Hello everyone, I'm reaching out to inquire if anyone has experience with executing Crank2 through the command line. I attempted utilizing the crank command, but it appears an XML input is required. To generate the XML file, I employed gcx with the following parameters:
gcx SEQIN /mnt/ssd/SAD/5uxx/rcsb_pdb_5UXX.fasta << END XTAL DEFAULT ATOM Se DNAM PEAK MTZI /mnt/ssd/SAD/5uxx/AUTOMATIC_DEFAULT_free.mtz outp gcx END Unfortunately, it seems that the heavy atom specification is not recognized by gcx. I have included the generated XML file for reference. Could anyone guide me on the correct procedure to run Crank using the command line, or point out what I might be missing? Thank you for your help. Best regards, Xin ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
<?xml version="1.0" standalone="yes"?> <crank> <parameters> <version>2.0.339</version> <description>gcx</description> <verbose>0</verbose> <code>crank</code> <solvent_content>0.589</solvent_content> <residues>231</residues> <nucleotides>0</nucleotides> <nmonomers>2</nmonomers> <bfactor>32.60</bfactor> <ref_crystal>1</ref_crystal> <ref_dataset>1</ref_dataset> <input_spacegroup> <name>P 31 2 1</name> <number>152</number> </input_spacegroup> <sequence> MMEGVKDFKQELLLVLPALRAFAISLSSKHDKAEDLVQDTLMKAWAKQDSFEMGSNLKAW LFTILRNEFYSQMRKRGREVQDSDGVFIESVAIHPAQYGSLDLQDFKKALNMLSADQREA IILIGASGFSYEDAAAICGCAIGTIKSRVSRARNRLQELLKVDRMNDCDEKNLTNHFTFG DDLLGVNSEIARKLRQFYLEIQEEALPARLLELLERLEQAERFGLNNAEKV </sequence> <input_intensity>0</input_intensity> <crystal id="1"> <native>1</native> <cell> <cell_a>92.260</cell_a> <cell_b>92.260</cell_b> <cell_c>127.624</cell_c> <cell_alpha>90.000</cell_alpha> <cell_beta>90.000</cell_beta> <cell_gamma>120.000</cell_gamma> </cell> <data id="1"> <type>PEAK</type> <anomalous>1</anomalous> <bfactor>32.60</bfactor> </data> </crystal> </parameters> <input_files> <file id="1"> <type>MTZ</type> <label>IN</label> <crystal id="1"> <data id="1"> <name>/mnt/ssd/SAD/5uxx/AUTOMATIC_DEFAULT_free.mtz</name> <f_plus>F(+)</f_plus> <sigf_plus>SIGF(+)</sigf_plus> <f_minus>F(-)</f_minus> <sigf_minus>SIGF(-)</sigf_minus> </data> </crystal> </file> </input_files> <output_files> <mtz_out> <name>(null)</name> </mtz_out> </output_files> <soap> <run> <directory>gcx</directory> <step id="1">PREP <name>PREP</name> <tag>1_PREP</tag> <step>1</step> <input> <exp_columns> <crystal id="1"> <data id="1"> <type>PEAK</type> <f_plus>F(+)</f_plus> <sigf_plus>SIGF(+)</sigf_plus> <f_minus>F(-)</f_minus> <sigf_minus>SIGF(-)</sigf_minus> <wavelength></wavelength> <anomalous>1</anomalous> </data> </crystal> </exp_columns> </input> <output> <exp_columns> <crystal id="1"> <data