But aren't the bump restraints re-evaluated at each iteration? That was my understanding (but I could be wrong), after all it's not a big deal to compute interatomic distances. One contribution that is not re-evaluated every iteration but only at iteration 1 is (I believe, but again I could be wrong) the solvent contribution, I guess because the assumption is that it doesn't change much.
All the same it's interesting that you mention that idea, because I have been trying precisely that with regular refinement and in some cases I get significantly lower final R-factors for the same total number of iterations if I split it into a series of short jobs of maybe only 3 or 4 iterations each (doesn't help every time though), each time feeding the output PDB from one job into the next one as you describe. I've no idea why it works though! Cheers -- Ian > -----Original Message----- > From: owner-ccp...@jiscmail.ac.uk [mailto:owner-ccp...@jiscmail.ac.uk] On > Behalf Of James Holton > Sent: 26 March 2009 01:08 > To: Kristof Van Hecke > Cc: CCP4BB@jiscmail.ac.uk > Subject: Re: [ccp4bb] Structure idealisation Refmac_5.5.0072 > > Kristof Van Hecke wrote: > > I want to optimize a DNA-helix with the function "Structure > > idealisation" in Refmac_5.5.00782 (CCP4_6.1.1). > > My question, is this performing just a geometry optimization (against > > a library), or is there also an energy-optimization of some kind > > involved,..? > What's the difference? > > > > And according to the number of cycles (default 10) used, different > > structural results are obtained, hence is there a means of estimating > > the ideal number of cycles to use..? > > > I generally keep re-inputting the output PDB back into refmac until the > input and output PDB files are "identical" to, say, withing 0.001 A. > This is my definition of "convergence". It is important to use a small > number of cycles for each run because if you don't atoms can move far > enough to start "bumping" into atoms that were not close enough to > trigger a "bump" restraint at the beginning. At least, this is how it > was back in "my day". > > -James Holton > MAD Scientist Disclaimer This communication is confidential and may contain privileged information intended solely for the named addressee(s). It may not be used or disclosed except for the purpose for which it has been sent. If you are not the intended recipient you must not review, use, disclose, copy, distribute or take any action in reliance upon it. If you have received this communication in error, please notify Astex Therapeutics Ltd by emailing i.tic...@astex-therapeutics.com and destroy all copies of the message and any attached documents. Astex Therapeutics Ltd monitors, controls and protects all its messaging traffic in compliance with its corporate email policy. The Company accepts no liability or responsibility for any onward transmission or use of emails and attachments having left the Astex Therapeutics domain. Unless expressly stated, opinions in this message are those of the individual sender and not of Astex Therapeutics Ltd. The recipient should check this email and any attachments for the presence of computer viruses. Astex Therapeutics Ltd accepts no liability for damage caused by any virus transmitted by this email. E-mail is susceptible to data corruption, interception, unauthorized amendment, and tampering, Astex Therapeutics Ltd only send and receive e-mails on the basis that the Company is not liable for any such alteration or any consequences thereof. Astex Therapeutics Ltd., Registered in England at 436 Cambridge Science Park, Cambridge CB4 0QA under number 3751674
