Chris Richardson wrote:
One of our group was having trouble getting AMoRe to use model coordinates as a
trial model. I've replicated this using the data from the tutorial at
http://www.ccp4.ac.uk/dist/examples/tutorial/html/mr-tutorial-amore.html
It fails using CCP4 6.1.13 on OS 10.6.7 (compiled from Fink) and Ubuntu 8.0.4
LTS (binary installation from ccp4.ac.uk).
The tutorial uses a PDB file of model coordinates (model.pdb). As I understand
it, AMoRe is supposed to generate an SF table file from this. Instead,
AutoAMoRe seems to be looking for an mtz file.
No, that would be the TABFUN step. You are running SORTFUN which takes your
experimental data and puts in the the .tab format required by the subsequent
routines. And with the HKLIN command line variable you are telling it to
get data from AmoreModel_MR_trial.mtz . Does that file exist, is it
readable, and path name correct?
The logs look like this:
***************************************************************************
* Information from CCP4Interface script
***************************************************************************
There is no SF Table file for the map of the model coordinates
Generating the file /home/foop/temp/amoretest/AmoreModel_MR_trial.tab
***************************************************************************
File: "/home/foop/temp/amoretest/AmoreModel_MR_trial.mtz"
Cannot be opened for reading
CCP4 library signal ccp4_general:Cannot find input file (Error)
raised in ccp4setenv<<<<<<
amore: Cannot find input file
Times: User: 0.0s System: 0.0s Elapsed: 0:00
***************************************************************************
* Information from CCP4Interface script
***************************************************************************
The program run with command: /sw/share/xtal/ccp4-6.1.13/bin/amore HKLIN
"/home/foop/temp/amoretest/AmoreModel_MR_trial.mtz" HKLPCK0
"/tmp/foop/AmoreTest_1_3_hkl.tmp" TABLE1
"/home/foop/temp/amoretest/AmoreModel_MR_trial.tab"
has failed with error message
Last system error message: No such file or directory
amore: Cannot find input file
***************************************************************************
The command script generating this is:
*******************************************************************
/tmp/foop/AmoreTest_1_4_com.tmp
*******************************************************************
title AmoreTest
sortfun -
MODEL -
resolution 60.0 -
3.0
labin FC=FC PHIC=PHIC
## This script run with the command ##########
# /sw/share/xtal/ccp4-6.1.13/bin/amore HKLIN "/home/foop/temp/amoretest/AmoreModel_MR_trial.mtz"
HKLPCK0 "/tmp/foop/AmoreTest_1_3_hkl.tmp" TABLE1
"/home/foop/temp/amoretest/AmoreModel_MR_trial.tab"
################################################
If anyone can suggest a way around this problem (other than using an
alternative MR program), I'd be grateful.
Regards,
Chris
--
Dr Chris Richardson :: Sysadmin, structural biology, icr.ac.uk
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