Running RESOLVE
Summary
To run RESOLVE, you need:
-
SOLVE and RESOLVE installed on your computer
-
the CCP4 suite
installed on your computer (or at least the file "symop.lib" somewhere)
-
A CCP4 mtz file with at least FP, PHI, FOM for your dataset
-
An estimate of the solvent content of your crystal
-
To set the CCP4 environmental variables for file control and symmetry
(modifying as appropriate for the location of symop.lib on your system):
setenv SYMOP /usr/local/lib/solve/symop.lib
setenv SYMINFO /usr/local/lib/solve/syminfo.lib
setenv CCP4_OPEN UNKNOWN |
The most basic RESOLVE script
(see the sample scripts for more
cases):
#!/bin/csh
#
# Here is a minimal script to run RESOLVE on MAD/MIR/SAD etc data:
#
# Set CCP4 variables for symmetry information and
# for file handling:
#
setenv SYMOP /usr/local/lib/solve/symop.lib
setenv SYMINFO /usr/local/lib/solve/syminfo.lib
setenv CCP4_OPEN UNKNOWN
#
# Now run RESOLVE:
#
resolve<<EOD
hklin solve.mtz
LABIN FP=FP PHIB=PHIB FOM=FOM HLA=HLA HLB=HLB HLC=HLC HLD=HLD
hklout resolve.mtz
solvent_content 0.4 ! your solvent content goes here.
! Next line is the file with your protein sequence.
seq_file protein.seq
EOD
#
# Now "resolve.mtz" has the output amplitudes, phases,
# and figure of merit in columns labelled: FP PHIM FOMM.
# A model of your structure is in resolve.pdb.
# |
-
RESOLVE will read from "solve.mtz" and write out new structure factor amplitudes
and phases.
-
If you have a file "ha.pdb" in your directory, RESOLVE will try to use
the PDB coordinates in it to identify and apply NCS.
-
Additionally, Hendrickson-Lattman coefficients are written.
-
A model of your structure is built and placed in resolve.pdb
-
You can use "resolve.mtz" in the same way as you use any mtz file in the
CCP4
suite.
Notes on input and output mtz files (see
the sample scripts
RESOLVE expects to read data from a CCP4 mtz file
-
at least FP, PHI, FOM are needed for MAD/MIR/SAD data
- for prime-and-switch, you need FP FC PHIC FOM, with optional FWT (from sigmaa)
- it works much better for MAD/MIR/SAD data if you also input Hendrickson-Lattman coefficients (HLA HLB HLC HLD)
- you specify the columns with the LABIN keyword as in the CCP4 suite
- LABIN FP=yourFPcolumn PHIB=yourPHIBestcolumn FOM=yourFOMcolumn HLA=yourHLAcolumn etc)
- If your input file has reflections with non-zero F within your resolution range, it will automatically attempt to phase all of them.
- You can input a FreeR_flag column.
RESOLVE will write a CCP4 mtz file
- The output columns of data are H K L FP SIGFP PHIM FOMM HLAM HLBM HLCM HLDM FreeR_flag
- FP is just what was input; SIGFP is 1.0 if not input. NOTE: the SIGFP behavior may not be what you expect: If you do not specify SIGFP in your labin statement, RESOLVE will write out SIGFP = 1.0. If you specify SIGFP=something, the data in column "something" will be copied out to SIGFP in the output file. If you use the default labin (FP=FP SIGFP=SIGFP PHIB=PHIB FOM=FOM
HLA=HLA HLB=HLB HLC=HLC HLD=HLD) it will copy it out correctly.
- PHIM is the modified "best" or centroid phase
- FOMM is the figure of merit of PHIM. Use in a map with F = FP * FOMIM * exp(i PHIM).
- HLAM, HLBM, HLCM, HLDM are Hendrickson-Lattman coefficients for the final phases.
- Reflections with FreeR_flag = 0 are used as the "free" set in RESOLVE.
Normally all reflections are used for all steps except the identification
of the solvent fraction and a database for density statistics (i.e., the
FreeR_flag is ignored for most steps).
