[phenixbb] Rosetta

Thu May 19 09:40:52 PDT 2011

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 
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>>>> 
>> 
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>
>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
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