Hi Nat,<div><br></div><div>Now I can make it. I just type labin="FP,SIGFP,DANO,SIGDANO". Then there is no error to find the labels. I think because I should give all columns together.</div><div><br></div><div>But there is another problem. When I run the script, it shows me:</div>
<div><div><br></div><div>...</div><div>File "/usr/local/phenix-1.7.1-743/phaser/phaser/phenix_interface/driver.py", line 694, in __init__</div><div> assert os.path.isfile(params.phaser.solution)</div><div>AssertionError</div>
</div><div><div>File "/usr/local/phenix-1.7.1-743/phaser/phaser/phenix_interface/driver.py", line 694, in __init__</div><div> assert os.path.isfile(params.phaser.solution)</div><div>AssertionError</div><div><br>
</div><div><br></div>Just stop at this step. What would be the reason and how to fix it? Any idea would be greatly appreciated.</div><div><br></div><div>Best regards,<br>GP</div><div><br></div><div><br></div><div><div class="gmail_quote">
On Tue, Jul 19, 2011 at 5:47 PM, Nathaniel Echols <span dir="ltr"><<a href="mailto:nechols@lbl.gov">nechols@lbl.gov</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
<div><div></div><div class="h5">On Tue, Jul 19, 2011 at 3:13 AM, G P <<a href="mailto:gysubscribe@gmail.com">gysubscribe@gmail.com</a>> wrote:<br>
> I am now writing a script for phenix.phaser.<br>
> In the input file params.eff there is a keyword labin which corresponds to<br>
> the labels inside input mtz files. The important columns in my ccp4 mtz file<br>
> are FP, SIGFP.<br>
> I edit the line of labin as:<br>
> labin F=FP SIGF=SIGFP<br>
> when running the script, it returns me: Syntax error: expected "=", found<br>
> "F" (file "params.eff", line 9)<br>
> So, I changed it like:<br>
> labin=FP SIGFP<br>
> when running, it gave me the message: Sorry: Couldn't find array FP SIGP in<br>
> file<br>
> I also tried: labin="FP" or labin = "FP SIGFP" or labin="labin F=FP" and so<br>
> on. With nothing it can find the right columns.<br>
> My mtz file should be not problem, I checked with mtzdmp, the columns FP and<br>
> SIGFP were there and with phenix GUI this file works well.<br>
> Would someone know exactly how to edit this line in params.eff?<br>
<br>
</div></div>labin="FP,SIGFP"<br>
<br>
The syntax used for these parameter files is much different from the<br>
CCP4 keyword input - this was necessary for incorporating Phaser into<br>
the Phenix GUI. Among other things, we specify data labels in groups,<br>
and internally "FP,SIGFP" is a single data structure containing both<br>
the amplitudes and sigmas. FYI, unlike the CCP4 version, with<br>
phenix.phaser you can use any type of data as input, so an anomalous<br>
Scalepack file will work too. (Of course you still need to know what<br>
labels to use - someday I intend to make the setup more automatic on<br>
the command line.)<br>
<br>
-Nat<br>
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</blockquote></div><br></div>