From: Lu Yu
Date: 18 February 2012 23:39
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
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From: George Sheldrick
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
Date: 18 February 2012 23:39
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
----------
From: George Sheldrick
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
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