diff options
Diffstat (limited to 'README')
| -rw-r--r-- | README | 50 |
1 files changed, 28 insertions, 22 deletions
@@ -37,12 +37,7 @@ above characteristics. The main programs are: single reflection list. - partialator, for merging patterns more accurately (and much more - slowly) using post refinement. - - - reintegrate, which is like "indexamajig" but without the indexing - step, instead getting the orientation matrix from the - output of a previous run of either "indexamajig" or - "reintegrate". + slowly) using post refinement. In addition, there is also: @@ -58,26 +53,34 @@ In addition, there is also: - check_hkl, for determining things like completeness. - - calibrate_detector, for summing patterns after peak detection to use - for calibrating your detector. + - sum_stack, for summing patterns after peak detection to use + for calibrating your detector. - cubeit, for summing patterns in 3D to inspect the peak profiles. - estimate_background, for calculating signal to noise ratios from the indexed peaks. - - render_hkl, for turning reflection lists into pretty graphics. + - calibrate_detector, which splits + + - reintegrate, which is like "indexamajig" but without the indexing + step, instead getting the orientation matrix from the + output of a previous run of either "indexamajig" or + "reintegrate". -And, because I'm so nice, included at no extra cost is: +Included at no extra cost are: - hdfsee, a simple viewer for images stored in HDF5 format. + - render_hkl, for turning reflection lists into pretty graphics. + There is also a big folder of scripts for achieving many related tasks. CrystFEL mostly works with images stored in HDF5 format, unit cell and atomic coordinate data in PDB format, and reflection lists in plain text format (i.e. -not MTZ). +not MTZ). There is a script for turning a plain text reflection list into an +MTZ file for later import into CCP4. For documentation on the individual programs and topics, see the files inside the "doc" directory. @@ -87,7 +90,7 @@ Installation ------------ See the "INSTALL" file for the generic instructions on how to use the build -system. In short, it's +system. In short, it's: $ ./configure $ make @@ -96,7 +99,7 @@ $ sudo make install You might want to substitute something based on one of the following for the first step: -$ ./configure --enable-opencl +$ ./configure --with-opencl $ ./configure --with-hdf5=/some/strange/location $ ./configure --with-libtiff=/some/strange/location $ ./configure --with-gsl=/some/strange/location @@ -117,25 +120,28 @@ Program name ------------ There seems to be a tendency to capitalise all the letters in the names of -programs in scientific publications. It's not 1970 any more, and programs can -have capitalisation any way we choose, not just all capitals. +programs in scientific publications. Sometimes the authors do this, other times +the journal capitalises them at the proof stage. It's as if they think it +somehow makes the name look more "computery", or perhaps "trademark-y". + +Well, it's not 1970 any more, and programs are no longer input on punched cards. +That means we can have capitalisation any way we choose. I hope you can forgive +me for being fussy about how my work is referred to in publications and talks. The name for the overall software suite is "CrystFEL", with this being the only acceptable capitalisation. The individual programs should always be referred to with all letters in lower case, exactly the same as the names of the binaries. -Put the names in quotes if this sounds strange to you. The only exception is if -the name of the program comes at the start of a sentence, or in a title, or -similar position where a word would normally be capitalised. +Put the names in quotes or italics if this sounds strange to you. The only +exception is if the name of the program comes at the start of a sentence, or in +a title, or similar position where a word would normally be capitalised. In most cases, it will be more appropriate to refer to the overall suite than to one of its constituent programs. The following are NOT acceptable forms: "CRYSTFEL", "crystFEL", "Crystfel", -"INDEXAMAJIG" and "PATTERN_SIM". +"INDEXAMAJIG" and "PATTERN_SIM". If you use any of these, the Capitalisation +Monster will hunt you down and eat you. In addition, CrystFEL is made up of "programs", not "routines" nor "procedures". (The "programs" in turn are made up from "routines" and "procedures", but unless you are exploring the source code, there's no need for you to know about that). - -I hope you can forgive me for being fussy about how my work is referred to in -publications and talks. |