[phenixbb] generating xplor map of specific size

Pavel Afonine pafonine at lbl.gov
Tue Feb 3 09:30:17 PST 2015


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:* phenixbb-bounces at phenix-online.org 
> [phenixbb-bounces at phenix-online.org] on behalf of Scott Horowitz 
> [horowsah at umich.edu]
> *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 <horowsah at umich.edu 
> <mailto:horowsah at umich.edu>> 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
>
>
> _______________________________________________
> phenixbb mailing list
> phenixbb at phenix-online.org
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