Re: [ccp4bb] FFT map coefficients only for certain chains
Like Herman, it was not apparent to me what exactly you want wanted. If you want a map that covers only [1] or excludes [2] a particular atom selection then you can do that in Coot. Extensions - Maps... - Mask Map by Atom Selection, e.g. to show only the A chain, use an atom selection of //A. You can then export the map using: Extensions - Maps... - Export Map or Extensions - Maps... - Export Local Map Fragment... If you really want structure factors from that then you can use sfall (MODE SFCALC MAPIN). Paul. [1] use mask inversion [2] don't use mask inversion *From:* CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] *On Behalf Of *zhang yu *Sent:* Sunday, February 19, 2012 11:47 PM *To:* CCP4BB@JISCMAIL.AC.UK *Subject:* [ccp4bb] FFT map coefficients only for certain chains Dear CCP4ers, Is that possible to generate map coefficients only for certain chains? For example, I have two chains, A and B, and I would like to output a map file only contains coefficients for chain A. The isomesh command in Pymol could generate similar images. But my purpose is not for presentation, I need a map file only contains coefficient for certain chains. In the interface of FFT tool in Phenix or CCP4, there is an option to include a PDB file and define atom selections. It describe that If a PDB is supplied, the output map will cover the model plus a buffer on all sides. The atom selection parameters can be used to specify a smaller region . If I define the selection as chain A when I run the FFT, the output map still covers a rectangular block containing chain A, instead of regions only surrounding chain A. Thanks. Yu -- Yu Zhang HHMI associate Waksman Institute, Rutgers University 190 Frelinghuysen Rd. Piscataway, NJ, 08904
Re: [ccp4bb] FFT map coefficients only for certain chains
Herman, Thanks for clarifying the difference between map coefficients and map files for me. What I really need are only map files, and I could generate those masked maps by following Paul's suggestion. Yu 2012/2/20 Paul Emsley paul.ems...@bioch.ox.ac.uk Like Herman, it was not apparent to me what exactly you want wanted. If you want a map that covers only [1] or excludes [2] a particular atom selection then you can do that in Coot. Extensions - Maps... - Mask Map by Atom Selection, e.g. to show only the A chain, use an atom selection of //A. You can then export the map using: Extensions - Maps... - Export Map or Extensions - Maps... - Export Local Map Fragment... If you really want structure factors from that then you can use sfall (MODE SFCALC MAPIN). Paul. [1] use mask inversion [2] don't use mask inversion -- *From:* CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UKCCP4BB@JISCMAIL.AC.UK] *On Behalf Of *zhang yu *Sent:* Sunday, February 19, 2012 11:47 PM *To:* CCP4BB@JISCMAIL.AC.UK *Subject:* [ccp4bb] FFT map coefficients only for certain chains Dear CCP4ers, Is that possible to generate map coefficients only for certain chains? For example, I have two chains, A and B, and I would like to output a map file only contains coefficients for chain A. The isomesh command in Pymol could generate similar images. But my purpose is not for presentation, I need a map file only contains coefficient for certain chains. In the interface of FFT tool in Phenix or CCP4, there is an option to include a PDB file and define atom selections. It describe that If a PDB is supplied, the output map will cover the model plus a buffer on all sides. The atom selection parameters can be used to specify a smaller region . If I define the selection as chain A when I run the FFT, the output map still covers a rectangular block containing chain A, instead of regions only surrounding chain A. Thanks. Yu -- Yu Zhang HHMI associate Waksman Institute, Rutgers University 190 Frelinghuysen Rd. Piscataway, NJ, 08904 -- Yu Zhang HHMI associate Waksman Institute, Rutgers University 190 Frelinghuysen Rd. Piscataway, NJ, 08904
[ccp4bb] FFT map coefficients only for certain chains
Dear CCP4ers, Is that possible to generate map coefficients only for certain chains? For example, I have two chains, A and B, and I would like to output a map file only contains coefficients for chain A. The isomesh command in Pymol could generate similar images. But my purpose is not for presentation, I need a map file only contains coefficient for certain chains. In the interface of FFT tool in Phenix or CCP4, there is an option to include a PDB file and define atom selections. It describe that If a PDB is supplied, the output map will cover the model plus a buffer on all sides. The atom selection parameters can be used to specify a smaller region . If I define the selection as chain A when I run the FFT, the output map still covers a rectangular block containing chain A, instead of regions only surrounding chain A. Thanks. Yu -- Yu Zhang HHMI associate Waksman Institute, Rutgers University 190 Frelinghuysen Rd. Piscataway, NJ, 08904
