Re: [ccp4bb] Local real-space refinement by phenix
Hi Hailiang, phenix.refine does local real-space refinement indeed. Here are the details about the algorithm: http://cci.lbl.gov/~afonine/rsr.pdf Slide #10 shows how to use it. Although it works fine in its present shape, there are still some things that need to be improved and some limitations to remove (work in progress). Pavel. P.S.: Second reminder: there is PHENIX mailing list to use for PHENIX related questions. On 8/25/10 1:58 PM, Hailiang Zhang wrote: Hi there: As I understand, phenix.refine do real-space refinement locally (by DiffMap), but from the documentation, I didn't find the keywords to specify the residue range to be refined. Thanks for any help! Best Regards, Hailiang
Re: [ccp4bb] Local real-space refinement by phenix
I would like to propose that we rename this list to the Phenix (and CCP4) Bulletin Board. What have people got against sending purely Phenix questions to the Phenix list? George PS. Since there is no SHELX list, if you have a specifically SHELX question you should just email me directly, as in fact most users do. Prof. George M. Sheldrick FRS Dept. Structural Chemistry, University of Goettingen, Tammannstr. 4, D37077 Goettingen, Germany Tel. +49-551-39-3021 or -3068 Fax. +49-551-39-22582 On Wed, 25 Aug 2010, Hailiang Zhang wrote: Hi there: As I understand, phenix.refine do real-space refinement locally (by DiffMap), but from the documentation, I didn't find the keywords to specify the residue range to be refined. Thanks for any help! Best Regards, Hailiang
Re: [ccp4bb] Local real-space refinement by phenix
On 8/25/10 2:11 PM, George M. Sheldrick wrote: I would like to propose that we rename this list to the Phenix (and CCP4) Bulletin Board. Sounds too Russian: after collapse of USSR many street names in Moscow, as well as metro station names, were renamed back to their original names they had almost one generation ago (70+ years) -:) All the best! Pavel.
Re: [ccp4bb] Local real-space refinement by phenix
Just realized there is a seperate phenix bb. Sorry guy... I would like to propose that we rename this list to the Phenix (and CCP4) Bulletin Board. What have people got against sending purely Phenix questions to the Phenix list? George PS. Since there is no SHELX list, if you have a specifically SHELX question you should just email me directly, as in fact most users do. Prof. George M. Sheldrick FRS Dept. Structural Chemistry, University of Goettingen, Tammannstr. 4, D37077 Goettingen, Germany Tel. +49-551-39-3021 or -3068 Fax. +49-551-39-22582 On Wed, 25 Aug 2010, Hailiang Zhang wrote: Hi there: As I understand, phenix.refine do real-space refinement locally (by DiffMap), but from the documentation, I didn't find the keywords to specify the residue range to be refined. Thanks for any help! Best Regards, Hailiang
Re: [ccp4bb] Local real-space refinement by phenix
Are you suggesting ccp4 is collapsing and people are coming back to the original source? Garib On 25 Aug 2010, at 22:17, Pavel Afonine wrote: On 8/25/10 2:11 PM, George M. Sheldrick wrote: I would like to propose that we rename this list to the Phenix (and CCP4) Bulletin Board. Sounds too Russian: after collapse of USSR many street names in Moscow, as well as metro station names, were renamed back to their original names they had almost one generation ago (70+ years) -:) All the best! Pavel.
Re: [ccp4bb] Local real-space refinement by phenix
Hey Garib, LOL... no of course, I was just saying that I'm a bit allergic to re-naming well established things, and some other people may be too -:) Why don't we rename you Mr. Refmac -:) ? Pavel. On 8/25/10 2:25 PM, Garib Murshudov wrote: Are you suggesting ccp4 is collapsing and people are coming back to the original source? Garib On 25 Aug 2010, at 22:17, Pavel Afonine wrote: On 8/25/10 2:11 PM, George M. Sheldrick wrote: I would like to propose that we rename this list to the Phenix (and CCP4) Bulletin Board. Sounds too Russian: after collapse of USSR many street names in Moscow, as well as metro station names, were renamed back to their original names they had almost one generation ago (70+ years) -:) All the best! Pavel.
Re: [ccp4bb] Local real-space refinement by phenix
On 25 Aug 2010, at 22:17, Pavel Afonine wrote: On 8/25/10 2:11 PM, George M. Sheldrick wrote: I would like to propose that we rename this list to the Phenix (and CCP4) Bulletin Board. Sounds too Russian: after collapse of USSR many street names in Moscow, as well as metro station names, were renamed back to their original names they had almost one generation ago (70+ years) -:) If 70+ years correspond to almost one generation ago, Russians must live very long and have children awfully late! Perhaps this is why they can accumulate such wisdom ... . With best wishes, Gerard. -- === * * * Gerard Bricogne g...@globalphasing.com * * * * Global Phasing Ltd. * * Sheraton House, Castle Park Tel: +44-(0)1223-353033 * * Cambridge CB3 0AX, UK Fax: +44-(0)1223-366889 * * * ===
Re: [ccp4bb] Local real-space refinement by phenix
The fault is entirely with those who respond to phenix questions. You can't blame the askers for guessing that CCP4BB will get a better response. I call this The Republican Fallacy. This fallacy is predicated on the assumption that it is easier to modify behavior than it is to modify the environment. James On Aug 25, 2010, at 2:07 PM, Pavel Afonine wrote: P.S.: Second reminder: there is PHENIX mailing list to use for PHENIX related questions.
