Thanks, Anastassis, "Solvent" is working now after installing the fixed file.
Cheers, Matt 2009/1/8 Anastassis Perrakis <[email protected]> > Hi - > Its a bug in version 7.0.1 that went (almost) unnoticed ... there was one > more complaint a year ago and I had fixed it but there was no release in > between. Sorry. > > Apart from simply doing the solvent building from the REFMAC interface > instead (either with arp_warp as since now or with Coot as since CCP4 6.1) I > will mail you the fixed file (which might work). Anyone else interested ask > me ; the fix will be in the imminent 7.1 release. > > A. > > > > On Jan 8, 2009, at 12:59, Matthew Chu wrote: > > 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 <[email protected]> > 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 <[email protected]> > >> 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 > > ---------------------------------------------------------------------------- > > > -- ---------------------------------------------------------------------------- Matthew LH Chu PhD Student School of Pharmacy and Pharmaceutical Sciences University of Manchester ----------------------------------------------------------------------------
