Hi, For Autobuild, you would put in both strands, separated by a blank line or a title line starting with ">". All the best, Tom T ________________________________________ From: [email protected] [[email protected]] on behalf of Randy Read [[email protected]] Sent: Wednesday, April 25, 2012 1:10 PM To: PHENIX user mailing list Subject: Re: [phenixbb] Inputting DNA for Phenix MR and/or Autobuild Hi, For Phaser, the second option (each strand on a different line) will be fine for specifying the composition. Since all Phaser is worried about is the composition, it wouldn't really matter if you put it all on one line. For AutoBuild, we'll have to wait for Tom T to answer, because I don't know how you say that two things are different strands. Regards, Randy ----- Randy J. Read Department of Haematology, University of Cambridge Cambridge Institute for Medical Research Tel: +44 1223 336500 Wellcome Trust/MRC Building Fax: +44 1223 336827 Hills Road E-mail: [email protected] Cambridge CB2 0XY, U.K. www-structmed.cimr.cam.ac.uk On 25 Apr 2012, at 19:48, Charles Allerston wrote:

Dear all,

I can’t find much in the way of documentation for this. Can someone point me to some please?

I basically want to know the correct format for entering DNA into the search for MR and inputting into Autobuild.

If I have a double stranded DNA do I enter it as

...

DNA1 AATT:AATT

...

DNA1 AATT TTAA

etc.

?

cheers,

charlie

Dr. Charles Allerston Genome Integrity & Repair Structural Genomics Consortium Nuffield Department of Medicine Old Road Campus University of Oxford OX3 7DQ http://www.thesgc.org/scientists/groups/oxford/genome-integrity-and-repair

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Dear All,   Do you have the expereince to install Phenix under Cygwin? Which version works?   Cheers,   Fenghui  

On 04/26/2012 09:11 PM, Nathaniel Echols wrote:

On Thu, Apr 26, 2012 at 7:52 AM, Dialing Pretty wrote:

...

Do you have the expereince to install Phenix under Cygwin? Which version works?

Why not installing a real operating system? Don't miss that chance! :)

Phenix won't run under Cygwin. We have a Windows installer available in the nightly builds which is very rudimentary; this is your only option right now, but a more intuitive installer will be available in the next couple of weeks.

-Nat _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb

Dialing, try phenix.mtz2map file_name.mtz format=xplor You will probably need to specify the labels too. Pavel On 5/1/12 5:42 AM, Dialing Pretty wrote:

Dear All, Currently I do not have the GUI interface. I have the windows CCI. I have a set PDB and MTZ which I do not want to refine anymore. Can you give me some suggestions on the command in phenix refine by"output.write_maps=True" so that I can get a copy of corresponding set of xplor file? Here I mean by which series of parameters of phenix refine, with the set of PDB and MTZ as inputs, I can get a set of xplor, which corresponds to the initial PDB and MTZ input file? Cheers, Dialing

On Thu, Apr 26, 2012 at 6:57 AM, Dialing Pretty wrote:

In the protein crystalographic paper, there is always a table on Crystallographic data and refinement statistics. Do you have some suggestions on which items should be contained in this item?

Yes, run phenix.table_one (I recommend using the GUI in the latest nightly build for this), supplying it your model, data, and integration/scaling log files, and it will generate a table that should be suitable for most journals. Many journals also have their own recommendations; check the author instructions for either NSMB, Structure, or Acta D, you should find some kind of template. (I cribbed from these when writing the program; they're all pretty similar, with minor differences.) -Nat

On Mon, Apr 30, 2012 at 1:12 AM, Sebastiano Pasqualato wrote:

I just wanted to let you know that when processing the data with XDS (in my case with xia2) and providing the CORRECT.LP logfile to phenix.table_one, the program fails to extract information on total reflections, multiplicity, Rsym.

I could have overlooked something. Could you please send me the logfile? (If you have one that is already published which we could use for regression testing, even better.) Does xia2 also extract something of this info automatically, e.g. for REMARK 200 records? If Graeme has already done some of the work I should just figure out how to use that instead of writing yet another logfile parser - although I guess people use XDS manually too.

I have a question, too. In the case the refinement resolution is different from the integration one, would the table give both series of values.

No, the assumption is that these are the same - this might seem a little unreasonable, but as a reader or reviewer I would want to know what was the mean I/sigma for the reflections *actually used in refinement*;.

I usually put in table 1 also the reflections not used in refinement (i.e. the Rfree set number of reflections). Would be nice to have it there.

I could probably find a place to fit this in, although this is the kind of information that I think is best put in the Methods section (which Phenix still won't write for you - yet). -Nat