Appion

On Mar 14, 2011, at 2:29 PM, Jeff Speir wrote:

Hi Lauren,

I had sent you the commands Gabe found for converting virus maps in viper icos orientation to EMAN icos orientation. Turns out there was a slight error. The 90 degree rotation in the second command should be -90. Didn't unravel this until EMAN spit back a good enough reconstruction to see that the icos symmetry wasn't exactly matching the model that went in. There also appears to be a bug in EMAN pdb2mrc such that when you specify low resolution for the output map it slows way, way down (final map is fine, just takes far too long to compute). A workaround was to produce the default map (1Å spacing) then low pass filter it. The simple script below embodies both fixes and is what I used. Thought it might be useful for you to know how I worked from Viper coordinates to an EMAN starting model in the end.

Cheers,

Jeff

#!/bin/tcsh

1. Compute map from model in Viper std icos orientation and
2. rotate to EMAN std icos orientation

1. generate map, 1A/voxel

pdb2mrc afhv_vprstd_particle.pdb tmp1.mrc

1. low pass filter map, lp=A/voxel (i.e. resolution)

proc3d tmp1.mrc tmp2.mrc apix=1.0 lp=25 edgenorm

1. rotate map from Viper std to EMAN std icos orientation

proc3d tmp2.mrc tmp3.mrc icos5fTo2f
proc3d tmp3.mrc afhv_25A_eman.mrc rot=0,0,-90

1. clean up intermediate maps

/bin/rm tmp1.mrc tmp2.mrc tmp3.mrc

Error message from /ami/data17/appion/11jan12a/models/accepted/file_11mar02p48/file_11mar02p48.appionsub.log:

 ... Time stamp: 11mar02p49
 ... Function name: uploadModel
 ... Appion directory: /usr/lib64/python2.4/site-packages
!!! WARNING: Using split database
Connected to database: 'ap292'
 ... Committing data to database
 ... Found project id=292 for session 11jan12a in 6.81 msec
 ... Looking up symmetry for input: 2
 ... Selected symmetry group: ICOS -- Icos (5 3 2) EMAN
 ... Run directory: /ami/data17/appion/11jan12a/models/accepted/file_11mar02p48
!!! WARNING: directory '/ami/data17/appion/11jan12a/models/accepted/file_11mar02p48' already exists.
 ... Writing function log to: uploadModel.log
 ... Found 4 processors on this machine
 ... Running Appion version 'r15281'
Naming density model: /ami/data17/appion/11jan12a/models/accepted/file_11mar02p48/upload-vni206_model_25A_vpr-11mar02p49
 ... copying original model to a new location: /ami/data17/appion/11jan12a/models/accepted/file_11mar02p48/upload-vni206_model_25A_vpr-11mar02p49.mrc

calculating dimensions...
Traceback (most recent call last):
  File "/opt/appion/bin/uploadModel.py", line 234, in ?
    uploadModel.start()
  File "/opt/appion/bin/uploadModel.py", line 217, in start
    apVolume.viper2eman(mrcname, mrcname, apix=self.params['apix'])
KeyError: 'apix'