[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
> http://phenix-online.org/mailman/listinfo/phenixbb
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