Re: [ccp4bb] AW: [ccp4bb] Twinned data and maps
But wouldn't detwinning be problematic with nearly perfectly twinned data? I'll post my own question about separately to not hijack the thread... On Mon, 2009-03-16 at 11:24 +0100, Clemens Steegborn wrote: > Hi Walter, > > You should definitely detwin data for map calculation if you have a > significant twinning fraction (and only for maps; keep using the twinned > data set for refinement). We use the CCP4 program detwin. BUT if Shelxl > gives bad density, maybe that's simply what you have, a bad density map - > because output from Shelx is already detwinned! > BTW, we observed that different programs handled different cases differently > well; I would suggest ALWAYS to try more than one program, and also to try > Phenix ... > > Best > Clemens > > > -Ursprüngliche Nachricht- > Von: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] Im Auftrag von > Walter Kim > Gesendet: Monday, March 16, 2009 7:22 AM > An: CCP4BB@JISCMAIL.AC.UK > Betreff: [ccp4bb] Twinned data and maps > > Hi again, > > Thanks for your insight into refinement tools for twinned data. I have a > couple of twinned data sets that are nearly perfectly pseudomerohedrally > twinned. I've begun to refine my data in Refmac5 (using the automated twin > refinement), CNS (using the twin inputs) and Shelxl; I'm testing out the > different refinement programs to evaluate the best strategy for the > refinement. However, I would like to start making maps. > > 1. Refmac5 - outputs an mtz that is model-biased > 2. CNS - maps made via model_map_twin.inp are poor > 3. Shelxl - the maps generated in coot from the.fcf file are poor > > Are there better ways to make cleaner maps with my twinnned data that are > less model-biased that I can try to build into? Should I detwin the data and > make maps from that (but continue to refine against the twinned data)? > > Thanks, > Walter -- Edwin Pozharski, PhD, Assistant Professor University of Maryland, Baltimore -- When the Way is forgotten duty and justice appear; Then knowledge and wisdom are born along with hypocrisy. When harmonious relationships dissolve then respect and devotion arise; When a nation falls to chaos then loyalty and patriotism are born. -- / Lao Tse /
[ccp4bb] AW: [ccp4bb] AW: [ccp4bb] Twinned data and maps
Yes, Phenix default output (for twinned data) is detwinned, like the one from Shelxl; didn't know for the new Refmac twin option - but I understand from this posting and Garib's that it also detwins if the twin option is used ... So considering that the Shelxl-derived density looked bad, I definitely agree with Tassos (and apparently didn't make that point clear enough) that other reasons for bad density than twinning have to be considered ... Best Clemens -Ursprüngliche Nachricht- Von: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] Im Auftrag von Eleanor Dodson Gesendet: Monday, March 16, 2009 12:52 PM An: CCP4BB@JISCMAIL.AC.UK Betreff: Re: [ccp4bb] AW: [ccp4bb] Twinned data and maps But dont all twinned refinement programs output detwinned terms for a map? Certainly REFMAC and SHELX do. Eleanor Clemens Steegborn wrote: > Hi Walter, > > You should definitely detwin data for map calculation if you have a > significant twinning fraction (and only for maps; keep using the twinned > data set for refinement). We use the CCP4 program detwin. BUT if Shelxl > gives bad density, maybe that's simply what you have, a bad density map - > because output from Shelx is already detwinned! > BTW, we observed that different programs handled different cases differently > well; I would suggest ALWAYS to try more than one program, and also to try > Phenix ... > > Best > Clemens > > > -Ursprüngliche Nachricht- > Von: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] Im Auftrag von > Walter Kim > Gesendet: Monday, March 16, 2009 7:22 AM > An: CCP4BB@JISCMAIL.AC.UK > Betreff: [ccp4bb] Twinned data and maps > > Hi again, > > Thanks for your insight into refinement tools for twinned data. I have a > couple of twinned data sets that are nearly perfectly pseudomerohedrally > twinned. I've begun to refine my data in Refmac5 (using the automated twin > refinement), CNS (using the twin inputs) and Shelxl; I'm testing out the > different refinement programs to evaluate the best strategy for the > refinement. However, I would like to start making maps. > > 1. Refmac5 - outputs an mtz that is model-biased > 2. CNS - maps made via model_map_twin.inp are poor > 3. Shelxl - the maps generated in coot from the.fcf file are poor > > Are there better ways to make cleaner maps with my twinnned data that are > less model-biased that I can try to build into? Should I detwin the data and > make maps from that (but continue to refine against the twinned data)? > > Thanks, > Walter > > > >
Re: [ccp4bb] AW: [ccp4bb] Twinned data and maps
