Simulated-1g1c: Difference between revisions

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but it traces only about 62 residues. The density looks somewhat reasonable, though.
but it traces only about 62 residues. The density looks somewhat reasonable, though.


The files [ftp://{{SERVERNAME}}/pub/xds-datared/1g1c/xds-simulated-1g1c-I.mtz xds-simulated-1g1c-I.mtz] and [ftp://{{SERVERNAME}}/pub/xds-datared/1g1c/xds-simulated-1g1c-F.mtz xds-simulated-1g1c-F.mtz] are available.
The files [https://{{SERVERNAME}}/pub/xds-datared/1g1c/xds-simulated-1g1c-I.mtz xds-simulated-1g1c-I.mtz] and [https://{{SERVERNAME}}/pub/xds-datared/1g1c/xds-simulated-1g1c-F.mtz xds-simulated-1g1c-F.mtz] are available.


I refined against 1g1c.pdb:
I refined against 1g1c.pdb:
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showing that the anomalous completeness, and even the quality of the anomalous signal, can indeed be increased. I doubt, however, that going to three or more frames would improve things even more.
showing that the anomalous completeness, and even the quality of the anomalous signal, can indeed be increased. I doubt, however, that going to three or more frames would improve things even more.


The MTZ files are at [ftp://{{SERVERNAME}}/pub/xds-datared/1g1c/xds-simulated-1g1c-F-2frames.mtz] and [ftp://{{SERVERNAME}}/pub/xds-datared/1g1c/xds-simulated-1g1c-I-2frames.mtz], respectively. They were of course obtained with XDSCONV.INP:
The MTZ files are at [https://{{SERVERNAME}}/pub/xds-datared/1g1c/xds-simulated-1g1c-F-2frames.mtz] and [https://{{SERVERNAME}}/pub/xds-datared/1g1c/xds-simulated-1g1c-I-2frames.mtz], respectively. They were of course obtained with XDSCONV.INP:
  INPUT_FILE=temp.ahkl
  INPUT_FILE=temp.ahkl
  OUTPUT_FILE=temp.hkl CCP4_I
  OUTPUT_FILE=temp.hkl CCP4_I
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</pre>
</pre>


Using the default (see above) phenix.refine job, I obtain against the [ftp://{{SERVERNAME}}/pub/xds-datared/1g1c/xds-simulated-1g1c-F-2frames.mtz MTZ file with amplitudes]:
Using the default (see above) phenix.refine job, I obtain against the [https://{{SERVERNAME}}/pub/xds-datared/1g1c/xds-simulated-1g1c-F-2frames.mtz MTZ file with amplitudes]:
  Start R-work = 0.3434, R-free = 0.3540
  Start R-work = 0.3434, R-free = 0.3540
  Final R-work = 0.2209, R-free = 0.2479
  Final R-work = 0.2209, R-free = 0.2479
and against the [ftp://{{SERVERNAME}}/pub/xds-datared/1g1c/xds-simulated-1g1c-I-2frames.mtz MTZ file with intensities]
and against the [https://{{SERVERNAME}}/pub/xds-datared/1g1c/xds-simulated-1g1c-I-2frames.mtz MTZ file with intensities]
  Start R-work = 0.3492, R-free = 0.3606
  Start R-work = 0.3492, R-free = 0.3606
  Final R-work = 0.2244, R-free = 0.2504
  Final R-work = 0.2244, R-free = 0.2504
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     total      165799  42025    43003      97.7%      11.7%    12.3%  162399  10.07    13.5%    14.8%    17%  0.908  16219
     total      165799  42025    43003      97.7%      11.7%    12.3%  162399  10.07    13.5%    14.8%    17%  0.908  16219


Using these data (stored in [ftp://{{SERVERNAME}}/pub/xds-datared/1g1c/xscale.oldversion]), I was finally able to solve the structure (see screenshot below) - SHELXE traced 160 out of 198 residues. All files produced by SHELXE are in [ftp://{{SERVERNAME}}/pub/xds-datared/1g1c/shelx].
Using these data (stored in [https://{{SERVERNAME}}/pub/xds-datared/1g1c/xscale.oldversion]), I was finally able to solve the structure (see screenshot below) - SHELXE traced 160 out of 198 residues. All files produced by SHELXE are in [https://{{SERVERNAME}}/pub/xds-datared/1g1c/shelx].


[[File:1g1c-shelxe.png]]
[[File:1g1c-shelxe.png]]