Dear Rajnesh, My experience with molecular replacement is that when you don’t have a model, you don’t get density. Only in exceptional cases (crystals with a very high solvent content) I see density for missing loops or domains, so missing density is very inconvenient, but no reason to be worried.
You say that with the 4 molecule search model you get a MR solution and density, but no density for the 5th molecule. With the model for the 5th molecule, you also get a MR solution, but no density for molecules 1-4. What happens if you load in coot both the solution for the 4 molecules and the solution for the 5th molecule? Does that produce a sensible crystal packing (e.g. no serious overlaps)? The solutions may be in different asymmetric units, so you may have to apply some crystallographic symmetry transformations to bring them together. If the crystal packing makes sense, you could merge the pdb files and see if you can refine the combined solutions. Best, Herman Von: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> Im Auftrag von Eleanor Dodson Gesendet: Mittwoch, 12. Februar 2020 14:04 An: CCP4BB@JISCMAIL.AC.UK Betreff: [EXTERNAL] Re: [ccp4bb] problem in structure solution of multidomain protein EXTERNAL : Real sender is owner-ccp...@jiscmail.ac.uk<mailto:owner-ccp...@jiscmail.ac.uk> At 3A finding missing domains is tricky.. Can you increase that resolution at all? Much easier at 2.5A! But I would refine and rebuild the 4 domains to the best possible maps, then see if there is any density unaccounted for. (You will have to lower the COOT default contour level I guess..) If there is you could use buccaneer to try and build it, keeping the fitted domains fixed .. That can work IF there is density to build into.. Presumably you know the sequence? MR from a modelling model is often tricky anyway. Eleanor On Wed, 12 Feb 2020 at 12:42, Boaz Shaanan <bshaa...@bgu.ac.il<mailto:bshaa...@bgu.ac.il>> wrote: Hi, One other option is to run MR in Phaser in one run with the tetramer made of the 4 monomers as model 1 and the single monomer as model 2. The gui offers this option and there is also an example in the documentaion. Cheers, Boaz Boaz Shaanan, Ph.D. Department of Life Sciences Ben Gurion University of the Negev Beer Sheva Israel On Feb 12, 2020 09:23, Rajnesh Kumari Yadav <rajn...@rcb.res.in<mailto:rajn...@rcb.res.in>> wrote: Hello everyone, I am working on a protein which have 5 domain in it, we have its 4 domain structure and 3.0 Angstrom data of 5 domain protein crystal. While doing the Molecular replacement we got solution with four domain with good electron density and space for last domain without any density. When we tried Molecular replacement with the missing domain (modelled) only we got solution shows density for this missing domain but not able see electron density for rest four domain even though room for 4 domain was visible in the solution. I need help or suggestion for this issue. ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1<https://urldefense.proofpoint.com/v2/url?u=https-3A__www.jiscmail.ac.uk_cgi-2Dbin_webadmin-3FSUBED1-3DCCP4BB-26A-3D1&d=DwMFaQ&c=Dbf9zoswcQ-CRvvI7VX5j3HvibIuT3ZiarcKl5qtMPo&r=HK-CY_tL8CLLA93vdywyu3qI70R4H8oHzZyRHMQu1AQ&m=4vtUDcuFQJn-BoiAKYaKMsM5J7zHOGXXMRBJ0RULCok&s=KRePI7bw61a69xpFtsZzRNxXJESoPyDf1XdfdsnLpKM&e=> ________________________________ To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1<https://urldefense.proofpoint.com/v2/url?u=https-3A__www.jiscmail.ac.uk_cgi-2Dbin_webadmin-3FSUBED1-3DCCP4BB-26A-3D1&d=DwMFaQ&c=Dbf9zoswcQ-CRvvI7VX5j3HvibIuT3ZiarcKl5qtMPo&r=HK-CY_tL8CLLA93vdywyu3qI70R4H8oHzZyRHMQu1AQ&m=4vtUDcuFQJn-BoiAKYaKMsM5J7zHOGXXMRBJ0RULCok&s=KRePI7bw61a69xpFtsZzRNxXJESoPyDf1XdfdsnLpKM&e=> ________________________________ To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1<https://urldefense.proofpoint.com/v2/url?u=https-3A__www.jiscmail.ac.uk_cgi-2Dbin_webadmin-3FSUBED1-3DCCP4BB-26A-3D1&d=DwMFaQ&c=Dbf9zoswcQ-CRvvI7VX5j3HvibIuT3ZiarcKl5qtMPo&r=HK-CY_tL8CLLA93vdywyu3qI70R4H8oHzZyRHMQu1AQ&m=4vtUDcuFQJn-BoiAKYaKMsM5J7zHOGXXMRBJ0RULCok&s=KRePI7bw61a69xpFtsZzRNxXJESoPyDf1XdfdsnLpKM&e=> ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
