Dear all, >> >> I tried to use ARP/wARP 7.0.1 GUI for solvent building, however it >> couldn't >> recognize my ligand library file (.cif), which works fine in refmac >> refinement. >> Apparently, the error message is: >> >> ===> Error: New ligand has been encountered. Stopping now >> Refmac_5.2.0019: New ligand has been encountered. Stopping now >> Your coordinate file has a ligand which has either minimum or no >> description >> in the library >> A new ligand description has been added to >> /tmp/mchu/refmac5_temp1.03957_lib.cif >> >> Even if I use the one refmac created after the error, it still can't >> recognize this new cif file... >> >> I also tried to run it from command line, another problem was raised. It >> couldn't recognize the FP label in my mtz when I used the keyword [fp >> F_New] >> [sigfp SIGF_New] [freer FreeR_flag] >> >> Error message: >> Label FP does not match the content of the datafile >> /home/mchu/ARP_wARP/solvent/L1.mtz >> Possible mtz labels are: F_New FC FWT DELFWT >> >> Does anyone have any idea why and how I can fix it? Thank you so much in >> advance! >> >> Kind regards, >> Matt >> >> >> >> > > -- ---------------------------------------------------------------------------- Matthew LH Chu PhD Student School of Pharmacy and Pharmaceutical Sciences University of Manchester ----------------------------------------------------------------------------