RESOLVE will write out a PDB file with a model of your structure
- The model will usually not be fully complete, depending on the quality
of the map
- Some loops won't be present in most cases
- Side chains will be built on the better parts of the model if you specify
a file with the protein sequence
- Side chains not in density will be truncated to CB
Keywords for resolve
KEYWORD DEFAULT WHAT IT IS
access_file solve2.access Name of solve2.access file. If it is not
in the /usr/local/lib/solve/ directory or
in the current directory or in the directory
$SOLVEDIR then you will want to tell RESOLVE
where it is
hklin solve.mtz mtz file with input phases and phase
probabilities
hklout resolve.mtz mtz file with output phases
LABIN FP=FP PHIB=PHIB FOM=FOM HLA=HLA HLB=HLB HLC=HLC HLD=HLD
LABIN statement identifying the columns of
data in the hklin mtz file
mask_cycles 5 Number of cycles in which masks are redone and
images are compared to map
minor_cycles 10 Number of minor cycles per mask_cycle
no_build Don't build a model
build_only Just build the model (no density modification)
assemble_only Just assemble the model and write it out
(using info in peak_file and fragment_file)
build_outside_model Just build the model outside the region
defined by model xxx.pdb
superquick_build Build the model as quickly as possible,
searching for fragments on coarse grid
works great for good maps and 10x faster
than version 2.03 model-building)
NOTE: superquick_build/quick_build/
thorough_build are 3 choices for
1 parameter
quick_build (Default) Standard model-building protocol
(3x faster than version 2.03)
thorough_build Look exhaustively for ways to build the model.
Similar to version 2.03.
Not always any better than "quick_build"
aggressive_build Build aggressively, allowing some incorrect
residues or even entirely incorrect residues.
Same as "macro_cycles 3". Not recommended.
conservative_build Build conservatively (same as version 2.03).
Same as "macro_cycles 1".
seq_file protein.seq File containing protein sequence
Format: 1-letter code sequence of each chain,
separated by lines starting with &rt&rt&rt.
No need to put in duplicate chains.
no_expand_ncs Don't expand number of copies of each chain
beyond what was found with ha sites
seq_prob_min 0.95 Minimum confidence of sequence match to place
side chains on a fragment
use_met_in_align Use heavy-atom positions as markers for MET
positions
dist_cut_met 2.0 Consider a heavy-atom close to SD of Met if
within this distance (default=2/3 of
resolution)
richardson_rotamers Use Richardson Penultimate rotamer library from
SC Lovell, JM Word, JS Richardson and DC
Richardson (2000) " The Penultimate Rotamer
Library" Proteins: Structure Function and
Genetics 40 389-408.
noget_peaks Skip searching for helices/strands and use
data from peak_file
noget_fragments Skip searching for fragments and use data
from fragment_file
peak_file resolve_peaks.dat Intermediate file with locations of all
helices/strands considered
fragment_file fragments.dat Intermediate file with coordinates of all
fragments considered in model-building
fom_cut 0.15 Set initial resolution for density
modification to be where the FOM is about .15
s_step 0.02 Steps in s=1/d to take during phase extension
solvent_content 0.3 Fraction of unit cell in solvent region (if
specified, do not search for optimal fraction)
use_input_solv Do not search for optimal solvent content
Use value from solvent_content if specified
Use value from resolve.solvent if it exists
and solvent_content is not specified.
resolution Resolution limits (default=whatever is in
input mtz file)
res_start 2.5 Start out density modification at this
resolution, then extend to maximum
phase_extend Start out density modification at resolution
res_start (set automatically), then extend
to maximum
no_phase_extend Start out density modification at final
resolution. This is default (changed
in version 2.09)
phases_from_solve Input phases are not yet density-modified
(default if "hklstart" is not set)
phases_from_resolve Input phases are already density-modified
(default if "hklstart" is set)
use_free_for_test Use free set for solvent content/histogram
tests (default unless Nfree<500)
use_all_for_test Use all data for solvent content/histogram
tests
create_free Create FreeR_flag if it does not exist
(default)(This does not mean that the
FreeR_flag is used)
include_free Use all data for main cycles (default)
exclude_free Do not include free data for main cycles
(does not work well)
no_damp do not damp shifts in phases
database 1 Use database entry #1 for histograms of
protein/solvent density
get_histograms Use the map calculated from hklin to generate
density histograms. These can be pasted in to
$SOLVEDIR/segments/rho.list (be sure to match the
number of lines in the other entries in this file)
and then accessed with "database nn" where this is the
nn'th entry in rho.list
use_input_db Do not search for optimal histogram from
database.
