Whilst I can input SAD SAD data ie two different SAD datasets using Group =1 and Group =2 with the "Wavelength" keyword, how do I input 2 different crystals using the "crystal_info" keyword which does not recognize Group = Inputting .sca unmerged anomalous data how do I input data for 2 different crystal_info keywords with different heavy atoms and different unit cells? thanks Nora Dr N B Cronin X-Ray Laboratory Manager Tel. (+44) 020 7153 5445 Section of Structural Biology Fax. (+44) 020 7153 5457 Chester Beatty Laboratories mobile: (+44) 07787554059 The Institute of Cancer Research 237 Fulham Road London SW3 6JB 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.
Hi Nora, AutoSol will only take a single "crystal_info", and assumes that all data that you give it is referring to a single crystal form, with (approximately) the same cell dimensions for all datasets. If you have multiple crystal forms, or crystals with substantially (more than about 1-2 percent) different cells, then you will want to solve them separately. You can then combine information with phenix.multi_crystal_average if you want. Let me know if that doesn't help with your two questions! All the best, -Tom T
Whilst I can input SAD SAD data ie two different SAD datasets using Group =1 and Group =2 with the "Wavelength" keyword, how do I input 2 different crystals using the "crystal_info" keyword which does not recognize Group =
Inputting .sca unmerged anomalous data how do I input data for 2 different crystal_info keywords with different heavy atoms and different unit cells?
thanks
Nora
Dr N B Cronin X-Ray Laboratory Manager Tel. (+44) 020 7153 5445 Section of Structural Biology Fax. (+44) 020 7153 5457 Chester Beatty Laboratories mobile: (+44) 07787554059 The Institute of Cancer Research 237 Fulham Road London SW3 6JB
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._______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb
I get an error in reading the .hhr file: Loading PDB and alignment files from /work/ncronin/cdc23/23_HG_14/xds_Cdc23-23_HG_14w1_run1_1/phenix/MR_ROSETTA_5/WORK_1/5791278_1/5791278_ed.hhr Log file for mr_model_preparation is: /work/ncronin/cdc23/23_HG_14/xds_Cdc23-23_HG_14w1_run1_1/phenix/MR_ROSETTA_5/WORK_1/5791278_1/mr_model_preparation.log ******************* ERROR ENDING *************** Uninterpretable: 'Q ss_pred hhhHHHHHHHHHhc---CCCcccHHHHHHHHHHHHhHhhhHhHHhhhcCCCccccchhHHHHHHHHHHHHhccCCCCchh\nQ 82 DCKEFERAAYTLQN---CKSSKSIFLRLYSKYLAGEKKSEEENETLLNTNLTLSSTNREFYYISEVLESLHYQGNKDPYL 158 (285)\nQ Consensus 82 ~~~~~~~A~~~l~~---~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~l~~a~~~~~~~~~~~~~~~~~~ 158 (285)\n ..|+|++|+..+++ .+.....+...+.......+..+ ++..++++++. .|.+..+\nT Consensus 35 elG~y~~Ai~~~~~al~~~p~~~~~~~~lg~~~~~~g~~~~--------------------A~~~~~~al~~-~p~~~~~ 93 (243)\nT 2q7f_A 35 EFGDYEKAAEAFTKAIEENKEDAIPYINFANLLSSVNELER--------------------ALAFYDKALEL-DSSAATA 93 (243)\nT ss_dssp -------CCTTHHHHHTTCTTCHHHHHHHHHHHHHTTCHHH--------------------HHHHHHHHHHH-CTTCHHH\nT ss_pred HcCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHCCCHHH--------------------HHHHHHHHHhc-CCccHHH\n\n\nQ ss_pred HHHHHHHHHHcCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHhcHHHHHHHH-------HhCCcccHHHHHHHHHHHHHH\nQ 159 LYLSGVVYRKRKQDSKAIDFLKSCVLKAPFFWSAWLELSLSIDSLETLTTVV-------SQLPSTHIMTKIFYVYASHEL 231 (285)\nQ Consensus 159 ~~~~g~~~~~~~~~~~A~~~~~~al~~~p~~~~~~~~l~~~~~~~~~~~~al-------~~~p~~~~~~~~~~~~~~~~~ 231 (285)\n +..+|.++...+++++|+..|.+++...|.+...+..++.++...++++.++ ...| ....+..+|.++...