As far as I know map coeffiicient correspond to detwinned data. But using detwinned data may not be a good idea. It would be good to see what are R factor. Another thing to consider is that different program may use different flags for free R and it may cause some problem. What are Rfactors, completeness, percentage of freeR reflections? These are printed by all programs. If your solution is wrong and you are using twin refinement even if you do not have twinned crystals your R factor can be as low as 50% (that is theoretical limit for random Rfactor when one data are from twinned and another from untwinned crystals). If you have perfect twin and you are modelling twin (using twin refinement) then your random Rfactors can be even smaller. regards Garib On 16 Mar 2009, at 11:51, Eleanor Dodson wrote: But dont all twinned refinement programs output detwinned terms for a map? Certainly REFMAC and SHELX do. Eleanor Clemens Steegborn wrote: Hi Walter, You should definitely detwin data for map calculation if you have a significant twinning fraction (and only for maps; keep using the twinned data set for refinement). We use the CCP4 program detwin. BUT if Shelxl gives bad density, maybe that's simply what you have, a bad density map - because output from Shelx is already detwinned! BTW, we observed that different programs handled different cases differently well; I would suggest ALWAYS to try more than one program, and also to try Phenix ... Best Clemens -Ursprüngliche Nachricht- Von: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] Im Auftrag von Walter Kim Gesendet: Monday, March 16, 2009 7:22 AM An: CCP4BB@JISCMAIL.AC.UK Betreff: [ccp4bb] Twinned data and maps Hi again, Thanks for your insight into refinement tools for twinned data. I have a couple of twinned data sets that are nearly perfectly pseudomerohedrally twinned. I've begun to refine my data in Refmac5 (using the automated twin refinement), CNS (using the twin inputs) and Shelxl; I'm testing out the different refinement programs to evaluate the best strategy for the refinement. However, I would like to start making maps. 1. Refmac5 - outputs an mtz that is model-biased 2. CNS - maps made via model_map_twin.inp are poor 3. Shelxl - the maps generated in coot from the.fcf file are poor Are there better ways to make cleaner maps with my twinnned data that are less model-biased that I can try to build into? Should I detwin the data and make maps from that (but continue to refine against the twinned data)? Thanks, Walter
Re: [ccp4bb] AW: [ccp4bb] Twinned data and maps
But dont all twinned refinement programs output detwinned terms for a map? Certainly REFMAC and SHELX do. Eleanor Clemens Steegborn wrote: Hi Walter, You should definitely detwin data for map calculation if you have a significant twinning fraction (and only for maps; keep using the twinned data set for refinement). We use the CCP4 program detwin. BUT if Shelxl gives bad density, maybe that's simply what you have, a bad density map - because output from Shelx is already detwinned! BTW, we observed that different programs handled different cases differently well; I would suggest ALWAYS to try more than one program, and also to try Phenix ... Best Clemens -Ursprüngliche Nachricht- Von: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] Im Auftrag von Walter Kim Gesendet: Monday, March 16, 2009 7:22 AM An: CCP4BB@JISCMAIL.AC.UK Betreff: [ccp4bb] Twinned data and maps Hi again, Thanks for your insight into refinement tools for twinned data. I have a couple of twinned data sets that are nearly perfectly pseudomerohedrally twinned. I've begun to refine my data in Refmac5 (using the automated twin refinement), CNS (using the twin inputs) and Shelxl; I'm testing out the different refinement programs to evaluate the best strategy for the refinement. However, I would like to start making maps. 1. Refmac5 - outputs an mtz that is model-biased 2. CNS - maps made via model_map_twin.inp are poor 3. Shelxl - the maps generated in coot from the.fcf file are poor Are there better ways to make cleaner maps with my twinnned data that are less model-biased that I can try to build into? Should I detwin the data and make maps from that (but continue to refine against the twinned data)? Thanks, Walter
Re: [ccp4bb] AW: [ccp4bb] Twinned data and maps
Hi - I thought that both phenix and refmac output map coefficients corresponding to de-twinned data - or do I get this wrong? I am also wondering what is the context of "poor" and if it has to do with twinning, or simply if the starting model is not so good. In what was are these "poor" maps different than the refmac5 "model biased" maps? From what I have seen also from your previous email its hard to advice. Its not clear if the Phaser solution is correct, how good the search model was, how the refinement goes. I would suggest to post these details so maybe we could send more detailed comments. Tassos On Mar 16, 2009, at 11:24, Clemens Steegborn wrote: Hi Walter, You should definitely detwin data for map calculation if you have a significant twinning fraction (and only for maps; keep using the twinned data set for refinement). We use the CCP4 program detwin. BUT if Shelxl gives bad density, maybe that's simply what you have, a bad density map - because output from Shelx is already detwinned! BTW, we observed that different programs handled different cases differently well; I