[ccp4bb] How to improve the density of another molecule in Asymmetric unit
Hello Everyone, I have a question about how to improve the electron density. I have two indepedent molecules in the asymmetric unit (1.9 A resolution). I solved the structure with PHASER and refined with CCP4i (Rfree = 0.29). For the first molecule, the density is very good, but for the second one, the density is much worse than the first one. Are there any ways to improve the density of the second molecule, such as some kinds of averaging? Why that happens? Thank you very much for your help! Sincerely, Sun Tang [EMAIL PROTECTED] - Never miss a thing. Make Yahoo your homepage.
Re: [ccp4bb] How to improve the density of another molecule in Asymmetric unit
ni hao, I have a question about how to improve the electron density. I have two indepedent molecules in the asymmetric unit (1.9 A resolution). I solved the structure with PHASER and refined with CCP4i (Rfree = 0.29). For the first molecule, the density is very good, but for the second one, the density is much worse than the first one. Are there any ways to improve the density of the second molecule, such as some kinds of averaging? Why that happens? there can be various causes for this such as undetected twinning or a spacegroup error. if you can exclude those possibilities, it could also be that the weak-density molecule has fewer packing interactions and thus is less well ordered, and therefore has a higher overall temperature factor. you can investigate this with SPANCSI (http://xray.bmc.uu.se/usf/spancsi_man.html#H5). --dvd ** Gerard J. Kleywegt [Research Fellow of the Royal Swedish Academy of Sciences] Dept. of Cell Molecular Biology University of Uppsala Biomedical Centre Box 596 SE-751 24 Uppsala SWEDEN http://xray.bmc.uu.se/gerard/ mailto:[EMAIL PROTECTED] ** The opinions in this message are fictional. Any similarity to actual opinions, living or dead, is purely coincidental. **
Re: [ccp4bb] How to improve the density of another molecule in Asymmetric unit
First you cannot normally expect two in the same AU have the same structure, so an over-weighted averaging may cause bias. It is likely that a rigid-body refinement down to two molecules or even domains may help improve in your case. On Jan 16, 2008, at 8:47 AM, Sun Tang wrote: Hello Everyone, I have a question about how to improve the electron density. I have two indepedent molecules in the asymmetric unit (1.9 A resolution). I solved the structure with PHASER and refined with CCP4i (Rfree = 0.29). For the first molecule, the density is very good, but for the second one, the density is much worse than the first one. Are there any ways to improve the density of the second molecule, such as some kinds of averaging? Why that happens? Thank you very much for your help! Sincerely, Sun Tang [EMAIL PROTECTED] Never miss a thing. Make Yahoo your homepage. Lijun Liu, PhD Institute of Molecular Biology HHMI Department of Physics University of Oregon Eugene, OR 97403 541-346-4080
