Leginon

First, we apologize, but we are not ready for a full trunk installation. The unblur link was left by the appion developer for his local condition.

Trunk is not always stable bcause of active development by multiple developers. There is a branch myami-beta which is slightly more controlled (used by NYSBC SEMC users). gctf implementation is there, too.

Regarding GPU stack frame alignment, the new makeDDRawFrameStack.py program in /usr/local/bin/ uses, according to your error tracing, the appionlib at /usr/local/lib/python2.7/site-packages/appionlib. It is likely that the particular appionlib is still an older version since setNewNumRunningAverageFrames is a recent addition. If you are sure the new .py files was copied successfully into the default /usr/local/lib/python2.7/site-packages/appionlib, check the .pyc files there for date. Maybe they were not recompiled for some reason.

Hi,

So I copied over the entire appionlib and appion/bin directory from trunk to the installation directories (/usr/local/.....).

For GPU alignment, I now get the dosefgpu_driftcorr (v2.1) not recognizing -nrw as input. Removing the "--nrw=1" from submit command did not work.
Setting "--nrw=0" worked.

For Gctf:
I am getting this error
-------------------------------------------------------------------------------------------------------------------------------
Tips: Better to run it outside the Micrographs/ directory to match typical Relion style.
-------------------------------------------------------------------------------------------------------------------------------
... ctf estimation completed in 24.28 sec
... reading filename_en-a_ctffind3.log
Traceback (most recent call last):
File "/usr/local/bin/gctf.py", line 397, in <module>
imgLoop.run()
File "/usr/local/lib/python2.7/site-packages/appionlib/appionLoop2.py", line 88, in run
results = self.loopProcessImage(imgdata)
File "/usr/local/lib/python2.7/site-packages/appionlib/appionLoop2.py", line 146, in loopProcessImage
return self.processImage(imgdata)
File "/usr/local/bin/gctf.py", line 280, in processImage
logf = open(ctfproglog, "r")
IOError: [Errno 2] No such file or directory: 'filename_en-a_ctffind3.log'

---------------
Do I need to install CTFFIND3 for Gctf to work? There is only CTFFIND4 on the workstation.

Thank you.

Hi Harry,

A fix for the --nrw bug is in the trunk now, revision r19808. In appionlib/apDDprocess.py, change line 1206 from

if self.getNewNumRunningAverageFrames() != 0:

to

if self.getNewNumRunningAverageFrames() > 1:

Gctf writes log files to ctffind3 format, you do not need to install ctffind3. If Gctf did not generate the ctffind3.log file, it probably didn't finish processing correctly. Can you check for either the line "All # files finished successfully" or any error messages in your terminal output? Thanks,

Carl

Hi Carl,

After editing line 1206 in appionlib/apDDprocess.py, GPU alignment works now. Thank you.

For Gctf, here is the output:

Opening filename_en-a.mrc for initial test and preperation ....... *******************************************************************************************
User input parameters:
--apix 1.255
--kv 300.00
--cs 2.26
--ac 0.07
--boxsize 1024
--resL 50.00
--resH 4.00
--defS 1000.00
--astm 0.10

All parameters to be used:
General options:
--apix 1.255
--dstep 14.000
--kv 300.00
--cs 2.26
--ac 0.07
Advanced options:
--bfac 150.00
--defL 5000.00
--defH 90000.00
--astm 0.10
--resL 50.00
--resH 4.00
--boxsize 1024
--overlap 0.50
--convsize 85
--do_validation 0
--do_basic_rotave 0
--do_EPA 0
--do_Hres_ref 0
--Href_resL 15.00
--Href_resH 4.00
--Href_bfac 50.00
Bfactor estimation options:
--B_resL 15.00
--B_resH 6.00
Movie options:
--mdef_ave_type 0
--mdef_aveN 7
--mdef_fit 0
Local refinement options:
--do_local_refine 0
--local_radius 1024.00
--local_boxsize 512
--local_overlap 0.50
--local_boxtype 1
--local_avetype 0
Tilt refinement options:
--refine_tilt 0
--init_tilt_ang 0.00
--init_tilt_err 0.00
Correction options:
--do_phase_flip 0
Validation options:
--do_validation 0
Input CTF parameters for refinement:
--refine_input_ctf 0
--defU_init 20000.00
--defV_init 20000.00
--defA_init 0.00
--B_init 200.00
--defU_err 500.00
--defV_err 500.00
--defA_err 15.00
--B_err 50.00
--input_ctfstar NULL
I/O options:
--ctfstar micrographs_all_gctf.star
--logsuffix _gctf.log
--boxsuffix _automatch.star
--write_local_ctf 0
--plot_res_ring 1
--gid 0
--do_unfinished 0

All 1 files to be searched and refined:
filename_en-a.mrc

TIME<<<<<< PREPARATION: 0.274411s

Reading file: filename_en-a.mrc
.

TIME<<<<<< READING: 0.095370s
TIME<<<<<< FFT: 0.984862s

Reading filename_en-a.mrc.
Processing file: filename_en-a.mrc

TIME<<<<<< 1D SEARCH: 0.000781s

Defocus_U Defocus_V Angle CCC
48213.96 48213.86 61.22 -0.002236 Final Values

TIME<<<<<< 2D REFINE: 0.054699s
TIME<<<<<< FITTING: 0.086936s

-------------------------------------------------------------------------------------------------------------------------------
Resolution limit estimated by EPA: 4.257
Estimated Bfactor: 1.36
-------------------------------------------------------------------------------------------------------------------------------

TIME<<<<<< VALIDATION: 0.000001s
TIME<<<<<< STACK_REFINE: 0.000000s
TIME<<<<<< LOCAL_REFINE: 0.000001s
TIME<<<<<< CTF_CORRECTION: 0.000000s

Processing done successfully.
-------------------------------------------------------------------------------------------------------------------------------

#################################################################################################################################
All 1 files finished successfully:

TIME<<<<<< TOTAL: 1.675650s

#################################################################################################################################

-------------------------------------------------------------------------------------------------------------------------------
Tips: For micrographs from 'Cs corrector' ,you can set the parameter --Cs to be 0 or near 0, e.g. 0.01.It does not affect the CTF results if you use 0 or 0.1.
-------------------------------------------------------------------------------------------------------------------------------
... ctf estimation completed in 1.82 sec
... reading filename_en-a_ctffind3.log
Traceback (most recent call last):
File "/usr/local/bin/gctf.py", line 398, in <module>
imgLoop.run()
File "/usr/local/lib/python2.7/site-packages/appionlib/appionLoop2.py", line 88, in run
results = self.loopProcessImage(imgdata)
File "/usr/local/lib/python2.7/site-packages/appionlib/appionLoop2.py", line 146, in loopProcessImage
return self.processImage(imgdata)
File "/usr/local/bin/gctf.py", line 281, in processImage
logf = open(ctfproglog, "r")
IOError: [Errno 2] No such file or directory: 'filename_en-a_ctffind3.log'

Hi Carl,

As you suggested, I downloaded trunk 19816, copied over gctf.py, edited the "exename" at line 93 to our installaion of Gctf, appion Gctf plugin works now.

Thank you.

Harry