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 <[log in to unmask]>
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
<[log in to unmask]>
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
--
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Matthew LH Chu
PhD Student
School of Pharmacy and Pharmaceutical Sciences
University of Manchester
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