Hi Tom, this doesn't help. The last 12 chains are simply thrown out in the editing step. Best wishes and thank! Kornelius On Tue, 18 Dec 2007 10:15:00 -0700 Tom Terwilliger wrote:

Hi Kornelius,

I am checking this out...but for the moment here is a solution:

You can use 2-character chain codes in phenix. They go in the usual column for chain ID and the column just before it.

So columns 21-22 in your PDB file could be: " A" (chain A, usual syntax) " B" " C" ...etc " 0" " 1" " 9" "AA" (chain AA, recognized only by hybrid-36 compatible programs) "AB" "AC" ...etc

-Tom T

At 06:34 AM 12/18/2007, you wrote:

...

Dear all,

I'm trying to refine/rebuild a structure of 48 identical chains. In Refmac the small letters a, b, c and 0 1 2 for the chains work quite well and are distinguished. However that does not apply to Phenix which sees A equal to a. What might be the solution to use?

Thanks and best wishes

Kornelius

---------------------------------------------- Kornelius Zeth Max Planck Institute for Developmental Biology Dept. Protein Evolution Spemannstr. 35 72076 Tuebingen, Germany [email protected] Tel -49 7071 601 323 Fax -49 7071 601 349 _______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb

Thomas C. Terwilliger Mail Stop M888 Los Alamos National Laboratory Los Alamos, NM 87545

Tel: 505-667-0072 email: [email protected] Fax: 505-665-3024 SOLVE web site: http://solve.lanl.gov PHENIX web site: http:www.phenix-online.org ISFI Integrated Center for Structure and Function Innovation web site: http://techcenter.mbi.ucla.edu TB Structural Genomics Consortium web site: http://www.doe-mbi.ucla.edu/TB

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---------------------------------------------- Kornelius Zeth Max Planck Institute for Developmental Biology Dept. Protein Evolution Spemannstr. 35 72076 Tuebingen, Germany [email protected] Tel -49 7071 601 323 Fax -49 7071 601 349

Hi phenix.autobuild users, I'm sorry to report a serious bug that I have just noticed that applies to MTZ files for autobuild containing intensities. The problem is fixed now. I'm very sorry about this mistake. All the best, -Tom T THE PROBLEM: In all alpha and beta versions of phenix up to now (up to 1.3b/rc6), there has been a bug in autobuild in which the command phenix.autobuild data.mtz model.pdb will misinterpret intensity data as amplitudes if the input file is an mtz file (for example if the mtz file has IMEAN,SIGIMEAN and F,SIGF). (This can also happen in the GUI version, but you will have been presented on screen 3 with a list of data types (FP SIGFP) and columns from the input data file to match them and it is not so likely that you will have chosen to match FP with IMEAN.) You can tell if this has happened in your case by looking for something like (search for the string "Input labels:"): Input labels: ['IMEAN', 'SIGIMEAN', 'None', 'None', 'None', 'None', 'None', 'None', 'FreeR_flag'] in your log file (where the None's don't matter, just the first 2 column names. The columns in this list should be amplitude-containing columns only. If everything is ok.it should look instead like: Input labels: ['F', 'SIGF', 'None', 'None', 'None', 'None', 'None', 'None', 'None'] THE SOLUTION: In existing versions, the solution to this is to either (1) only have amplitude arrays in your mtz file, or (2) use the GUI and select the correct amplitude arrays, or (3) specify what amplitude columns to use with a command like: input_labels="F SIGF". Note that you cannot use intensity data from an mtz file with the existing versions of autobuild, only amplitude data. In the corrected version (1.3b/rc7, not yet out) , you will be able to use an mtz file with intensity data as long as there is no amplitude data in the same mtz file. Note also that all this applies equally to the refinement_file and hires_file data. Also note that if the file type is not mtz, then this bug does not apply (because the file is always imported and converted from intensities to amplitudes automatically). Thomas C. Terwilliger Mail Stop M888 Los Alamos National Laboratory Los Alamos, NM 87545 Tel: 505-667-0072 email: [email protected] Fax: 505-665-3024 SOLVE web site: http://solve.lanl.gov PHENIX web site: http:www.phenix-online.org ISFI Integrated Center for Structure and Function Innovation web site: http://techcenter.mbi.ucla.edu TB Structural Genomics Consortium web site: http://www.doe-mbi.ucla.edu/TB

Hi Peter, That one should take intensities just fine. There is an explicit step to convert intensities to amplitudes in the wizard. I will have to check however as to whether an MTZ file with intensities will have been passed on to the AutoBuild wizard correctly... -Tom T

Hi Tom,

What about the AutoMR wizard. Can I use intensities there instead of amplitudes? I always get confused.

Thanks,

Peter

2007/12/18, Tom Terwilliger :

...

Hi phenix.autobuild users, I'm sorry to report a serious bug that I have just noticed that applies to MTZ files for autobuild containing intensities. The problem is fixed now. I'm very sorry about this mistake. All the best, -Tom T

THE PROBLEM:

In all alpha and beta versions of phenix up to now (up to 1.3b/rc6), there has been a bug in autobuild in which the command

phenix.autobuild data.mtz model.pdb

will misinterpret intensity data as amplitudes if the input file is an mtz file (for example if the mtz file has IMEAN,SIGIMEAN and F,SIGF). (This can also happen in the GUI version, but you will have been presented on screen 3 with a list of data types (FP SIGFP) and columns from the input data file to match them and it is not so likely that you will have chosen to match FP with IMEAN.)

You can tell if this has happened in your case by looking for something like (search for the string "Input labels:"):

Input labels: ['IMEAN', 'SIGIMEAN', 'None', 'None', 'None', 'None', 'None', 'None', 'FreeR_flag']

in your log file (where the None's don't matter, just the first 2 column names. The columns in this list should be amplitude-containing columns only. If everything is ok.it should look instead like:

Input labels: ['F', 'SIGF', 'None', 'None', 'None', 'None', 'None', 'None', 'None']

THE SOLUTION:

In existing versions, the solution to this is to either (1) only have amplitude arrays in your mtz file, or (2) use the GUI and select the correct amplitude arrays, or (3) specify what amplitude columns to use with a command like:

input_labels="F SIGF".

Note that you cannot use intensity data from an mtz file with the existing versions of autobuild, only amplitude data. In the corrected version (1.3b/rc7, not yet out) , you will be able to use an mtz file with intensity data as long as there is no amplitude data in the same mtz file.

Note also that all this applies equally to the refinement_file and hires_file data. Also note that if the file type is not mtz, then this bug does not apply (because the file is always imported and converted from intensities to amplitudes automatically).

Thomas C. Terwilliger Mail Stop M888 Los Alamos National Laboratory Los Alamos, NM 87545

Tel: 505-667-0072 email: [email protected] Fax: 505-665-3024 SOLVE web site: http://solve.lanl.gov PHENIX web site: http:www.phenix-online.org ISFI Integrated Center for Structure and Function Innovation web site: http://techcenter.mbi.ucla.edu TB Structural Genomics Consortium web site: http://www.doe-mbi.ucla.edu/TB

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