SHELX C/D/E: Difference between revisions

SHELX C/D/E (edit)

Revision as of 09:30, 7 June 2023

1,127 bytes added , 7 June 2023

m

→‎Minimum distance between atoms (MIND): remove "(as in the above thaumatin example" because that does not exist

Kay

Bureaucrats

1,334

edits

@@ Line 97: / Line 97: @@
 A common 'user error' is to set MIND -3.5 even though the distances between heavy atoms are less than 3.5 Å.  For example, in a Fe<sub>4</sub>S<sub>4</sub> cluster the Fe...Fe distance is about 2.7 Å, so MIND -2 would be appropriate. A disulfide bond has a length of 2.03 Å so then MIND -1.5 could be used to resolve the sulfur atoms, however if DSUL is used for this purpose MIND -3.5 is required.
-If heavy atoms can lie on special positions (as is the case with an iodide soak in a space group with twofold axes) the rejection of atoms on special positions should be switched off by giving the second MIND parameter as -0.1 (as in the above thaumatin example).
+If heavy atoms can lie on special positions (as is the case with an iodide soak in a space group with twofold axes) the rejection of atoms on special positions should be switched off by giving the second MIND parameter as -0.1 .
 === Interpretation of results ===
@@ Line 178: / Line 178: @@
 (or xx_i.hat).
-=== Full list of SHELXE options (defaults in brackets) ===
+=== Full list of SHELXE options ( Version 2021/1; defaults in brackets) ===
   -aN - N cycles autotracing [off]
- -AX - maximum random initial rotation in deg. for -O [-A3.0]
   -bX - B-value to weight anomalous map (xx.pha and xx.hat) [-b5.0]
+ -B1 - anti-parallel beta sheet, -B2 parallel and -B3 both [off]
   -cX - fraction of pixels in crossover region [-c0.4]
   -dX - truncate reflection data to X Angstroms [off]
+ -D  - fuse disulfides before looking for NCS [off]
   -eX - add missing 'free lunch' data up to X Angstroms [dmin+0.2]
   -f  - read F rather than intensity from native .hkl file [off]
@@ Line 200: / Line 201: @@
   -mN - N iterations of density modification per global cycle [-m20]
   -n or -nN - apply N-fold NCS to traces [off]
- -O or -ON - N random-start rigid-group domain searches [off]
   -o or -oN - prune up to N residues to optimize CC for xx.pda [off]
-  -q  - search for alpha-helices [off]
+  -O  - trace side chains [off]
+ -p or -pN - search for N DNA or RNA phosphates (-p = -p12) [off]
+  -qN - search for alpha-helices of length 6<N<15; -q sets -q7 [off]
+ -Q  - search for 12-helix,' extended by sliding (overrides -q) [off]
   -rX - FFT grid set to X times maximum indices [-r3.0]
   -sX - solvent fraction [-s0.45]
-  -tX - time factor for helix and peptide search [-t1.0]
+ -SX - radius of sphere of influence. Increase for low res [-S2.42]
+  -tX - time for initial searches (-t3 or more if difficult) [-t1.0]
   -uX - allocable memory in MB for fragment optimization [-u500]
   -UX - abort if less than X% of initial CA stay within 0.7A [-U0]
@@ Line 212: / Line 216: @@
   -x  - diagnostics, requires PDB reference file xx.ent [off]
   -yX - highest resol. in Ang. for calc. phases from xx.pda [-y1.8]
- -YX - SAD phase shift factor [-Y0.5]
   -zN - substructure optimization for a maximum of N atoms [off]
-  -z - substructure optimization, number of atoms not limited [off]
+  -z  - substructure optimization, number of atoms not limited [off]
-  -ZX - maximum shift in Ang. from initial position for -O [-Z1.0]
+  -t values of 3.0 or more switch to more accurate but appreciably
+ slower tracing algorithms, this is recommended when the resolution
+ is poor or the initial phase information is weak; -a10 is preferred.
+ In case of side chain tracing with -O, sequence will be docked
+ and output only once CC>30 so poly-alanine tracing scores
+ can be used to identify solutions as before.
+ Please cite: I. Uson & G.M. Sheldrick (2018), "An introduction to
+ experimental phasing of macromolecules illustrated by SHELX;