would suggest ALWAYS to try more than one program, and also to try Phenix ... Best Clemens -Ursprüngliche Nachricht- Von: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] Im Auftrag von Walter Kim Gesendet: Monday, March 16, 2009 7:22 AM An: CCP4BB@JISCMAIL.AC.UK Betreff: [ccp4bb] Twinned data and maps Hi again, Thanks for your insight into refinement tools for twinned data. I have a couple of twinned data sets that are nearly perfectly pseudomerohedrally twinned. I've begun to refine my data in Refmac5 (using the automated twin refinement), CNS (using the twin inputs) and Shelxl; I'm testing out the different refinement programs to evaluate the best strategy for the refinement. However, I would like to start making maps. 1. Refmac5 - outputs an mtz that is model-biased 2. CNS - maps made via model_map_twin.inp are poor 3. Shelxl - the maps generated in coot from the.fcf file are poor Are there better ways to make cleaner maps with my twinnned data that are less model-biased that I can try to build into? Should I detwin the data and make maps from that (but continue to refine against the twinned data)? Thanks, Walter P please don't print this e-mail unless you really need to Anastassis (Tassos) Perrakis, Principal Investigator / Staff Member Department of Biochemistry (B8) Netherlands Cancer Institute, Dept. B8, 1066 CX Amsterdam, The Netherlands Tel: +31 20 512 1951 Fax: +31 20 512 1954 Mobile / SMS: +31 6 28 597791
[ccp4bb] AW: [ccp4bb] Twinned data and maps
Hi Walter, You should definitely detwin data for map calculation if you have a significant twinning fraction (and only for maps; keep using the twinned data set for refinement). We use the CCP4 program detwin. BUT if Shelxl gives bad density, maybe that's simply what you have, a bad density map - because output from Shelx is already detwinned! BTW, we observed that different programs handled different cases differently well; I would suggest ALWAYS to try more than one program, and also to try Phenix ... Best Clemens -Ursprüngliche Nachricht- Von: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] Im Auftrag von Walter Kim Gesendet: Monday, March 16, 2009 7:22 AM An: CCP4BB@JISCMAIL.AC.UK Betreff: [ccp4bb] Twinned data and maps Hi again, Thanks for your insight into refinement tools for twinned data. I have a couple of twinned data sets that are nearly perfectly pseudomerohedrally twinned. I've begun to refine my data in Refmac5 (using the automated twin refinement), CNS (using the twin inputs) and Shelxl; I'm testing out the different refinement programs to evaluate the best strategy for the refinement. However, I would like to start making maps. 1. Refmac5 - outputs an mtz that is model-biased 2. CNS - maps made via model_map_twin.inp are poor 3. Shelxl - the maps generated in coot from the.fcf file are poor Are there better ways to make cleaner maps with my twinnned data that are less model-biased that I can try to build into? Should I detwin the data and make maps from that (but continue to refine against the twinned data)? Thanks, Walter
Re: [ccp4bb] Twinned data and maps
I am not sure if there is any way of avoiding model bias if the coordinates are included regardless of whether there is twinning or not - my preferred method is to set the occupancies of suspect regions to 0.00 then do refinement of the better parts of the model and then check maps again and rebuild as the maps indicate.. Eleanor Walter Kim wrote: Hi again, Thanks for your insight into refinement tools for twinned data. I have a couple of twinned data sets that are nearly perfectly pseudomerohedrally twinned. I've begun to refine my data in Refmac5 (using the automated twin refinement), CNS (using the twin inputs) and Shelxl; I'm testing out the different refinement programs to evaluate the best strategy for the refinement. However, I would like to start making maps. 1. Refmac5 - outputs an mtz that is model-biased 2. CNS - maps made via model_map_twin.inp are poor 3. Shelxl - the maps generated in coot from the.fcf file are poor Are there better ways to make cleaner maps with my twinnned data that are less model-biased that I can try to build into? Should I detwin the data and make maps from that (but continue to refine against the twinned data)? Thanks, Walter
[ccp4bb] Twinned data and maps
Hi again, Thanks for your insight into refinement tools for twinned data. I have a couple of twinned data sets that are nearly perfectly pseudomerohedrally twinned. I've begun to refine my data in Refmac5 (using the automated twin refinement), CNS (using the twin inputs) and Shelxl; I'm testing out the different refinement programs to evaluate the best strategy for the refinement. However, I would like to start making maps. 1. Refmac5 - outputs an mtz that is model-biased 2. CNS - maps made via model_map_twin.inp are poor 3. Shelxl - the maps generated in coot from the.fcf file are poor Are there better ways to make cleaner maps with my twinnned data that are less model-biased that I can try to build into? Should I detwin the data and make maps from that (but continue to refine against the twinned data)? Thanks, Walter
