Please tell us what worked. Eleanor On 6 June 2017 at 04:52, Shankar Prasad Kanaujia <[email protected]> wrote:
> Dear All, > > I am very happy to inform you that I have finally solved the structure. > Thanks to all for your kind suggestions. > > With best regards, > Shankar > > On Wed, Aug 3, 2016 at 8:35 PM, Sudipta Bhattacharyya < > [email protected]> wrote: > >> Dear Shankar, >> >> The high TFZ and LLG you mentioned indeed indicate a possible solution. >> However, how certain are you about the number of ensembles placed in the >> ASU? Also this high Rfree value sometime indicates the presence of >> t-NCS/twining, Did you check that (the presence of large off origin t-NCS >> peak)? Although phaser should detect it and correct it accordingly but only >> if you are searching for even number of ensembles in the ASU. >> >> Good luck, >> Sudipta. >> >> On Wed, Aug 3, 2016 at 9:14 AM, Shankar Prasad Kanaujia < >> [email protected]> wrote: >> >>> Dear All, >>> >>> As suggested, I tried several things. I am getting MR solutions with TFZ >>> > 8.0 (e.g. 12, 16) and high LLG (e.g. 150, 160). However, Rw/Rf remains >>> above 0.50 after first round of refinement. In some cases, after some >>> manual model building, Rw falls up to 0.46, however, Rf remains above 0.50. >>> >>> Any suggestions for further model building. The data is of ~1.9 Angst >>> processed in P1211. >>> >>> With best regards, >>> Shankar >>> >>> On Mon, Aug 1, 2016 at 1:48 PM, <[email protected]> wrote: >>> >>>> Dear Schankar, >>>> >>>> >>>> >>>> you could also try automatic packages like Balbes or Morda. However, it >>>> might not be a bad idea to try a more rational approach as well. With 27% >>>> sequence identity, you template may or may not have the same fold. With 27% >>>> sequence identity AND a similar biological function (e.g. similar reaction >>>> catalysed, binding to a similar receptor etc.), your bets are much better. >>>> (Except cases with large conformational changes like antibodies and >>>> calmodulin). >>>> >>>> >>>> >>>> If molecular replacement fails, you should also look very carefully in >>>> the space group assignment and in case of ambiguity try all possible space >>>> groups for your MR searches. >>>> >>>> >>>> >>>> Best, >>>> >>>> Herman >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> *Von:* CCP4 bulletin board [mailto:[email protected]] *Im Auftrag >>>> von *Sivakumar N >>>> *Gesendet:* Montag, 1. August 2016 08:30 >>>> *An:* [email protected] >>>> *Betreff:* Re: [ccp4bb] Molecular replacement with template having low >>>> sequence identity >>>> >>>> >>>> >>>> Dear Shankar, >>>> >>>> How do you appreciate this approach of generating an Ensemble of >>>> superposed homologous structures as a MR search probe? I found the FUGUE >>>> server helpful in pulling out the distantly related structural homologues >>>> for a given query sequence. Also, a manual or an automated method of >>>> refining or sieving the superposed homologues to cut out the residues that >>>> fall in the loop regions and possibly other residues at loci that introduce >>>> any noisy-correspondences between the superposed structures can be useful, >>>> in order to arrive at a better RMSD values between the equivalent Cα atoms >>>> of this hybrid MR search probe. >>>> >>>> Regards >>>> >>>> Sivakumar,N. >>>> >>>> >>>> >>>> On Sat, Jul 30, 2016 at 6:20 PM, Shankar Prasad Kanaujia < >>>> [email protected]> wrote: >>>> >>>> Dear All, >>>> >>>> Is it possible to solve the structure of a protein having template with >>>> a sequence identity of 27%. If yes, what is the best possible method. >>>> >>>> Any program which can automatically give some clue. >>>> >>>> With best regards, >>>> >>>> Shankar >>>> >>>> >>>> >>> >>> >>> >>> -- >>> Shankar Prasad Kanaujia, Ph.D. >>> Assistant Professor >>> Department of Biosciences and Bioengineering >>> Indian Institute of Technology Guwahati >>> Guwahati - 781039 Assam, India >>> Tele: 0361 258 2228 >>> Fax: 0361 258 2249 >>> Email: [email protected] >>> Homepage: http://www.iitg.ernet.in/spkanaujia/ >>> Google Scholar: https://scholar.google.com/cit >>> ations?user=Zt4JSNYAAAAJ&hl=en >>> >> >> > > > -- > Shankar Prasad Kanaujia, Ph.D. > Associate Professor > Department of Biosciences and Bioengineering > Indian Institute of Technology Guwahati > Guwahati - 781039 Assam, India > Tele: 0361 258 2228 > Fax: 0361 258 2249 > Email: [email protected] > Homepage: http://www.iitg.ernet.in/spkanaujia/ > Google Scholar: https://scholar.google.com/citations?user=Zt4JSNYAAAAJ&; > hl=en >
