Hi Scott, another alternative: phenix.map_box can cut out a box around selected atoms. Inputs: - map in xplor or ccp4 format, or MTZ wih Fourier map coefficients; - PDB model; - atom selection string; Output: - PDB with selected atoms in a box; - three map files (ccp4, xplor and MTZ) with map in a box. Examples: phenix.map_box model.pdb map_coefficients.mtz selection="chain A and resseq 1:10" Pavel On 2/3/15 8:16 AM, Terwilliger, Thomas Charles wrote:

Hi Scott, Yes, I think that phenix.cut_out_density should do something close to what you need, if you specify the same box and padding for each case. The output of cut_out_density is a set of map coefficients in a P1 cell; you then would need to just create a map of the whole "unit cell" from those coefficients. All the best, Tom T ------------------------------------------------------------------------ *From:* [email protected] [[email protected]] on behalf of Scott Horowitz [[email protected]] *Sent:* Tuesday, February 03, 2015 8:09 AM *To:* PHENIX user mailing list *Subject:* Re: [phenixbb] generating xplor map of specific size

This may be answering my own question: should cut_out_density do this if I make the original map bigger than necessary and then pare it down?

Scott

On Tue, Feb 3, 2015 at 9:48 AM, Scott Horowitz mailto:[email protected]> wrote:

Hi all,

Sorry for yet another map question: what I'd like to do is be able to generate xplor maps with an explicitly defined size and shape from the command line using phenix. Just choosing a buffer around a selection will result in slightly different sizes for different PDB files, which I'd like to avoid. In my comparisons, having exactly the same dimensions and centering for maps I'm calculating from multiple slightly different variants would be very helpful. Is there a way to do this?

Thanks, Scott

-- Scott Horowitz, Ph.D. Research Associate Howard Hughes Medical Institute

University of Michigan Department of Molecular, Cellular, and Developmental Biology Bardwell lab 830 N. University Ave, Room 4007 Ann Arbor, MI 48109 phone: 734-647-6683 fax: 734-615-4226

-- Scott Horowitz, Ph.D. Research Associate Howard Hughes Medical Institute

University of Michigan Department of Molecular, Cellular, and Developmental Biology Bardwell lab 830 N. University Ave, Room 4007 Ann Arbor, MI 48109 phone: 734-647-6683 fax: 734-615-4226

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