I did a single crystal XRD experiment for one crystal. I got res.file and hkl.file and ins.file by using these files bond connectivity and exact crystal structure how should I get it.
@Pcrao,
Your question is not clear. If you have already got .res file, it means that you already solved the structure. Then you need to refine the structure so as to achieve good agreement parameters. WinGX could help you in this. Diamond is a good software for structure visualization but, as far as I know, it is not made for structure solution and refinement.
Dr.Gregory, sorry I get the Cif file.From that file how to solve the crystal structure.When I opened the cif.file in mercury software, what I'm getting is not the exact crystal structure. what is the procedure for solving?
Structure determination procedure includes some stages. 1. unit cell determination; 2. data collection; 3. structure solution 4. structure refinement. At the end of the procedure you have to get final CIFile (crystallographic information file) which will contain all information and experimental and calculated results of the all stages. Quality of your results in CIF you have to check here:
http://checkcif.iucr.org/index.html
After checking, you can get hints (syntax errors or alerts of different levels) how is possible to improve your results in order to make them public-able. If your CIF gives alerts of sufficiently low levels and R-factor or other agreement parameters is sufficiently good, it means that you have got the structure of your crystal. If you did it, then what d'you mean that it "is not the exact crystal structure"?
Visualization of the structure is not directly related to the definition of the structure. Of course, you have to depict the structure (from CIF, RES or other files that contain atomic parameters and symmetry elements) for publication. it is also very useful to visualize it in intermediate stages of refinement in order to find your right direction. Many programs (Mercury, Diamond, CrystalMaker ...) could do it. They have many different options and styles that you can visualize the structure in different ways. If your problem lies here, choose any of these programs, read its guide and find options for an image that is suitable for a particular composition and structure of your crystal.
Question: how can you have a .res or .cif file before having solved and refined the crystal stucture?
What you should do is to start from the .ins and .hkl files and use a full structure determination software to solve and refine you crystal. There are many of them, e.g., ShelXle (http://ewald.ac.chemie.uni-goettingen.de/shelx/eingabe.php), PLATON (http://www.crystal.chem.uu.nl/distr/PLATON.html), SIR201x (http://wwwba.ic.cnr.it/content/sir2011-v10), WinGX (http://www.chem.gla.ac.uk/~louis/software/wingx/), but I believe that the easiest tool for you to use is Olex2 (http://www.olex2.org/) which tries to guide you as much as possible throughout the process.
At the end of the solution and refinement stages you wil get a .cif file that you can check using the link reported above to improve the quality of your results.
Thomas is right. You can have a cif file generated automatically from the diffractometer software, but this cif file cannot be used to solve the crystal structure.
Structure solution can be done initially through your diffractometer software.For example-the Apex software for Bruker machine would give you the .hkl file( essentially the integrated reflections data), the .ins file (The instructions file). You can solve the structure the automated way and assign all the labels afterwards and thus end up with a .res file and also a .cif file.If the structure is not what you expected or some distortion is there,you might want to either refine it using other softwares like XP,OLEX,WingX or you can even start from scratch using only the .ins and .hkl files to solve the structure.I suggest you go through the SHELX manuals to gain mastery over the commands through which you can solve structures.I also suggest taking help from some of your seniors or faculty members .
Softwares like mercury and diamond help you to just visualise the structures.They would be great if you want to understand the interactions within the crystal and how the molecules are packed within the lattice.However,they cannot solve any structure!
If you're concerned about any extra or deficient no. of bonds/atoms in the structure,you have to go back and work on the structure a bit.The.res file that you use to open these visulaisation softwares is just a result file.
All the best!