\nT Consensus 94 ~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~~-~~~~~~~~l~~~~~~~ 172 (243)\nT 2q7f_A 94 YYGAGNVYVVKEMYKEAKDMFEKALRAGMENGDLFYMLGTVLVKLEQPKLALPYLQRAVELNE-NDTEARFQFGMCLANE 172 (243)\nT ss_dssp HHHHHHHHHHTTCHHHHHHHHHHHHHHTCCSHHHHHHHHHHHHHTSCHHHHHHHHHHHHHHCT-TCHHHHHHHHHHHHHH\nT ss_pred HHHHHHHHHHhccchhhHHHHHHHHhhhhhhHHHHHHHHHHHHHHHhHHHHHHHHHHHHHhCC-ccHHhhhhhhhhhhhc\n\n\nQ ss_pred hcchHHHHHHHHHHHhhCCCChHHHHHHHHHHHHhcCHHHHHHHHHHHHHHCcC\nQ 232 HQVNSSAYEKLAEAEIIFPNSRYLKTQRALLTYDSRDFDEAESLFENILTNDPA 285 (285)\nQ Consensus 232 ~~~~~A~~~~~~~al~~~p~~~~~~~~la~~~~~~~~~~~A~~~~~~al~~~P~ 285 (285)\n +++++|+ .++++++..|+++.++..+|.++..+|++++|+.+|+++++++|+\nT Consensus 173 ~~~~~A~-~~~~~ai~~~p~~~~~~~~lg~~~~~~g~~~~A~~~~~kal~l~P~ 225 (243)\nT 2q7f_A 173 GMLDEAL-SQFAAVTEQDPGHADAFYNAGVTYAYKENREKALEMLDKAIDIQPD 225 (243)\nT ss_dssp TCCHHHH-HHHHHHHHHCTTCHHHHHHHHHHHHHTTCTTHHHHHHHHHHHHCTT\nT ss_pred ccHHHHH-HHHHHHHHHCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCC' ******************* ERROR ENDING *************** Can you help Best regards Nora On 19 Apr 2011, at 16:25, Thomas C. Terwilliger wrote:
Hi Nora,
AutoSol will only take a single "crystal_info", and assumes that all data that you give it is referring to a single crystal form, with (approximately) the same cell dimensions for all datasets.
If you have multiple crystal forms, or crystals with substantially (more than about 1-2 percent) different cells, then you will want to solve them separately. You can then combine information with phenix.multi_crystal_average if you want.
Let me know if that doesn't help with your two questions! All the best,
-Tom T
Whilst I can input SAD SAD data ie two different SAD datasets using Group =1 and Group =2 with the "Wavelength" keyword, how do I input 2 different crystals using the "crystal_info" keyword which does not recognize Group =
Inputting .sca unmerged anomalous data how do I input data for 2 different crystal_info keywords with different heavy atoms and different unit cells?
thanks
Nora
Dr N B Cronin X-Ray Laboratory Manager Tel. (+44) 020 7153 5445 Section of Structural Biology Fax. (+44) 020 7153 5457 Chester Beatty Laboratories mobile: (+44) 07787554059 The Institute of Cancer Research 237 Fulham Road London SW3 6JB
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._______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb
_______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb
Dr N B Cronin X-Ray Laboratory Manager Tel. (+44) 020 7153 5445 Section of Structural Biology Fax. (+44) 020 7153 5457 Chester Beatty Laboratories mobile: (+44) 07787554059 The Institute of Cancer Research 237 Fulham Road London SW3 6JB 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.
Hi Nora, Sorry for the trouble! The hhr-parser falls over, because your query sequence name is empty: Q 82 DCKEFERAAYTLQN---CKSSKSIFLRLYSKYLAGEKKSEEENETLLNTNLTLSSTNREFYYISEVLESLHYQGNKDPYL 158 (285) This is now fixed, and will be available in the next nightly build, but you can carry on using the version you have as long as you edit your hhr-file to include a name, e.g. the following should work: Q foo 82 DCKEFERAAYTLQN---CKSSKSIFLRLYSKYLAGEKKSEEENETLLNTNLTLSSTNREFYYISEVLESLHYQGNKDPYL 158 (285) Let me know if there are any more problems! BW, Gabor On May 19 2011, Nora Cronin wrote:
I get an error in reading the .hhr file:
Loading PDB and alignment files from /work/ncronin/cdc23/23_HG_14/xds_Cdc23-23_HG_14w1_run1_1/phenix/MR_ROSETTA_5/WORK_1/5791278_1/5791278_ed.hhr Log file for mr_model_preparation is: /work/ncronin/cdc23/23_HG_14/xds_Cdc23-23_HG_14w1_run1_1/phenix/MR_ROSETTA_5/WORK_1/5791278_1/mr_model_preparation.log
