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Processing SmgGDS 558 and farnesylated RhoA complex data

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keitaroyam edited this page Feb 2, 2019 · 1 revision

References

  • Original paper
    • Shimizu et al. (2018) "GEF mechanism revealed by the structure of SmgGDS-558 and farnesylated RhoA complex and its implication for a chaperone mechanism." PNAS doi: 10.1073/pnas.1804740115
  • PDB: 5ZHX
  • Raw data: Zenodo#1134209

How data were processed in the original paper

All datasets were given to kamo, and then clustering & merging procedures were performed using blend and cc. To find the best cluster that gives clear electron density of all prenyl groups, following scripts were used.

First, structure refinement was performed for each data. The electron density view of each ligand was created using the PyMOL script.

for d in $PWD/*3.5*/cluster_*/run_03/ccp4
do
 mkdir -v $d/refine0
 cat <<+ > $d/refine0/refine0.sh
copy_free_R_flag.py -r /path-to-reference/reference.mtz ../xscale.mtz
phenix.refine \\
 xscale_copy_free.mtz \\
 strategy=rigid_body+individual_sites+individual_adp \\
 /path-to-reference/xscale_KAMO_cluster55_refmac9_omitside.pdb \\
 /path-to-reference/FCS_mon_lib.cif \\
 ncs_search.enabled=True write_geo=false
pymol -cpqk < $PWD/draw_map.pml
+
done

+
 qsub -wd $d/refine0 -j y $d/refine0/refine0.sh
done

The PyMOL script draw_map.pml looks like this:

run /path/loadmtz.py
bg_color white
set ignore_case_chain
set mesh_width, 1
set ray_trace_fog, 0
set depth_cue, 0
set ray_shadows, 0

load /path-to-reference/xscale_KAMO_cluster55_refmac9.pdb, org
load xscale_KAMO_cluster55_refmac9_omitside_refine_001.pdb, refined
as sticks
util.color_chains("elem C")

print run_loadmtz("xscale_KAMO_cluster55_refmac9_omitside_refine_001.mtz", "all", labels="FOFCWT,PHFOFCWT", isolevel=2.5)

python
while 1:
 if any(map(lambda x: "msh_" in x, cmd.get_names())):
  print "msh OK!"
  break
 print "waiting.."
 time.sleep(1)

python end

color green, msh*
hide everything, (org or refined) and not resn FCS

python
for c in "efgh":
 print cmd.align("org and chain %s"%c, "refined and chain %s"%c)
 print cmd.zoom("chain %s and resn FCS"%c)
 print cmd.orient("chain %s and resn FCS"%c)
 print cmd.clip("slab", 5)
 print cmd.png("FCS_2.5s_%s.png"%c, ray=1)

python end

print cmd.get_names()
quit

Finally, the following script was used to make html file

out=omit_maps_3.5a.html
cat <<+ > $out
<html>
<head></head>
<body>
<table>
+

for d in *3.5*/cluster_*/run_03/ccp4/refine0
do
 log=$d/xscale_KAMO_cluster55_refmac9_omitside_refine_001.log
 r_wf=`grep "^Final R" $log`
 bave=`awk '/end: /{print $8}' $log`
 cc12ou=`grep "STATISTICS OF INPUT DATA SET" -B4 $d/../../XSCALE.LP | head -n1 | awk '{print $11}'`
 name=`echo $d | sed -e "s,/run.*,,"`
 cat <<+ >> $out
<tr>
 <td>$name<br>$r_wf<br>&lt;B&gt;=$bave<br>CC1/2.ou=$cc12ou</td>
 <td><img src="$d/FCS_2.5s_e.png" width=320></td>
 <td><img src="$d/FCS_2.5s_f.png" width=320></td>
 <td><img src="$d/FCS_2.5s_g.png" width=320></td>
 <td><img src="$d/FCS_2.5s_h.png" width=320></td>
</tr>
+
done

cat <<+ >> $out
</table>
</body>
+
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