Re: [ccp4bb] "reset" a structure before re-refinement

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Re: [ccp4bb] "reset" a structure before re-refinement

Cheers, Robbie Sent from my Windows 10 phone From: Andrew Leslie Sent: 17 August 2017 17:29 To: CCP4BB@JISCMAIL.AC.UK Subje

Re: [ccp4bb] "reset" a structure before re-refinement

8:40 AM, Robbie Joosten wrote: In most cases resetting the B-factors would be enough to perturb the model. Cheers, Robbie Sent from my Windows 10 phone *From: *Andrew Leslie <mailto:and...@mrc-lmb.cam.ac.uk> *Sent: *17 August 2017 17:29 *To: *CCP4BB@JISCMAIL.AC.UK <mailto:CCP4BB@

Re: [ccp4bb] "reset" a structure before re-refinement

Frank, Given that experimental electron density maps resulting from structure factors with a figure of merit of 0.5 are still interpretable, I don't think that "wiggling" the phases will be so bad. Fom of 0.5 corresponds to a phase error of 60 degrees, which is a pretty big shift. Interesting

Re: [ccp4bb] "reset" a structure before re-refinement

Hi Andrew, as far as I understand, PDBSET only affects the coordinates. The WIGL command in SHELXL also add noise to the ADPs, which has a dramatic effect on the resulting R1-value. See Figure S5 A vs. S5 B in doi: 10.1073/pnas.1502136112 At least one should reset the B-values in refmac, I

Re: [ccp4bb] "reset" a structure before re-refinement

On the same question, asked some time ago, Eleanor (or James?) pointed out that the this perturbation changes the phases only of the higher resolution reflections. I believe the implied conclusion was that "resetting" a structure does not have the same effect on all phases as randomising them

Re: [ccp4bb] "reset" a structure before re-refinement

Dear all, Many thanks for all of your suggestions - it seems that I was looking with the wrong search terms (perturb => shake) and there are indeed many tools out there for performing this. Problem solved :-) Best wishes Graeme > On 17 Aug 2017, at 18:18, Victor Lamzin

Re: [ccp4bb] "reset" a structure before re-refinement

Dear Graeme, You can also type the following on a command line, optional commands are given in square parentheses. Victor $warpbin/arp_warp mode shakemodel allatoms files ccp4 xyzin FILENAME.pdb xyzout FILENAME.pdb symmetry SPACEGROUP shakemodel [ bexclude B1 ] [ breset B1 B2 ] [ randomise X

Re: [ccp4bb] "reset" a structure before re-refinement

Dear Graeme, The WIGL instruction in SHELXL does exactly that, and has some useful options. http://shelx.uni-ac.gwdg.de/SHELX/shelxl_html.php#WIGL Best wishes, George On 08/17/2017 05:17 PM, Graeme Winter wrote: Dear All, Is there a protocol out there to gently perturb atomic positions so

Re: [ccp4bb] "reset" a structure before re-refinement

p4bb] "reset" a structure before re-refinement Hi Graeme, You can do this with PDBSET, keyword NOISE Cheers, Andrew > On 17 Aug 2017, at 16:17, Graeme Winter <graeme.win...@diamond.ac.uk> wrote: > > Dear All, > > Is there a protocol out there to gently per

Re: [ccp4bb] "reset" a structure before re-refinement

Hi Graeme, You can do this with PDBSET, keyword NOISE Cheers, Andrew > On 17 Aug 2017, at 16:17, Graeme Winter wrote: > > Dear All, > > Is there a protocol out there to gently perturb atomic positions so that > re-running refinement can essentially put them

[ccp4bb] "reset" a structure before re-refinement

Dear All, Is there a protocol out there to gently perturb atomic positions so that re-running refinement can essentially put them back without bias from the original refinement? In particular, if trying to perform the Karplus and Diederichs paired refinement protocol, I do not want to run the