[ccp4bb] AMoRe
Hi, Has anyone tried the tutorial on the CCP4 website for AMoRe? http://www.ccp4.ac.uk/examples/tutorial/html/mr-tutorial-amore.html I am trying to learn how to use the package in CCP4 and it fails and I am wondering if the tutorial has become outdated? Thank you, George
Re: [ccp4bb] AMoRe fails to use model coordinates
Hmm - I use this quite a bit. ifier. You cant start Autoamore for a particular model until that has been entered into the model database - the first Q you are asked from the GUI is Which model? But you can certainly close the model database once you have entered the model name with a unique identifier. The orde of operations is: sortfun to reformat the observed data tabfun to generate SFs from the model rotfun trafun fitfun However if you have already run sortfun or tabfun with that input the gui will not repeat the steps. Could you have used the same name for different models perhaps - that will get the software well confused! Eleanor On 04/27/2011 04:26 PM, Chris Richards: on wrote: On 27 Apr 2011, at 15:02, Edward A. Berry wrote: 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 file doesn't exist, it's a figment of the GUI's imagination. After some poking around, I've now got it to work properly. The problem seems to be that the GUI is very sensitive to the order in which you enter data. When you choose to run AMoRe, it pops up an AMoRe window and a Model Database window. If you enter data into these in the order specified in the tutorial, it will run the scripts for a model in the form of SFs from an MTZ, even though the Model Database window claims to be using a model in the form of coordinates. The trick to getting it to work seems to be: 1) Open the Model Database window. Enter your pdb filename. Don't even think about clicking Close, despite what the tutorial says. Click SaveExit, and never open the window again. If you do have to open it again, Restore Default Parameters and start from scratch. 2) Open the AMoRe window, set up the job parameters and run the job. Doing this will get it to run TABFUN on your pdb file rather than SORTFUN on a non-existent mtz file. Most of the time. Thanks to Stefano Trapani and Jorge Navaza for pointing us in the direction of the standalone AMoRe. Chris -- Dr Chris Richardson :: Sysadmin, structural biology, icr.ac.uk The Institute of Cancer Research: Royal Cancer Hospital, a charitable Company Limited by Guarantee, Registered in England under Company No. 534147 with its Registered Office at 123 Old Brompton Road, London SW7 3RP. This e-mail message is confidential and for use by the addressee only. If the message is received by anyone other than the addressee, please return the message to the sender by replying to it and then delete the message from your computer and network.
[ccp4bb] AMoRe fails to use model coordinates
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. 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 The Institute of Cancer Research: Royal Cancer Hospital, a charitable Company Limited by Guarantee, Registered in England under Company No. 534147 with its Registered Office at 123 Old Brompton Road, London SW7 3RP. This e-mail message is confidential and for use by the addressee only. If the message is received by anyone other than the addressee, please return the message to the sender by replying to it and then delete the message from your computer and network.
Re: [ccp4bb] AMoRe fails to use model coordinates
You could try the stand-alone version of AMoRe from Jorge Navaza's web site. http://mem.ibs.fr/JORGE/index.html Stefano TRAPANI Maître de Conférences Centre de Biochimie Structurale (CBS) CNRS UMR 5048; UM1; UM2; INSERM UMR 554 29 rue de Navacelles 34090 MONTPELLIER Cedex - France Tel : +33 (0)4 67 41 77 29 Fax : +33 (0)4 67 41 79 13 http://www.cbs.cnrs.fr/spip.php?rubrique182PERS=Stefano%20Trapani On Wed, April 27, 2011 13:14, 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. 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 The Institute of Cancer Research: Royal Cancer Hospital, a charitable Company Limited by Guarantee, Registered in England under Company No. 534147 with its Registered Office at 123 Old Brompton Road, London SW7 3RP. This e-mail message is confidential and for use by the addressee only. If the message is received by anyone other than the addressee, please return the message to the sender by replying to it and then delete the message from your computer and network. -- Passerelle antivirus CBS -- Passerelle antivirus CBS
Re: [ccp4bb] AMoRe fails to use model coordinates
On 27 Apr 2011, at 15:02, Edward A. Berry wrote: 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 file doesn't exist, it's a figment of the GUI's imagination. After some poking around, I've now got it to work properly. The problem seems to be that the GUI is very sensitive to the order in which you enter data. When you choose to run AMoRe, it pops up an AMoRe window and a Model Database window. If you enter data into these in the order specified in the tutorial, it will run the scripts for a model in the form of SFs from an MTZ, even though the Model Database window claims to be using a model in the form of coordinates. The trick to getting it to work seems to be: 1) Open the Model Database window. Enter your pdb filename. Don't even think about clicking Close, despite what the tutorial says. Click SaveExit, and never open the window again. If you do have to open it again, Restore Default Parameters and start from scratch. 2) Open the AMoRe window, set up the job parameters and run the job. Doing this will get it to run TABFUN on your pdb file rather than SORTFUN on a non-existent mtz file. Most of the time. Thanks to Stefano Trapani and Jorge Navaza for pointing us in the direction of the standalone AMoRe. Chris -- Dr Chris Richardson :: Sysadmin, structural biology, icr.ac.uk The Institute of Cancer Research: Royal Cancer Hospital, a charitable Company Limited by Guarantee, Registered in England under Company No. 534147 with its Registered Office at 123 Old Brompton Road, London SW7 3RP. This e-mail message is confidential and for use by the addressee only. If the message is received by anyone other than the addressee, please return the message to the sender by replying to it and then delete the message from your computer and network.