Use value from "database" if specified
Use value from resolve.database if it exists
and "database" is not specified.
wang_radius_cycle 6. 4. (default: variable start; 4 end) Starting and
ending radius (A) in Wang method for getting
solvent mask
NOTE: RESOLVE will automatically set this
for you in a reasonable way if you don't
specify it.
wang_radius_finish 4. (default: 4.0) Ending radius(A)in Wang method
for getting solvent mask
wang_radius_start 6. (default: variable) Starting radius(A)in Wang
method for getting solvent mask
wang_radius 6. Radius to be used for all cycles
NOTE: In RESOLVE you don't want or need a
small radius for getting the solvent
probability. It works better with a medium-
large radius (but really it makes very little
difference what radius you use)
hklstart mtz file with a starting set of phases.
RESOLVE will start with these phases (but use
probabilities from hklin). Useful for running
a few cycles, getting an output resolve_1.mtz,
then continuing on from there. Goes with
labstart.
labstart FP=FP PHIB=PHIB FOM=FOM LABIN statement for hklstart. only PHIB
and FOM used.
hklperfect mtz file with a model set of phases
labperfect FP=FP PHIB=PHIB FOM=FOM LABIN statement for hklperfect
difference_map calculate difference map FP hklin-FP
hklperfect
phase_with_perf use PHIB and FOM from hklperfect in
diff map (default is use PHIB and FOM
from hklin)
cc_ratio 0.1 Cut off prime-and-switch phasing at resolution
where CC of FP with FC < cc_ratio
verbose print out a lot of data every cycle, not just
at first and last.
nohl don't calculate HL coefficients at end of
RESOLVE (saves time)
new_ncs_group start a new group of NCS operators
ncs_domain_pdb domain_1.pdb PDB file identifying all points in the
asymmetric unit that are part of this NCS
group. See also rad_mask.
rota_matrix rotation matrix for NCS symmetry. Three
rota_matrix lines define a matrix:
Enter the identity as first molecule 1.
rota_matrix 1 0 0
rota_matrix 0 1 0
rota_matrix 0 0 1
The rotation matrix applies to orthogonal
Angstrom coordinates.
The matrix and translation maps molecule
j on to molecule 1.
This is what you get from the ccp4 program
lsqkab if molecule 1 is the reference
(xyzin1) and molecule j is the working
molecule (xyzin2)
tran_orth Translation vector for NCS symmetry element,
in orthogonal Angstroms
Enter after rota_matrix
center_orth Approximate center of mass of NCS symmetry
element, in orthogonal Angstroms
Enter after rota_matrix. Required only
for element 1
fraction_ncs 0.15 fraction of asymmetric unit occupied by 1
molecule (default = fraction protein / N )
invert Invert NCS matrices (they correspond to
mapping molecule 1 on to molecule j)
fix_ncs Do not refine NCS operators
ncs_restrict n Only consider NCS if there are n operators.
ncs_restrict 3 looks only for trimers.
force_ncs Use input or heavy-atom-site NCS symmetry even
if there is very low correlation
rad_ncs_mask_max 6. Do not allow NCS mask to have radius greater
than rad
overlap_min 0.1 minimum overlap extrapolated to center of molecule
to keep NCS
rho_overlap_min 0.3 minimum mean overlap <rho1*rho2> to keep NCS
fraction_ncs_min 0.05 minimum fraction of au involved in NCS to keep it
ha_file ha.pdb Use the entries in this file (PDB format) to
look for non-crystallographic symmetry.
If se_file is not given, also used to identify
Se positions for alignment of SeMet residues.
se_file se.pdb Use the entries in this file (PDB format) to
mark positions of Se in SeMet residues
(overrides sites in ha_file and is required if multiple
NCS groups are used)
compare_file xxx.pdb Use coords in this file to define asymmetric
unit for output resolve_compare.pdb
NOTE: has no effect on contents of resolve.pdb
no_find_ncs Don't try to find NCS from heavy-atom sites
even if the file "ha.pdb" exists
ncs_only Find NCS and do nothing else (no density
modification, nothing)
do_all_cycles Do all the assigned cycles, even if nothing
is happening
no_fill Don't fill in missing reflections (default)
(best usually)
fill Fill in missing reflections (risky)
r_match (Default=1.0) Maximum distance between CA in
different fragments to link during assembly
r_min (Default=1.) Lowest minimum rho/sigma for
main-chain atoms
r_min_side (Default=0.3) Lowest minimum rho/sigma for
side-chain atoms
r_overall (Default=0.75) Minimum rho_bar/avg for
starting a segment in model-building
r_end (Default=0.5) Minimum rho_bar/avg for
continuing a segment in model-building
z_cut (Default=0.5) Minimum Z-score to keep a
fragment after refinement
z_cut_extend (Default=-0.5) Minimum Z-score to keep a
fragment after extension
macro_cycles 3 (Default = 2) Number of iterations of lowering
thresholds in model-building.
