Re: [ccp4bb] solving structure of which 70% is known

Protein crystallography Programs for crystallography X-ray detectors
Basic tutorials:
Protein Peptide

CCP4bb navigation

CCP4bb <-- 2007 <-- September 2007 <-- 04 September 2007

Previous message:
Subject: Why is RANGES restricted to <60 in TRUNCATE ?
From: "Juergen J {- dot -} Mueller" jjm {- at -} MDC-BERLIN {- dot -} DE
Date: 2007-09-04

Next message:
Subject: covalently bonded Ligand fit
From: U Sam us_x {- at -} HOTMAIL {- dot -} COM
Date: 2007-09-04

Subject: Re: solving structure of which 70% is known
From: Christian Biertumpfel biertumpfelc {- at -} NIDDK {- dot -} NIH {- dot -} GOV
Date: 2007-09-04

Hi Raya,
My reply comes late but maybe it is still relevant to you. I have a few
suggestions for molecular replacement in phaser:

* Input both protein models in your search (define both known structures
as ensembles and search for both)
* Give higher values (let's say 1.0, 1.2, 1.4) for the "rms difference"
in "Similarity of PDB"
* Allow a number of clashes as packing tolerance (check your log files
how many clashes the "top solutions" have)
* Run phaser with "all choices of alternative space group"
(as mentioned before)

Good luck,
christian

Raja Dey wrote:
> Hello,
> I am trying to solve a multi-protein DNA complex structure from a 3.6 A native data set. The target structure is a dimer (95 aa in each monomer) in complex with DNA( 15 base pairs) plus a second protein of 131 aa. The data has been scaled to P6(1)22 sp. gr. and one target structure is expected to be in the asymmetric unit that corresponds to 68% solvent content. 70 % of the target structure is known in two parts(two different pdb structures previously solved contributing 55% and 15% of the target structure). I tried with molrep and phaser considering the first part(55%) as the search model but it turned out to no good solution which all clashes with symmetry related copies. If I assume the sp. gr. is not the case what else I can try. Any suggestion is well appreciated.
> Thanks...
> Raja
>

_______________________________________________________________________

Dr. Christian Biertümpfel
Laboratory of Molecular Biology

NIDDK/National Institutes of Health phone: +1 301 402 4647
9000 Rockville Pike, Bldg. 5, Rm. B1-03 fax: +1 301 496 0201
Bethesda, MD 20892-0580
USA
_______________________________________________________________________

CCP4bb navigation

CCP4bb <-- 2007 <-- September 2007 <-- 04 September 2007

Previous message:
Subject: Why is RANGES restricted to <60 in TRUNCATE ?
From: "Juergen J {- dot -} Mueller" jjm {- at -} MDC-BERLIN {- dot -} DE
Date: 2007-09-04

Next message:
Subject: covalently bonded Ligand fit
From: U Sam us_x {- at -} HOTMAIL {- dot -} COM
Date: 2007-09-04