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Running RESOLVE

Summary

To run RESOLVE, you need:

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.  

#

Notes on input and output mtz files (see the sample scripts

RESOLVE expects to read data from a CCP4 mtz file

RESOLVE will write a CCP4 mtz file

RESOLVE will write out a PDB file with a model of your structure

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

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