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*To*: ccp4bb@dl.ac.uk*Subject*: [ccp4bb]: model bias in refmac5?*From*: Jinsong Liu <jsliu@tularik.com>*Date*: Mon, 04 Jun 2001 14:47:00 -0700*References*: <3B1BB244.73B428DB@dundee.ac.uk>*Sender*: owner-ccp4bb@dl.ac.uk

*** For details on how to be removed from this list visit the *** *** CCP4 home page http://www.ccp4.ac.uk *** Dear All, I would like to get some opinions from people using refmac5 about how serious the model bias the map coefficient (FWT, PHWT) would be. I have a low resolution data, complete to 96% at 3.7A. Using molrep, I get different solutions from different homology models. Then I put these models in refmac5 for one cycle of rigid body (I got two molecules per ASU, each one as one rigid body) to calculate a 2fofc map. In most cases, the map looks too good to be true. But remember, these are all different MR solutions and only one can be real. I even throw in a totally different protein for Molrep, and refmac5, the map looks beautiful. The R-factor for those refmac are around 51%-53% range, considered the model is only about 1/3 of the total size of the protein I am working on this R-factor is not too bad for this resolution. Using exact same script, refmac (instead of refmac5) generated a worse map , though I can still see obvious model bias. Using CNX model_map.inp, the calculated map is unthinkable for one case I tested, that is clearly not my solution based on the map. In my memory, refmac map showed very little model bias except there are lots of missing data which is not the case I have here. This is the first time I saw such a heavy model bias in refmac. I used the standard script from the refmac5 example which is at the end of this mail. Can anyone give me some hints? Thanks Following is the rigid.csh script I used: refmac5 \ HKLIN $inmtz \ HKLOUT ${name}${curr}.mtz \ XYZOUT ${name}${curr}.pdb \ XYZIN ${name}${last}.pdb \ << eop>${name}${curr}.log # # Input mtz labels LABI FP=F SIGFP=SIGF FREE=FreeR_flag LABOUT FC=FC PHIC=PHIC # # Refinement parameters. Maximum likelihood refinement. # Reflections between 15 and 2.0Å will be used # REFI TYPE RIGID RESI MLKF RESO 20 4.0 # # Scaling parameters. For rigid body sometimes bulk solvent based # on constant value could be switched off #SOLVent NO # # Fixing Babinet's bulk solvent parameters sometimes helps to # stabilise scaling # SCALe TYPE BULK LSSC ANIS FIXBulk BBULk 200.0 # # Rigid body parameters # # Number of cycles # RIGIdbody NCYCle 1 # # Domain definition. Each group is one rigid body. It may consist of # several unconnected pieces of chain # RIGIdbody GROUp 1 FROM 285 A TO 453 A RIGIdbody GROUp 2 FROM 285 B TO 453 B # # First cycle will give R, free R over resolution. Last cycle also # will give rotation matrices and angles and translations # NOHARVEST MONI MEDIum END eop -- ----------------------------------------------------------------------- "The DAO is not a real DAO when it can be talked about." ---(DAO DE JING) Jinsong Liu, Ph.D. Tularik Inc. Phone: 650 825-7054 Two Corporate Drive Fax: 650 825-7320 South San Francisco, CA 94080, USA Email: jsliu@tularik.com -----------------------------------------------------------------------

**Follow-Ups**:**Re: [ccp4bb]: model bias in refmac5?***From:*Jinsong Liu <jsliu@tularik.com>

**Re: [ccp4bb]: model bias in refmac5?***From:*"Eleanor J. Dodson" <ccp4@ysbl.york.ac.uk>

**References**:**[ccp4bb]: New Version of PDB mode for Emacs***From:*Charlie Bond <C.S.Bond@dundee.ac.uk>

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