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NCS and Refmac
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Hello All,
Is there anything peculiar to incorporating NCS restraints from protin
with Refmac (v3.3--it's the latest we have installed). Whenever I attempt
to do this (and ONLY with NCS- without NCS restraints refmac runs just
fine) I get the following error:
libfpe: PID 4912 aborting; limit reached for trap type INVALID
IOT Trap
refmac_mlk.com[75]: 4912 Abort
[2] Exit 134 refmac_mlk.com > junk_13.log
This error occurs at the beginning, right after refmac reports the VDW and
torsion information, right at the point where it should report the NCS
information. Protin seems to run just fine.
Also, is there a way to impose bulk solvent corrections (i.e. scale and
anisotropic tensors) from XPLOR in order to do anisotropic bulk solvent
scaling in refmac? XPLOR seems to yield slightly better results than
refmac for this (I suspect because of the intermediate resolution of my
data, 20-2, and the fact that XPLOR uses an explicit mask).
Thanks in advance for any suggestions.
Felix Vajdos
My refmac input script follows:
#!/bin/sh
set -e
#
# Set parameters
#
crdin=refmac_12.pdb
inmtz=../analysis_utah/h87a20_f5_unq.mtz
crdout=junk_13.pdb
outmtz=junk_13.mtz
#
protin \
XYZIN $crdin \
PROTOUT protout.dat \
PROTCOUNTS counts.dat \
<<eof
TITL CypA_CA146(H87A) in p21 + 536 waters
CHNNAM ID A CHNTYP 1
CHNNAM ID B CHNTYP 2
CHNNAM ID C CHNTYP 3
CHNNAM ID D CHNTYP 3
CHNNAM ID E CHNTYP 4
CHNTYP 1 NTERM 1 MET 3
CHNTYP 1 CTERM 165 GLU 2
CHNTYP 1 SECO 30 41 1
CHNTYP 1 SECO 120 122 2
CHNTYP 1 SECO 136 143 1
CHNTYP 1 SECO 5 12 6
CHNTYP 1 SECO 15 24 6
CHNTYP 1 SECO 55 57 6
CHNTYP 2 NTERM 2 VAL 3
CHNTYP 2 CTERM 165 GLU 2
CHNTYP 2 SECO 30 41 1
CHNTYP 2 SECO 120 122 2
CHNTYP 2 SECO 136 143 1
CHNTYP 2 SECO 5 12 6
CHNTYP 2 SECO 15 24 6
CHNTYP 2 SECO 55 57 6
CHNTYP 3 NTERM 1 PRO 3
CHNTYP 3 CTERM 146 SER 2
CHNTYP 3 SECO 17 28 1
CHNTYP 3 SECO 36 42 1
CHNTYP 3 SECO 49 56 1
CHNTYP 3 SECO 65 83 1
CHNTYP 3 SECO 101 104 1
CHNTYP 3 SECO 111 118 1
CHNTYP 3 SECO 126 141 1
CHNTYP 4 WAT
NONX 2 CHNID C D NSPANS 1 12 140 1
SYMMETRY 4
LIST FEW
END
eof
#
# Refmac step. Refine
#
refmac \
HKLIN $inmtz \
HKLOUT $outmtz \
PROTOUT protout.dat \
PROTCOUNTS counts.dat \
PROTSCR counts.scr \
XYZIN $crdin \
XYZOUT $crdout \
<< eor
LABI FP=FP SIGFP=SIGFP FREE=FreeR_flag
LABO FC=FC PHIC=PHIC FWT=FWT DELFWT=DELFWT
!Refinement parameters
REFI TYPE REST
REFI RESI MLKF RESO 20.0 2.02
REFI BREF ISOT RESO 20.0 2.02
WEIG MATR 0.2
!Scaling parameters
SCALE TYPE BULK LSSC ANIS
!FREE 1.0
NCYC 20
MONI FEW
BINS 20
end
eor
#
------------------------------------------------------------------------
Felix F. Vajdos (801)585-3921
University of Utah felix@alta.med.utah.edu
Dept. of Biochemistry
50 North Medical Drive
Salt Lake City, UT 84132
------------------------------------------------------------------------
"Truth is the child of time, not of authority. Our ignorance is
infinite, let's whittle away just one cubic millimeter. Why should
we still want to be so clever when at long last we have a chance of
being a little less stupid?"-----Bertolt Brecht's Life of Galileo
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