Hi Nat, 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. But there is another problem. When I run the script, it shows me: ... File "/usr/local/phenix-1.7.1-743/phaser/phaser/phenix_interface/driver.py", line 694, in __init__ assert os.path.isfile(params.phaser.solution) AssertionError File "/usr/local/phenix-1.7.1-743/phaser/phaser/phenix_interface/driver.py", line 694, in __init__ assert os.path.isfile(params.phaser.solution) AssertionError Just stop at this step. What would be the reason and how to fix it? Any idea would be greatly appreciated. Best regards, GP On Tue, Jul 19, 2011 at 5:47 PM, Nathaniel Echols wrote:

On Tue, Jul 19, 2011 at 3:13 AM, G P wrote:

...

I am now writing a script for phenix.phaser. In the input file params.eff there is a keyword labin which corresponds to the labels inside input mtz files. The important columns in my ccp4 mtz file are FP, SIGFP. I edit the line of labin as: labin F=FP SIGF=SIGFP when running the script, it returns me: Syntax error: expected "=", found "F" (file "params.eff", line 9) So, I changed it like: labin=FP SIGFP when running, it gave me the message: Sorry: Couldn't find array FP SIGP in file I also tried: labin="FP" or labin = "FP SIGFP" or labin="labin F=FP" and so on. With nothing it can find the right columns. My mtz file should be not problem, I checked with mtzdmp, the columns FP and SIGFP were there and with phenix GUI this file works well. Would someone know exactly how to edit this line in params.eff?

labin="FP,SIGFP"

The syntax used for these parameter files is much different from the CCP4 keyword input - this was necessary for incorporating Phaser into the Phenix GUI. Among other things, we specify data labels in groups, and internally "FP,SIGFP" is a single data structure containing both the amplitudes and sigmas. FYI, unlike the CCP4 version, with phenix.phaser you can use any type of data as input, so an anomalous Scalepack file will work too. (Of course you still need to know what labels to use - someday I intend to make the setup more automatic on the command line.)

-Nat _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb

Hi Nat, Thank you so much! That's cool. I just wrote a None to that solution and it works!! Now I have some new problems: At beginning, I only have phenix installed. I do not have CCP4 installed. Then I run "phenix.phaser params.eff" to call phenix run phaser from script params.eff. It works well. Then, I installed CCP4 with its own phaser inside. Then I run again "phenix.phaser params.eff". The computer start to import files (should be some libraries and supporting files, not input data) from CCP4 installation directory. It seems so strange for me. And because some of the .so files in CCP4 directory are for 32bit, phenix.phaser gave me error message: wrong ELF class: ELFCLASS32 and refused to keep running. Is there anyway to set some kind of PATH variables to let phenix.phaser params.eff run like without CCP4 installed. (which I did at beginning). Sorry for so many questions. Don't worry to reply if you do not have time. I fully understand and thanks a lot for your reply. regards, GP On Wed, Jul 20, 2011 at 8:27 PM, Nathaniel Echols wrote:

On Wed, Jul 20, 2011 at 3:46 AM, G P wrote:

...

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.

Right, sorry, that's another thing that CCTBX does automatically. This command will show you what array labels Phenix recognizes:

iotbx.reflection_file_reader data.mtz

...

But there is another problem. When I run the script, it shows me: ... File "/usr/local/phenix-1.7.1-743/phaser/phaser/phenix_interface/driver.py", line 694, in __init__ assert os.path.isfile(params.phaser.solution) AssertionError File "/usr/local/phenix-1.7.1-743/phaser/phaser/phenix_interface/driver.py", line 694, in __init__ assert os.path.isfile(params.phaser.solution) AssertionError

Look for a parameter called "solution" - this needs to be left as None. (I don't think there's any way to use this from the command line right now - it's very specific to the GUI.)

-Nat _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb

Hi Nat, Thanks for you help. I solved that problem with Ralf's help now. Just reset the $PATH make phenix.phaser appearing before CCP4's. GP On Wed, Jul 20, 2011 at 8:39 PM, Nathaniel Echols wrote:

I think this is a known problem, but I'm not sure how to fix it - I am downloading the latest CCP4 now to try for myself. Ralf probably knows more. Did you source the setup file in the CCP4 installation?

-Nat

...

Hi Nat, Thank you so much! That's cool. I just wrote a None to that solution and it works!! Now I have some new problems: At beginning, I only have phenix installed. I do not have CCP4 installed. Then I run "phenix.phaser params.eff" to call phenix run phaser from

...

params.eff. It works well. Then, I installed CCP4 with its own phaser inside. Then I run again "phenix.phaser params.eff". The computer start to import files (should be some libraries and supporting files, not input data) from CCP4 installation directory. It seems so strange for me. And because some of the .so files in CCP4 directory are for 32bit, phenix.phaser gave me error message: wrong ELF class: ELFCLASS32 and refused to keep running. Is there anyway to set some kind of PATH variables to let phenix.phaser params.eff run like without CCP4 installed. (which I did at beginning). Sorry for so many questions. Don't worry to reply if you do not have time. I fully understand and thanks a lot for your reply. regards, GP

On Wed, Jul 20, 2011 at 8:27 PM, Nathaniel Echols wrote:

...

On Wed, Jul 20, 2011 at 3:46 AM, G P wrote:

...

Now I can make it. I just type labin="FP,SIGFP,DANO,SIGDANO". Then

On Wed, Jul 20, 2011 at 11:35 AM, G P wrote: script there

...

...

...

is no error to find the labels. I think because I should give all columns together.

Right, sorry, that's another thing that CCTBX does automatically. This command will show you what array labels Phenix recognizes:

iotbx.reflection_file_reader data.mtz

...

But there is another problem. When I run the script, it shows me: ... File

"/usr/local/phenix-1.7.1-743/phaser/phaser/phenix_interface/driver.py",

...

line 694, in __init__ assert os.path.isfile(params.phaser.solution) AssertionError File

"/usr/local/phenix-1.7.1-743/phaser/phaser/phenix_interface/driver.py",

...

line 694, in __init__ assert os.path.isfile(params.phaser.solution) AssertionError

Look for a parameter called "solution" - this needs to be left as None. (I don't think there's any way to use this from the command line right now - it's very specific to the GUI.)

-Nat _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb

_______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb

_______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb