Hi Melanie, Mapmask was suggested. The XYZLIM command of mapmask takes values in grid points or fractional coordinates. You could make a 300A cube by giving fractional coordinates of 300/(current cell edge), But since that doesn't change the grid it won't change the thickness of your slices. I don't think mapmask (old name "extend") can change the grid.
Maprot was also mentioned, and I think this should work. You need to generate a 300x300x300 target map (WORKIN) and perhaps a mask (could be your entire current cell). Use the identity rot-trans operator, or with some non-zero translation if necessary to get your model entirely in one cell. But it might be much easier to just recalculate your map from structure factors with equal grid spacings using fft. So if you want half-angstrom slices, set the grid values (nx,ny,nz) to twice the cell dimensions in Angstroms. The FFT has some restrictions on the grid so you may not be able to choose exactly what you want, but could get pretty close to even spacing. (In fact programs that write maps tend to make approximately equal spacing, like 1/2 or 1/3 of the resolution, by default- so it would be surprising if your current map has drastically different spacing along the different axes). If you expand your data to P1 before fft, then the only restrictions are that nz be an even number (and none of the nx,ny,nz have prime factors greater than 19). You should be able to get very nearly equal spacing with that. I wonder if there is any program that uses conventional FT and allows arbitrary grid choices? eab On 07/16/2018 11:28 AM, melanie.voll...@diamond.ac.uk wrote:
Thanks everyone who replied to my post. I got a wealth of ideas. Melanie Hello everyone, I have a question about manipulating map files. I want to use my map derived from X-ray diffraction and create a standard volume for it, say 300A3. This is to be able to create slices of equal dimensions along all three directions of the electron density stored in the map file. Currently my slices differ in dimensions as the default volume is defined by the unit cell. I don't think there is anything in the map tools from the X-ray field I know. I had a play with Chimera and I think there is a tool in there to use some form of reference cell created from coordinates. But I don't want to make use of a coordinates file. I just want to inflate my unit cell to a standard volume. Any ideas would be very welcome. Thanks Melanie -- This e-mail and any attachments may contain confidential, copyright and or privileged material, and are for the use of the intended addressee only. If you are not the intended addressee or an authorised recipient of the addressee please notify us of receipt by returning the e-mail and do not use, copy, retain, distribute or disclose the information in or attached to the e-mail. Any opinions expressed within this e-mail are those of the individual and not necessarily of Diamond Light Source Ltd. Diamond Light Source Ltd. cannot guarantee that this e-mail or any attachments are free from viruses and we cannot accept liability for any damage which you may sustain as a result of software viruses which may be transmitted in or with the message. Diamond Light Source Limited (company no. 4375679). Registered in England and Wales with its registered office at Diamond House, Harwell Science and Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom ######################################################################## ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
