regarding refinement of large molecule

[kuldeepmahiya]

Dear All,
I have a question regarding the size of molecule. If suppose a molecule under examination or for the data collection have more than 100 carbon atoms, then the usual refinement that we employed for small molecule is also appropriate for a such big molecules too ? I am using wingx version 1.80.05 and shelxl-97 for structure solution and refinements.

Kuldeep
Bio inorganic Research Laboratory,
Department of Chemistry,
University of Delhi
India.

[johnewarren]

Most refinement packages can handle in excess of 100 non-hydrogen atoms quite readily. The issues only come if your trying to have specific naming conventions.

Crystals seems to allow more than 4 character naming whilst shelx is limited to 4 characters so. This means if you have an atom with two characters in the name say Cl or Xe of Pb etc you can have maximum of 99 numeric versions whilst if you have a single character name you can have 999. But of course you can also swtich to a pseudo hex format and have 0A etc and exceed the 99 limit. Then if you have say C101 and from it H101A, H101B and H101C it will not work as you exceeded the number of characters. It is a rather week point in shelx and stems from the old days of fortran and economy of coding.

Rather amusingly though shelx only defines an atom from its relevant SFAC card number you could label all you atoms randomly, Fred is ok, so is John, Mary, June etc. Shelxl will refine just fine as long as you do not have two atoms with the same name. If you are using a program that uses the atom name to define the atom type in the viewer it won't work but other will so you can have Paul (which is a Pb) and John, Ring, Geor as it coordinating oxygens etc.

If you have a really big structure then the matrix setup in shelxl is too small for refinement - you will get a warning so you will need shelxh or if you have the commercial versions apparantly it is no longer an issue. If you search the forumfor shelxh you will see reference to this.

Also quite interestingly direct methods has now been successfully used to solve a structure with over 1000 non hydrogen atoms.

In sort, you'll be fine with over 100 atoms in your refinement, as long as your data is good enough (same rule as for most things).

[kuldeepmahiya]

Thank you so much Sir for your kind help.