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Re: using xh to refine a large small molecule

PostPosted: 11 Mar 2010, 10:32
by johnewarren
I should note that shelxh/shelxl are the same as XL/XH for all intents of this posting. Also I believe there is now a parallel version for windows but only for commercial package users that is the SHELXTL license owners.

PS

Moving this post to software/shelx

Re: using xh to refine a large small molecule

PostPosted: 11 Mar 2010, 11:31
by Rudi
As far as the difference between SHELXL and SHELXH is concerned, this thread might be of help:

viewtopic.php?f=124&t=464&hilit=SHELXH

In short: With the latest version of SHELXL, SHELXH should become redundant.

Re: using xh to refine a large small molecule

PostPosted: 11 Mar 2010, 16:20
by ecs
thanks!
as I don't have the latest shelxl, I will be happy doing my refinement with xh :)

Re: using xh to refine a large small molecule

PostPosted: 11 Mar 2010, 19:15
by pmueller
ecs wrote:thanks!
as I don't have the latest shelxl, I will be happy doing my refinement with xh :)

As SHELXL is free, there should be no excuse for not having the latest version.

Re: using xh to refine a large small molecule

PostPosted: 11 Mar 2010, 20:59
by johnewarren
Peter unless something has change very recently it is still version 97 and shelxl and shelxh.

Re: using xh to refine a large small molecule

PostPosted: 11 Mar 2010, 21:12
by johnewarren
From the shelx website (11/03/2010):

The current full release of the complete SHELX system is still 97-2 (24 March 1998), but the new macromolecular phasing programs SHELXC, SHELXD and SHELXE been added and the Linux and Windows executables have been recompiled with the new Intel Fortran-95 compiler and are particularly fast on Pentium-4 systems (see benchmarks). The new Windows executables should run under Windows 95, 98, ME, NT, 2000 and XP but not under DOS or Windows 3.1. They should be started from a MSDOS input window. The SHELX users' list has been added to this homepage and is being updated at regular intervals. Please let me know if your email address is given incorrectly or if you wish to be removed from the list for any reason. SHELXC and SHELXE are still at beta-test stage and will expire at the end of 2003 (and will then be replaced by a new version). Registered users of SHELX-97 may download SHELXC, SHELXD and SHELXE using the same procedure as before, no further application form is required. The documentation for these programs is in the files fastphas.pdf and shelx-de.pdf.

As mentioned in the previous post Rudi refers to above:
SHELXH - version of SHELXL for very large structures

SHELXH is a special version of SHELXL for the refinement of very large structures (with more than about 10000 unique atoms). The only difference between shelxh.f and shelxl.f is the first FORTRAN statement in which the array dimensions are specified by means of a PARAMETER statement. If even SHELXH is not large enough, you will need to change the dimensions of the arrays A and B as explained in the comments at the start of the source file. Large versions of SHELXS, SHELXPRO and SHELXA may be created in the same way, but it is rather unlikely that they will ever be required. Further details are provided by comments in the respective sources. SHELXL will print a suitable error message if it is necessary to increase the dimensions of the large arrays A or B.

A little care and fine-tuning may be required so that such large structures can be refined efficiently. If the computer does not have enough physical memory available, or if the 'maximum vector length' is set too large, SHELXH will run in disk exercising mode. This 'maximum vector length' refers to the number of reflections that are processed in one vector run, which may be smaller than the number in the input/output buffer. Some trial and error is needed to set the maximum allowed value so that the physical memory is fully exploited with a minimum of disk I/O for the virtual memory swap file. This number is set as the fourth parameter on the L.S. or CGLS instruction, and should be a multiple of 8; a good value to try for a 64MB computer is 64 (the third number on the L.S. or CGLS instruction is almost always zero). The array B is used as working space for these vectors (CGLS and L.S.) as well as for the least-squares matrix (L.S.). If the array B is not big enough, the program will use a smaller maximum vector run.

Re: using xh to refine a large small molecule

PostPosted: 11 Mar 2010, 21:19
by pmueller
suit yourself

Re: using xh to refine a large small molecule

PostPosted: 11 Mar 2010, 21:43
by Rudi
@John: I guess Peter refers to this version:

Code: Select all
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
+  XL     -     CRYSTAL STRUCTURE REFINEMENT    -    SHELXTL Version 2008/4  +
+  Copyright(c) 2008 Bruker Analytical X-ray Solutions  All Rights Reserved  +
+  test                                  started at 06:24:56 on 03-Apr-2009  +
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++


viewtopic.php?f=124&t=464&hilit=SHELXH#p2232

I think we have already discussed this issue in the thread quoted.

Re: using xh to refine a large small molecule

PostPosted: 12 Mar 2010, 09:26
by johnewarren
pmueller wrote:suit yourself

Not that I would not love to have a new version of the free academic version but there is not one I can just get at this time. Unless you can pull some strings Peter :D
Rudi wrote:@John: I guess Peter refers to this version:

Yep, I've heard a lot about the newer commercial versions but there is a bit of a lag between the two. I should have asked George about it when I was at the ACA - never mind.
On a related note the new Olex2 refinement package is looking very, very nice this is the SMTBX based one that is shall we say SHELX independent. I can not wait for it to be released.
PS Rudi
johnewarren wrote:As mentioned in the previous post Rudi refers to above:

I had not missed your post, we are sort of covering old ground here again. Probably worthwhile merging the two threads into one bigger post. I will do that now.