id="1"> <f>1_PREP_X1_D1_F</f> <sigf>1_PREP_X1_D1_SIGF</sigf> <f_plus>1_PREP_X1_D1_F+</f_plus> <sigf_plus>1_PREP_X1_D1_SIGF+</sigf_plus> <f_minus>1_PREP_X1_D1_F-</f_minus> <sigf_minus>1_PREP_X1_D1_SIGF-</sigf_minus> </data> </crystal> </exp_columns> <freer_columns> <freer>1_PREP_FREER</freer> </freer_columns> </output> <prep> <input_rfree>0</input_rfree> <rfree_label>Unassigned</rfree_label> <rfree_fraction>0.05</rfree_fraction> <rescale_f>1</rescale_f> <ncyc>100</ncyc> <lores>10</lores> <hires>1000.00</hires> <mode>ANISOTROPIC</mode> <wilson>0</wilson> <weight>0</weight> </prep> </step> <step id="2">AFRO <name>AFRO</name> <tag>2_AFRO</tag> <step>2</step> <input> <exp_columns> <crystal id="1"> <data id="1"> <f>1_PREP_X1_D1_F</f> <sigf>1_PREP_X1_D1_SIGF</sigf> <f_plus>1_PREP_X1_D1_F+</f_plus> <sigf_plus>1_PREP_X1_D1_SIGF+</sigf_plus> <f_minus>1_PREP_X1_D1_F-</f_minus> <sigf_minus>1_PREP_X1_D1_SIGF-</sigf_minus> </data> </crystal> </exp_columns> </input> <output> <ea_columns> <ea>2_AFRO_EA</ea> <sigea>2_AFRO_SIGEA</sigea> </ea_columns> <fa_columns> <fa>2_AFRO_FA</fa> <sigfa>2_AFRO_SIGFA</sigfa> </fa_columns> <alpha_columns> <alpha>2_AFRO_ALPHA</alpha> </alpha_columns> </output> <afro> <manual_reso>>0</manual_reso> <hires_cutoff>1000.50</hires_cutoff> <target>GIAC</target> <sigf>2.0</sigf> <manual_sigmas>0</manual_sigmas> </afro> </step> <step id="3">CRUNCH2 <name>CRUNCH2</name> <tag>3_CRUNCH2</tag> <step>3</step> <input> <exp_columns> <crystal id="1"> <data id="1"> <f>1_PREP_X1_D1_F</f> <sigf>1_PREP_X1_D1_SIGF</sigf> <f_plus>1_PREP_X1_D1_F+</f_plus> <sigf_plus>1_PREP_X1_D1_SIGF+</sigf_plus> <f_minus>1_PREP_X1_D1_F-</f_minus> <sigf_minus>1_PREP_X1_D1_SIGF-</sigf_minus> </data> </crystal> </exp_columns> <ea_columns> <ea>2_AFRO_EA</ea> <sigea>2_AFRO_SIGEA</sigea> </ea_columns> <fa_columns> <fa>2_AFRO_FA</fa> <sigfa>2_AFRO_SIGFA</sigfa> </fa_columns> </input> <output> <substructure>3_CRUNCH2</substructure> </output> <crunch2> <patt_search>1</patt_search> <patt_trials>150</patt_trials> <score_threshold>1.000</score_threshold> <ncycles>400</ncycles> <deviation>2.25</deviation> <bp3_verify>3</bp3_verify> <scattering_power>15</scattering_power> <hi_res>1000.50</hi_res> <min_atoms>3</min_atoms> <ntrials>20</ntrials> </crunch2> </step> <step id="4">BP3 <name>BP3</name> <tag>4_BP3</tag> <step>4</step> <input> <substructure>3_CRUNCH2</substructure> <exp_columns> <crystal id="1"> <data id="1"> <f>1_PREP_X1_D1_F</f> <sigf>1_PREP_X1_D1_SIGF</sigf> <f_plus>1_PREP_X1_D1_F+</f_plus> <sigf_plus>1_PREP_X1_D1_SIGF+</sigf_plus> <f_minus>1_PREP_X1_D1_F-</f_minus> <sigf_minus>1_PREP_X1_D1_SIGF-</sigf_minus> </data> </crystal> </exp_columns> </input> <output> <substructure>4_BP3</substructure> <phase_columns> <f>4_BP3_F</f> <sigf>4_BP3_SIGF</sigf> <phib>4_BP3_PHIB</phib> <fom>4_BP3_FOM</fom> </phase_columns> <hl_columns> <hla>4_BP3_HLA</hla> <hlb>4_BP3_HLB</hlb> <hlc>4_BP3_HLC</hlc> <hld>4_BP3_HLD</hld> </hl_columns> </output> <bp3> <phase>0</phase> <no_hand>0</no_hand> <difference_map>1</difference_map> <stop_fom>0.075</stop_fom> </bp3> </step> <step