Dear Lu Yu,
Most readers of this list will only be familiar with the use of SHELXD
to find heavy atom sites for experimental phasing, but it appears that
you are using it for small molecule direct methods, which in fact is
what the program was originally written for. For small molecule direct
methods you MUST have a resolution at which the atoms are resolved from
each other, i.e. 1.2A or better, and 1.0A is a big improvement over
1.2A. For experimental phasing the heavy atoms are further apart and so
much lower resolution may succeed, I have heard of cases where even 10A
data were sufficient to find heavy atom clusters.
For small molecule direct methods you will need an name.hkl file
containing h,k,l,I and sigma(I) (HKLF 4 format) or h,k,l,F and sigma(F)
(HKLF 3 format), as specified by the HKLF instruction at the end of the
name.ins file for SHELXD. If possible you should use intensities, most
integrating and scaling systems can write the HKLF 4 directly without
going through mtz format. Note that all SHELX programs merge equivalents
and reject systematic absences as required and that the reflections may
be in any order.
If SHELXD says "the cell is too small to put atoms randomly" then you
are asking it to find more atoms (the FIND instruction) than fit into
the asymmetric unit. You should ask for less, check the CELL instruction
for a typo or maybe you have a salt crystal. Note that the space group
P1 is specified by LATT -1 and no SYMM cards. If you put in LATT 1 or
leave it out the space group P-1 will be assumed.
For such a small structure it might be better to use small molecule
programs for the refinement, otherwise you will have problems when you
try to deposit and publish the structure. I would (of course) recommend
SHELXL plus the SHELXLE GUI for this, but you should also try to find an
experienced small molecule crystallographer to help you to get started,
almost every chemistry department has at least one. If this does not
resolve your problems I would be happy to look at your data.
Best wishes, George
On 02/19/2012 12:39 AM, Lu Yu wrote:
Hi all,
I was trying to use SHELXD program for protein peptides (6-7 residues)
for the very first time, and I got the .pdb file which should be the
correct solution. However, in the .pdb file, the atoms are labeled as
ABC and they are not recognized as amino acids.
My question is normally what program can I run after SHELXD, to put
those atoms into residues in the correct order so that I can use
refmac to refine the structure?
Another question is, I have another peptide which has P1 space group,
and the SHELXD won't start and it said "the cell is too small to put
atoms randomly", in this case, can I still use SHELXD for the
structure solving and what should I do? If not, what other programs
can I use to solve small peptide structures with 6-7 residues?
Thanks for your help!!
Lu