+ new autotracing features" Acta Cryst. D74, 106-116
+ (Open Access) if SHELXE proves useful.
 Meaning of additional output when using the -x option:
@@ Line 387: / Line 401: @@
 == Obtaining the SHELX programs ==
-SHELXC/D/E and test data may be downloaded from the [http://shelx.uni-goettingen.de/bin/ SHELX fileserver]. First fill the application form at  http://shelx.uni-goettingen.de/register.php  Password and downloading instructions will then be emailed to the address given on the form.  The programs are free to academics but a small license fee is required for 'for-profit' use.
+SHELXC/D/E are distributed with [https://www.ccp4.ac.uk/ CCP4].
+The programs and test data may also be downloaded from the [http://shelx.uni-goettingen.de/bin/ SHELX fileserver]. First fill the application form at  http://shelx.uni-goettingen.de/register.php  Password and downloading instructions will then be emailed to the address given on the form.  The programs are free to academics but a small license fee is required for 'for-profit' use.
 Beta-test versions are also available from time to time. They are announced by George Sheldrick and are available from the beta-test directory. The username and password for accessing these may be obtained from GS.
-[[hkl2map]] can be downloaded from a website at EMBL Hamburg.
+[[hkl2map]] can be downloaded from a website at EMBL Hamburg. XDSGUI can be downloaded from its [[xds:XDSGUI|XDSwiki article]].
 == References ==
 If these programs prove useful, you may wish to cite (and read!):<br>
-[http://scripts.iucr.org/cgi-bin/paper?sc5010 Sheldrick, G.M. (2008). "A short history of SHELX", ''Acta Crystallogr''. '''D64''', 112-122] [''Standard reference for all SHELX* programs''].<br>
 Sheldrick, G.M., Hauptman, H.A., Weeks, C.M., Miller, R. & Usón, I. (2001). "Ab initio phasing". In ''International Tables for Crystallography'', Vol. F, Eds. Rossmann, M.G. & Arnold, E., IUCr and Kluwer Academic Publishers, Dordrecht pp. 333-351 [''Full background to the dual-space recycling used in SHELXD''].<br>
@@ Line 407: / Line 421: @@
 Nanao, M.H., Sheldrick, G.M. & Ravelli, R.B.G. (2005). "Improving radiation-damage substructures for RIP", ''Acta Crystallogr''. '''D61''', 1227-1237 [''Practical details of RIP phasing with SHELXC/D/E''].<br>
-Uson, I., Stevenson, C.E.M., Lawson, D.M. & Sheldrick, G.M. (2007). "Structure determination of the O-methyltransferase NovP using the `free lunch algorithm' as implemented in SHELXE", ''Acta Crystallogr''. '''D63''', 1069-1074 [''Implementation of the FLA in SHELXE''].<br>
+Usón, I., Stevenson, C.E.M., Lawson, D.M. & Sheldrick, G.M. (2007). "Structure determination of the O-methyltransferase NovP using the `free lunch algorithm' as implemented in SHELXE", ''Acta Crystallogr''. '''D63''', 1069-1074 [''Implementation of the FLA in SHELXE''].<br>
+[http://scripts.iucr.org/cgi-bin/paper?sc5010 Sheldrick, G.M. (2008). "A short history of SHELX", ''Acta Crystallogr''. '''D64''', 112-122] [''Standard reference for all SHELX* programs''].<br>
 [http://dx.doi.org/10.1107/S0907444909038360 Sheldrick, G.M. (2010). "Experimental phasing with SHELXC/D/E: combining chain tracing with density modification", ''Acta Cryst'' '''D66''', 479-485.]
-[https://doi.org/10.1107/S0907444913027534 A. Thorn and Sheldrick, G.M. (2013) Extending molecular-replacement solutions with SHELXE. ''Acta Cryst'' '''D69''', 2251-2256.]
+[https://doi.org/10.1107/S0907444913027534 A. Thorn and Sheldrick, G.M. (2013). Extending molecular-replacement solutions with SHELXE. ''Acta Cryst'' '''D69''', 2251-2256.]
+[https://journals.iucr.org/d/issues/2018/02/00/ba5271/ba5271.pdf Usón, I. & Sheldrick, G. M. (2018). An introduction to experimental phasing of macromolecules illustrated by SHELX; new autotracing features. ''Acta Cryst.'' '''D74''', 106-116.]
 <br>
 See also the [http://shelx.uni-goettingen.de/ SHELX homepage]
 <br>