NOTE: normally do not use more than 3 or the
model becomes poor. Each cycle beyond 1 r_min
and r_min_side decrease by 0.5 and z_cut and
z_cut_extend decrease by 1.
no_unassigned Do not write out residues not assigned to
sequence in model-building
rad_mask 2.5 Radius for calculation of solvent mask and for
inclusion in image-based phasing and for NCS
region identification
image Use map calculated from PDB file
("composite_pdb") or from input phases as
target for electron density. Only density
within rad_mask of atoms used if from PDB
file.
image_only Do not do solvent flattening/NCS etc. Just
use the image as a target. Requires the
keyword "image" as well. Produces phases
similar to "sigmaa".
prior_weight 1.0 (Default=1.0) Weight on the input phases.
Prior_weight 0 is used in prime-and-switch
phasing.
prime_and_switch Use prime-and-switch phasing. Use input phases
only to calculate initial map.
Input phase probabilities not used at all.
no_erase_protein Do not let P(protein) be less than the
starting value in prime-and-switch phasing.
n_image_cycle Number of cycles of using the image (map)
based on a model in density modification
composite_pdb xxx.pdb_ root name of a set of PDB files to be used to
construct a composite image
composite_pdb_first 0 first PDB file for composite is xxx.pdb_0
composite_pdb_last 20 last PDB file for composite is xxx.pdb_20
pdb_in refmac.pdb Name of PDB file to be used in starting
model-building
extend_only Just trim and extend the chains in pdb_in;
don't rebuild from scratch
no_merge_ncs_copies Do not merge NCS copies during extend
(default = merge_ncs_copies)
side_avg_min 0.0 Truncate side-chain atoms in model-building if
mean density is < side_avg_min
LABIN FP=FP FC=FC PHIC=PHIC FOM=WCMB FWT=FWT LABIN statement suitable for prime-
and-switch using SIGMAA phases.
FWT is optional; if present initial map
calculated with FWT exp(i PHIC).
pattern_phase Use image in cc_map_file as target for
image-based phasing (no prior phase
information, no solvent flattening, no NCS.
cc_map_file recovered_map.dat binary file with map for pattern_phase
targeting (only read by RESOLVE)
coarse_grid Use coarse grid (same as RESOLVE 2.02) for
maps. Must match RESOLVE_PATTERN
n_restore 1 Number of times to restart density
modification using mask from previous run
but starting with original phases.
Default = 0 (no restarting)
no_restore Same as n_restore 0
scale_refl 0.5 Weighting on map probability function
(default = 0.5)
scale_refl_start 0.05 Weighting on map probability function
(default = 0.5) on first cycle of density
modification
scale_refl_end 0.5 Weighting on map probability function
(default = 0.5) on last cycle of density
modification
trim Trim pdb_in file back to match density
(default)
no_trim Take main-chain of pdb_in file as is and use
as a basis for model-building without trimming
i_ran_seed value of random seed
no_cut_up_model Don't cut up pdb_in into little pieces
(default)
cut_up_model Cut pdb_in up into little and big pieces and
try them all as starting points for
model-building
build_image Use FFT-based search to find helices/strands
and create an output map (dump.map)with
reconstructed image of the map. You can then
use dump.map with "pattern_phase"
evaluate_model Compare the model defined by the model
keyword with the map calculated from hklin
model resolve_best.pdb model to evaluate with evaluate_model
mask_as_mtz modifies ncs_mask_file and protein_mask_file to
write out as an mtz file instead
ncs_mask_file mask.mtz write out a CCP4-style mtz file with FP PHIM
FOM that yield a map showing the NCS
asymmetric unit. NOTE: only the asymmetric unit
of NCS is shown, but crystallographic symmetry is
applied to it, which can make interpretation of
the mask a little confusing.
