Re: [ccp4bb] fixing position in the refinement: Shelx, refmac5
For SHELX there are two ways to fix selected atoms: either put AFIX 1 in front of the fixed atoms and AFIX 0 after them, or use the BLOC instruction. e.g. BLOC 1 N_1 C_53 N_57 C61 N_62 CA_62 C_62 O_62 N_63 LAST BLOC -1 N_1 C_53 N_57 C61 N_62 CA_62 C_62 O_62 N_63 LAST would fix residues 54-56 and the side-chain of residue 62 (but you may need to consider the order of atoms). This would be easier than using AFIX if you are already using AFIX for riding hydrogens, however it is OK to fix atoms with AFIX 1 and then use HFIX in the same job to add hydrogens. I have deliberately chosen a complicated example to show how easy it is! More details on SHELXL refinements are now available from the CCP4 Wiki: http://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php/SHELXL and for SHELXC, D and E see: http://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php/SHELX_C/D/E Note that since this is a Wiki, users are encouraged to contribute! George Prof. George M. Sheldrick FRS Dept. Structural Chemistry, University of Goettingen, Tammannstr. 4, D37077 Goettingen, Germany Tel. +49-551-39-3021 or -3068 Fax. +49-551-39-2582 On Thu, 3 Apr 2008, U Sam wrote: How one can fix position of few residues when refining in SHELX or Refmac5. Thanks. Sam. _ Use video conversation to talk face-to-face with Windows Live Messenger. http://www.windowslive.com/messenger/connect_your_way.html?ocid=TXT_TAGLM_WL_Refresh_messenger_video_042008
Re: [ccp4bb] fixing position in the refinement: Shelx, refmac5
No. Better way is restraining internal degrees of freedom. Something like elastic network model: Tirion MM (1996) Phys Rev Letters 77 pp 1905-1908 But care should be taken with weights and which distances should be restrained. Fiixing position is not good way of using prior information (In my view of course, which is debatable) Garib On 4 Apr 2008, at 06:56, Frank von Delft wrote: Is that also how you would restrain refinement at low resolution when using a high-resolution model? (e.g. a 1.8A model into 4A data) phx. Garib Murshudov wrote: In newer version of refmac you can use harmonic restraints. Take the new stable version of refmac from www.ysbl.york.ac.uk/YSBLPrograms/index.jsp and use harmonic restraints as described in: http://www.ysbl.york.ac.uk/~garib/refmac/data/refmac_news.html http://www.ysbl.york.ac.uk/%7Egarib/refmac/data/refmac_news.html Keyword is: external harmonic residues from [residue_number] [chain_name] to [residue_number] [chain_name] sigma [value] sigma 0.1 With the current ccp4i version you can use developers option and add an external keyword file that contains this keyword for residues you want to fix. I hope it helps. Garib On 4 Apr 2008, at 00:39, U Sam wrote: How one can fix position of few residues when refining in SHELX or Refmac5. Thanks. Sam. _ Use video conversation to talk face-to-face with Windows Live Messenger. http://www.windowslive.com/messenger/connect_your_way.html? ocid=TXT_TAGLM_WL_Refresh_messenger_video_042008
Re: [ccp4bb] fixing position in the refinement: Shelx, refmac5
Is that also how you would restrain refinement at low resolution when using a high-resolution model? (e.g. a 1.8A model into 4A data) phx. Garib Murshudov wrote: In newer version of refmac you can use harmonic restraints. Take the new stable version of refmac from www.ysbl.york.ac.uk/YSBLPrograms/index.jsp and use harmonic restraints as described in: http://www.ysbl.york.ac.uk/~garib/refmac/data/refmac_news.html http://www.ysbl.york.ac.uk/%7Egarib/refmac/data/refmac_news.html Keyword is: external harmonic residues from [residue_number] [chain_name] to [residue_number] [chain_name] sigma [value] sigma 0.1 With the current ccp4i version you can use developers option and add an external keyword file that contains this keyword for residues you want to fix. I hope it helps. Garib On 4 Apr 2008, at 00:39, U Sam wrote: How one can fix position of few residues when refining in SHELX or Refmac5. Thanks. Sam. _ Use video conversation to talk face-to-face with Windows Live Messenger. http://www.windowslive.com/messenger/connect_your_way.html?ocid=TXT_TAGLM_WL_Refresh_messenger_video_042008