******************* ERROR ENDING *************** Uninterpretable: 'Q ss_pred hhhHHHHHHHHHhc---CCCcccHHHHHHHHHHHHhHhhhHhHHhhhcCCCccccchhHHHHHHHHHHHHhccCCCCchh\nQ 82 DCKEFERAAYTLQN---CKSSKSIFLRLYSKYLAGEKKSEEENETLLNTNLTLSSTNREFYYISEVLESLHYQGNKDPYL 158 (285)\nQ Consensus 82 ~~~~~~~A~~~l~~---~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~l~~a~~~~~~~~~~~~~~~~~~ 158 (285)\n ..|+|++|+..+++ .+.....+...+.......+..+ ++..++++++. .|.+..+\nT Consensus 35 elG~y~~Ai~~~~~al~~~p~~~~~~~~lg~~~~~~g~~~~--------------------A~~~~~~al~~-~p~~~~~ 93 (243)\nT 2q7f_A 35 EFGDYEKAAEAFTKAIEENKEDAIPYINFANLLSSVNELER--------------------ALAFYDKALEL-DSSAATA 93 (243)\nT ss_dssp -------CCTTHHHHHTTCTTCHHHHHHHHHHHHHTTCHHH--------------------HHHHHHHHHHH-CTTCHHH\nT ss_pred HcCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHCCCHHH--------------------HHHHHHHHHhc-CCccHHH\n\n\nQ ss_pred HHHHHHHHHHcCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHhcHHHHHHHH-------HhCCcccHHHHHHHHHHHHHH\nQ 159 LYLSGVVYRKRKQDSKAIDFLKSCVLKAPFFWSAWLELSLSIDSLETLTTVV-------SQLPSTHIMTKIFYVYASHEL 231 (285)\nQ Consensus 159 ~~~~g~~~~~~~~~~~A~~~~~~al~~~p~~~~~~~~l~~~~~~~~~~~~al-------~~~p~~~~~~~~~~~~~~~~~ 231 (285)\n +..+|.++...+++++|+..|.+++...|.+...+..++.++...++++.++ ...| ....+..+|.++...\nT Consensus 94 ~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~~-~~~~~~~~l~~~~~~~ 172 (243)\nT 2q7f_A 94 YYGAGNVYVVKEMYKEAKDMFEKALRAGMENGDLFYMLGTVLVKLEQPKLALPYLQRAVELNE-NDTEARFQFGMCLANE 172 (243)\nT ss_dssp HHHHHHHHHHTTCHHHHHHHHHHHHHHTCCSHHHHHHHHHHHHHTSCHHHHHHHHHHHHHHCT-TCHHHHHHHHHHHHHH\nT ss_pred HHHHHHHHHHhccchhhHHHHHHHHhhhhhhHHHHHHHHHHHHHHHhHHHHHHHHHHHHHhCC-ccHHhhhhhhhhhhhc\n\n\nQ ss_pred hcchHHHHHHHHHHHhhCCCChHHHHHHHHHHHHhcCHHHHHHHHHHHHHHCcC\nQ 232 HQVNSSAYEKLAEAEIIFPNSRYLKTQRALLTYDSRDFDEAESLFENILTNDPA 285 (285)\nQ Consensus 232 ~~~~~A~~~~~~~al~~~p~~~~~~~~la~~~~~~~~~~~A~~~~~~al~~~P~ 285 (285)\n +++++|+ .++++++..|+++.++..+|.++..+|++++|+.+|+++++++|+\nT Consensus 173 ~~~~~A~-~~~~~ai~~~p~~~~~~~~lg~~~~~~g~~~~A~~~~~kal~l~P~ 225 (243)\nT 2q7f_A 173 GMLDEAL-SQFAAVTEQDPGHADAFYNAGVTYAYKENREKALEMLDKAIDIQPD 225 (243)\nT ss_dssp TCCHHHH-HHHHHHHHHCTTCHHHHHHHHHHHHHTTCTTHHHHHHHHHHHHCTT\nT ss_pred ccHHHHH-HHHHHHHHHCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCC'
******************* ERROR ENDING ***************
Can you help
Best regards
Nora
On 19 Apr 2011, at 16:25, Thomas C. Terwilliger wrote:
Hi Nora,
AutoSol will only take a single "crystal_info", and assumes that all data that you give it is referring to a single crystal form, with (approximately) the same cell dimensions for all datasets.
If you have multiple crystal forms, or crystals with substantially (more than about 1-2 percent) different cells, then you will want to solve them separately. You can then combine information with phenix.multi_crystal_average if you want.
Let me know if that doesn't help with your two questions! All the best,
-Tom T
Whilst I can input SAD SAD data ie two different SAD datasets using Group =1 and Group =2 with the "Wavelength" keyword, how do I input 2 different crystals using the "crystal_info" keyword which does not recognize Group =
Inputting .sca unmerged anomalous data how do I input data for 2 different crystal_info keywords with different heavy atoms and different unit cells?
thanks
Nora
Dr N B Cronin X-Ray Laboratory Manager Tel. (+44) 020 7153 5445 Section of Structural Biology Fax. (+44) 020 7153 5457 Chester Beatty Laboratories mobile: (+44) 07787554059 The Institute of Cancer Research 237 Fulham Road London SW3 6JB
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._______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb
_______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb
Dr N B Cronin X-Ray Laboratory Manager Tel. (+44) 020 7153 5445 Section of Structural Biology Fax. (+44) 020 7153 5457 Chester Beatty Laboratories mobile: (+44) 07787554059 The Institute of Cancer Research 237 Fulham Road London SW3 6JB
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.
-- ################################################## Dr Gabor Bunkoczi Cambridge Institute for Medical Research Wellcome Trust/MRC Building Addenbrooke's Hospital Hills Road Cambridge CB2 0XY ##################################################
participants (3)
-
Dr G. Bunkoczi -
Nora Cronin -
Thomas C. Terwilliger