protein_mask_file mask.mtz write out a CCP4-style mtz file with FP PHIM
FOM that yield a map showing the protein
region. NOTE: only the asymmetric unit
of the protein mask is shown, but crystallographic
symmetry is applied to it, which can make
interpretation of the mask a little confusing.
add_mask Require that the region defined by the PDB file
read in with model xxx.pdb is protein use
rad_mask radius in definition of region
no_ha do not write heavy-atom sites out to the
resolve. pdb model file
ha_occ 1.0 set occ of heavy-atoms written out from
ha.pdb to resolve.pdb to this value
(default=0.0)
start_chain 1 23 start chain 1 with residue number 23
(default = 1)
start_segment n read segments files starting with number "n"
max_segment m read up to "m" segments files. These are files
with information about helices/strands etc.
score_only score an electron density map (skew, ha_ncs,
correlation of map from map-probability phases
with original map, correlation of local rms)
score_tert score tertiary structure
loop_only Fit a loop only. Requires pdb_in and
extend_only
n_random_loop 20 Number of loop conformations to try. If
negative, try only randomized configurations.
rms_random_loop 0.3 RMS random variation in loop coordinates
n_random_frag 0 Number of randomized fragment conformations
to try
rms_random_frag 0.3 RMS random variation in frag coordinates
pieces_only 10 Used with cut_up_model;
do not include the uncut part and cut into sizes pieces_only. If negative,
start at every amino acid and make a fragment of length pieces_only
and try to extend.
skip_hetatm Ignore HETATM records in PDB files.
cut_1 0.5 Minimum rho for residue/average to continue
segment
cut_2 0.75 Minimum rho for residue/average to start/stop
a segment
dist_close 1.0 (0.5 for cross of 2 models) Maximum distance of CA to be
considered the same (A)
rebuild_in_place Rebuild the model in segments, preserving
sequence alignment.
n_try_rebuild 1 Number of times to try to find each segment
replace_existing Replace existing segments in rebuild_in_place
even if worse than starting coordinates
(default is to keep existing if better)
rho_min_main_low 1.0 Minimum density at atoms in loop. Default=1,
try 0.5; goes with rho_min_main_base
rho_min_main_base 1.0 Minimum density at atoms in loop. Default=1,
try 0.5; goes with rho_min_main_low
no_sub_segments Fit entire segments to sequence (do not break
up)
omit_box n Omit all points in omit box n from density
modification
n_box_target m Try to set up m omit boxes
omit_boundary 2.0 Increase the size of the omit region defined by
omit_box in all directions by this amount
complete_omit Do not include solvent flattening or histogram
matching in omit region (default)
no_complete_omit Include solvent flattening and histogram
matching even in omit region
complete_omit_hist Include histogram matching even in omit region
leave_out [123] xx In generation of data with errors,
leave out planes of reflections in direction 1=h 2=k 3=l
to throw away a fraction xx of the total. Part of
(goes with fom_target and sigma_target)
strict_match match atoms with identical names and residues only in
comparison of two PDB files
modify modify the density near ha sites to be < 2.5 sigma
at start of density modification (useful for cases
where very high ha sites are present)
modify_outside modify the density outside region defined by
model in model_2 but inside "protein" region
(requires model_2 to be set). Density in this region
will be renormalized to make the distribution of
density match that in the region that is defined
by the model. This is useful to "bring up" density
that really is in the protein region but has no
phase information from the model.
scale_cut region of ligand is defined in evaluate_ligand
as the region actually occupied by the ligand,
and any adjacent contiguous density at least
scale_cut * sigma of map.
max_copies number of copies of chain in side_chain will be
limited to max_copies (side_chain estimates how
many copies from the number of segments with the
same sequence; this will override that value.
Different than ncs_restrict, which applies to estimation
of the number of ncs copies estimated from heavy-atom
sites.
keep_f_mag If set, the hklstart dataset will keep |F|. Otherwise
this is overwritten with F from hklin.