id="5">SOLOMON <name>SOLOMON</name> <tag>5_SOLOMON</tag> <step>5</step> <input> <exp_columns> <crystal id="1"> <data id="1"> <f>1_PREP_X1_D1_F</f> <sigf>1_PREP_X1_D1_SIGF</sigf> <f_plus>1_PREP_X1_D1_F+</f_plus> <sigf_plus>1_PREP_X1_D1_SIGF+</sigf_plus> <f_minus>1_PREP_X1_D1_F-</f_minus> <sigf_minus>1_PREP_X1_D1_SIGF-</sigf_minus> </data> </crystal> </exp_columns> <hl_columns> <hla>4_BP3_HLA</hla> <hlb>4_BP3_HLB</hlb> <hlc>4_BP3_HLC</hlc> <hld>4_BP3_HLD</hld> </hl_columns> <substructure>4_BP3</substructure> </input> <output> <substructure>5_SOLOMON</substructure> <phase_columns> <f>5_SOLOMON_F</f> <sigf>5_SOLOMON_SIGF</sigf> <phib>5_SOLOMON_PHIB</phib> <fom>5_SOLOMON_FOM</fom> </phase_columns> <hl_columns> <hla>5_SOLOMON_HLA</hla> <hlb>5_SOLOMON_HLB</hlb> <hlc>5_SOLOMON_HLC</hlc> <hld>5_SOLOMON_HLD</hld> </hl_columns> </output> <solomon> <trunc_low>0.4</trunc_low> <trunc_high>1.0</trunc_high> <radius>3</radius> <no_hand>0</no_hand> <hand_cycles>10</hand_cycles> <margin>0.003</margin> <optimize_solvent>0</optimize_solvent> <opt_cycles>5</opt_cycles> <density_modify>1</density_modify> <ncycles>20</ncycles> <combined_dmmb>0</combined_dmmb> <phase_comb>DIRECT</phase_comb> <keep_mtz>0</keep_mtz> </solomon> </step> <step id="6">ARPWARP <name>ARPWARP</name> <tag>6_ARPWARP</tag> <step>6</step> <input> <exp_columns> <crystal id="1"> <data id="1"> <f>1_PREP_X1_D1_F</f> <sigf>1_PREP_X1_D1_SIGF</sigf> <f_plus>1_PREP_X1_D1_F+</f_plus> <sigf_plus>1_PREP_X1_D1_SIGF+</sigf_plus> <f_minus>1_PREP_X1_D1_F-</f_minus> <sigf_minus>1_PREP_X1_D1_SIGF-</sigf_minus> </data> </crystal> </exp_columns> <phase_columns> <f>5_SOLOMON_F</f> <sigf>5_SOLOMON_SIGF</sigf> <phib>5_SOLOMON_PHIB</phib> <fom>5_SOLOMON_FOM</fom> </phase_columns> <substructure>5_SOLOMON</substructure> <freer_columns> <freer>1_PREP_FREER</freer> </freer_columns> </input> <output> <pdb>6_ARPWARP</pdb> <substructure>6_ARPWARP</substructure> <phase_columns> <f>6_ARPWARP_F</f> <sigf>6_ARPWARP_SIGF</sigf> <phib>6_ARPWARP_PHIB</phib> <fom>6_ARPWARP_FOM</fom> </phase_columns> <freer_columns> <freer>1_PREP_FREER</freer> </freer_columns> </output> <arpwarp> <use_six>0</use_six> <no_use_pdb>1</no_use_pdb> <side_after>7</side_after> <small_cycles>5</small_cycles> <big_cycles>10</big_cycles> <combined_dmmb>0</combined_dmmb> <ncycles>3</ncycles> <exclude_freer>Y</exclude_freer> <phase_restrain>DIRECT</phase_restrain> <cv_sigmaa>Y</cv_sigmaa> <phase_blur>1.0</phase_blur> <damp_p>0.99</damp_p> <damp_b>0.99</damp_b> <weight_mode>AUTO</weight_mode> <wmat></wmat> <scale>BULK</scale> <scanis>Y</scanis> <refmac_ref_set>Y</refmac_ref_set> <solvent>0</solvent> <tlsonoff>0</tlsonoff> </arpwarp> </step> </run> </soap> </crank>