track_libs Keep track of the libraries used to build models
build_rna ! interpret chains as RNA polymers and use RNA library if avail
build_dna ! interpret chains as DNA polymers and use DNA library if avail
proxy N O5' ! interpret O5' as if it were N (the first atom in a residue)
! expected values: N C CA O CB
i_res_max 3 ! max number of residues in fragments in input fragment library
factor_sd 1.0 !Scale on SD of target density for model-based density modification
background_map !Input map coefficients for hklin will be used for all undefined points in omit map (instead of zeros)
background_offset 0.0 ! offset for background map
scale_background 1.0 ! scale for background map
dist_ca_approach 0.0 ! how close CA (or equivalent proxy atom) on
! different chains can approach
dist_cut_assemble 3.5 ! min distance between atoms in different fragments
compare_main ! Requiring main_chain atoms in assemble to be at least
dist_cut_assemble from all those in existing chains
compare_all ! Requiring all atoms in assemble to be at least
dist_cut_assemble from all those in existing chains
max_residue_sep 6. ! residues with CA or equiv within this distance of each
! other are considered connected in reuse-chain
i_res_max 7 allows fragments up to length 7 from input fragment library.
proxy N O ! interpret O as if it were N (the first atom in a residue)
! expected values: N C CA O CB
i_res_max 3 ! max number of residues in fragments in input fragment library
factor_sd 1.0 !Scale on SD of target density for model-based density modification
background_map !Input map coefficients for hklin will be used for all undefined points in omit map (instead of zeros)
background_offset 0.0 ! offset for background map
scale_background 1.0 ! scale for background map
dist_ca_approach 0.0 ! how close CA (or equivalent proxy atom) on
! different chains can approach
dist_cut_assemble 3.5 ! min distance between atoms in different fragments
compare_main ! Requiring main_chain atoms in assemble to be at least
dist_cut_assemble from all those in existing chains
compare_all ! Requiring all atoms in assemble to be at least
dist_cut_assemble from all those in existing chains
max_residue_sep 6. ! residues with CA or equiv within this distance of each
! other are considered connected in reuse-chain
no_prior_in_align ! do not include relative frequency of amino acids in
! sequence when computing alignment probabilities
Keywords for RESOLVE helices_strands and Trace (PHENIX only)
cc_strand_min Minimum CC of strand density to keep (0.5)
require_direction Only strands with direction defined kept
keep_direction If has strand has direction defined only keep that direction (default)
any_direction Keep both directions of strands
any_strand Take any strand, good or not (not default)
strand_length_min Minimum strand length (A) to keep (2.)
rad_value_strand Radius (A) around strand for CC (0.5)
ca_value_strand Radius (A) around strand for periodicity (1.5)
n_period_ca_strand Number of grid points/period of strand (12)
dist_ca_strand Period (A) of strand (6.74)
no_prior_in_align Do not use amino acid composition in side-chain ID (not default)
make_pseudo_fom HKLSTART dataset will keep F and Phase (not default)
skew_in_target include skew in the target function (not tested)
i_use_sum sum with regular target function (not tested)
i_use_tanh Use tanh-modified skew (not tested)
weight_skew weighting on skew target (not tested)
range_skew allowed range of skew for i_use_tanh (not tested)
dist_ca_sep Trace-chain CA-CA separation (4.0)
target_helix_ip3 Helix target distance for CA-CA distance i to i-plus-3 (5.5)
target_strand_ip3 Strand target distance for CA-CA distance i to i-plus-3 (10.5)
tol_helix_ip3 Tolerance in target_helix_ip3 (1.25)
tol_strand_ip3 Tolerance in target_strand_ip3 (1.25)
n_min_helix Minimum residues in helix for trace_chain (6)
n_min_strand Minimum residues in strand for trace_chain (5)
tol_helix Tolerance in obs-idealized helix CA positions for trace_chain (1.5)
n_cycle_message Cycles of message-passing in trace_chain (100)
n_point_min Minimum CA in chain in trace_chain (10)
n_overlap Number of overlapping CA to consider in joining nonamers (2)
rat_pair_min Minimum density between 2 points in trace_chain (ratio, 0.5)
a_cut_min Minimum density at atoms for trace_chain (ratio to sigma,1.0)
target_ratio Target ratio of atoms to place:non-H atoms in structure in trace_chain (1.5)
dist_ca_tol Tolerance of CA-CA distance in trace_chain (0.5)
n_sift_nona Number of nonamers per atom in trace_chain (0=auto)
w_rmsd_line Weight on rmsd from line in trace_chain (1.)
w_rmsd_target Weight on rmsd from target distance in trace_chain (1.)
w_density Weight on density in trace_chain (12.)
dist_max_consider Maximum distance of a point from line to consider in trace_chain (2.)
trace_chain Use trace_chain algorithm to rapidly obtain CA positions from a map
quick_trace Quickly trace chains
medium_trace Standard trace chains (default)
thorough_trace Thorough trace chains
unique_chains only write out unique chains in trace_chain (not default)
cutoff_trace fract of top peaks to reject, assuming they are not protein (0.001)
ncut_trace_min number of top peaks to reject, assuming they are not protein (0)
trace_ratio_long ratio of tolerance in + to - directions for CA-CA dist (0.33)
cutoff_trace fract of top peaks to reject, assuming they are not protein (0.001)
ncut_trace_min number of top peaks to reject, assuming they are not protein (0)
trace_ratio_long ratio of tolerance in + to - directions for CA-CA dist (0.33)
Keywords for RESOLVE ligand fitting
ligand_file ligand.pdb PDB file with N copies of a ligand in random
stereochemically ideal conformations. All
atoms must be in the same order in all copies
n_ligand_pos 300 Number of rotation/translation positions for a
ligand to consider
n_ligand_pos_ref 100 Number of rotation/translation positions for a
ligand to refine
n_group_search 3 Number of large groups within ligand to search
for. If zero, groups from input file used
without rotation/translation to start fitting
group_search xx Use group xx in ligand to start ligand fitting
n_keep_plac 100 Number of placements of groups to keep in
ligand search
n_indiv_tries_min 20 Minimum number of top placements of large groups
to try individually in ligand search
n_indiv_tries_max 20 Maximum number of top placements of large groups
to try individually in ligand search
ligand_resno 20 Residue # for ligand
n_template_atom 45 Number of atoms in ligand (overrides guess
made by resolve)
no_local_search Search whole map for ligand
search_dist 10 Search within this distance of top rms region in
map for local searches
search_center 3 10 5 Local search is around this point (in A)
fit_phi_range -20 20 Try angles from -20 to 20 degrees relative to
the torsion angles in ligand_file
fit_phi_inc 20 Sample angles in range fit_phi_range with
increment fit_phi_inc
delta_phi_ligand 50 Rotation angle to sample overall placements
of large groups in ligand fitting
acceptable_offset 1.0 Maximum allowed offset of atoms from overlapping
placements in ligand search (i.e., placements
of an atom from each of 2 directions in a
cyclic molecule)
cut_close 1.5 Minimum allowed separation between atoms in
separate rigid groups.
ignore_map Ignore the map and just generate a random
conformation.
model xxx.pdb Generate FC from model and use Fo-Fc map
to fit ligand.
rad_mask_ligand mask for "protein" region will be defined by all points
within rad_mask_ligand of an atom in the model. This
mask is used to exclude ligand atoms from places where
the protein is located.
density_offset The density in the map is offset by density_offset*sigma
in ligand fitting. This is useful for allowing a
ligand to be fitted even with low density
density_min The lowest density where a ligand atom may be placed
is density_min (except in the final stages when
any remaining atoms are placed whereever they fit.)
dist_fixed 0.3 In generating allowed ligand conformations for
ligand fitting, if multiple conformations are input
in ligand_file, then assume that a set of atoms that has
an rmsd among configurations of less than dist_fixed
is always staying in a fixed relative configuration.
Normally use 0.3 A. If small changes in configuration
are input a smaller value may be useful (0.05 A).
Keywords for resolve_pattern
KEYWORD DEFAULT WHAT IT IS
access_file solve2.access Name of solve2.access file. If it is not i
the /usr/local/lib/solve/ directory or in the
current directory or in the directory
$SOLVEDIR then you will want to tell RESOLVE
where it is
hklin solve.mtz mtz file with input phases and phase
probabilities
hklout resolve.mtz mtz file with output phases
LABIN FP=FP PHIB=PHIB FOM=FOM HLA=HLA HLB=HLB HLC=HLC HLD=HLD
LABIN statement identifying the columns of
data in the hklin mtz file
resolution Resolution limits (default=whatever is in
input mtz file)
Use value from resolve.database if it exists
and "database" is not specified.
recover_image Analyze map calculated with hklin phases and
amplitudes for local patterns; write out
binary map with the recovered image to
cc_map_file
cc_map_file recovered_map.dat File with recovered map (binary file; only
read by RESOLVE)
coarse_grid Use coarse grid (same as RESOLVE 2.02) for
maps. Must match RESOLVE
path_patterns $SOLVEDIR/patterns/ Location of library files for RESOLVE_PATTERN