[ccp4bb] AW: Twinning problem - almost solved.
Dear Bulletin Board, After some headbanging (Refmac5 had helpfully created gap records for all insertions and deletions present in the structure), I got refmac5 running with the TWIN option. Refmac5 also found the k,h,-l domain and rejected the other possible domains because they were too small. The Rfactor's are now extremely good: ~14% and the Rfree's are for me acceptable: ~24%. Since I found the difference between R and Rfree somewhat large, I have been playing with the weighting. By using a weight of 0.01, I can bring the Rfactor up to 18%, but the Rfree stays about the same or even gets a little worse. My question: is there a way to bring R and Rfree closer together, or is it related to the twinned data and is it something we have to live with? Best regards, Herman -Ursprüngliche Nachricht- Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von Miller, Mitchell D. Gesendet: Donnerstag, 20. Juni 2013 17:43 An: CCP4BB@JISCMAIL.AC.UK Betreff: Re: [ccp4bb] Twinning problem You are welcome. Let me also for the benefit of others who may search the archives in the future, let me correct two errors below - (typo and a miss-recollection). Specially, I was thinking that phenix.refine was now able to refine multiple twin laws, but according to Nat Echols on the phenix mailing list http://phenix-online.org/pipermail/phenixbb/2013-March/019538.html phenix.refine only handles 1 twin law at this time. (My typo was that and our second structure was 3nuz with twin fractions 0.38, 0.32, 0.16 and 0.14 -- not 2nuz). A useful search for deposited structures mentioning tetartohedral http://www.ebi.ac.uk/pdbe-srv/view/search?search_type=all_texttext=TETARTOHEDRALLY+OR+TETARTOHEDRAL Regards, Mitch -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of herman.schreu...@sanofi.com Sent: Thursday, June 20, 2013 8:04 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] AW: Twinning problem Dear Mitch (and Philip and Phil), It is clear that I should give refmac a go with the non-detwinned F's and just the TWIN command. Thank you for your suggestions, Herman -Ursprüngliche Nachricht- Von: Miller, Mitchell D. [mailto:mmil...@slac.stanford.edu] Gesendet: Donnerstag, 20. Juni 2013 16:18 An: Schreuder, Herman RD/DE Betreff: RE: Twinning problem Hi Herman, Have you considered the possibility of your crystals being tetartohedral twinned. That is more than one of the twin laws may apply to your crystals. E.g. in P32 it is possible to have tetartohedral twinning which would have 4 twin domains - (h,k,l), (k,h,-l), (-h,-k,l) and (-k,-h,-l). Perfect tetartohedral twinning of P3 would merge in P622 and each twin domain would have a faction of 0.25. We have had 2 cases like this (the first 2PRX was before there was support for this type of twinning except for in shelxl and we ended up with refined twin fractions of 0.38, 0.28, 0.19, 0.15 for the deposited crystal and a 2nd crystal that we did not deposit had twin fractions of 0.25, 0.27, 0.17, 0.31). The 2nd case we had was after support for twining (including tetartohedral twinning) was added to refmac (and I think phenix.refine can also handle this). For 2NUZ, it was P32 with refined twin fractions of 0.25, 0.27, 0.17, 0.31. Pietro Roversi wrote a review of tetartohedral twinning for the CCP4 proceedings issues of acta D http://dx.doi.org/10.1107/S0907444912006737 I would try refinement with refmac using the original (non-detwinned F's) with just the TWIN command to see if it ends up keeping twin fractions for all 3 operators (4 domains) -- especially with crystals 1 and 3 which appear to have the largest estimates of the other twin fractions. Regards, Mitch == Mitchell Miller, Ph.D. Joint Center for Structural Genomics Stanford Synchrotron Radiation Lightsource 2575 Sand Hill Rd -- SLAC MS 99 Menlo Park, CA 94025 Phone: 1-650-926-5036 FAX: 1-650-926-3292 -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of herman.schreu...@sanofi.com Sent: Thursday, June 20, 2013 6:47 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Twinning problem Dear Bulletin Board, Prodded by pdb annotators, which are very hesitant to accept coordinate files when their Rfactor does not correspond with our Rfactor, I had a look again into some old data sets, which I suspect are twinned. Below are the results of some twinning tests with the Detwin program (top value: all reflections, lower value: reflections Nsig*obs (whatever that may mean). The space group is P32, the resolution is 2.3 - 2.6 Å and data are reasonable complete: 95 - 100%. From the Detwin analysis, it seems that the crystals are twinned with twin operator k,h,-l with a twinning fraction of 0.3 for crystal 1, 0.15 for crystal 2 and 0.4 for crystal 3. Crystal 2 can be refined while ignoring twinning to get
Re: [ccp4bb] AW: Twinning problem - almost solved.
I have found PDB_REDO is an efficient way of tweaking structure solutions. Among other things, it sorts through various MATRIX and BFAC weights and tests effectiveness of TLS if not used already. It usually improves typical final structure solutions for our group by about 1% or so Rfree and reduces the Rfree-R spread, as well as improves a variety of other structural measures. You can of course adjust weights and TLS manually, but if you can get a local version of PDB_REDO running it saves a lot of time, and has some extra features. I've modified v. 5.0.9 for this purpose. Depending on the packages you do or don't have, it is a little tricky to get running locally. Roger Rowlett On Jun 21, 2013 4:42 AM, herman.schreu...@sanofi.com wrote: Dear Bulletin Board, After some headbanging (Refmac5 had helpfully created gap records for all insertions and deletions present in the structure), I got refmac5 running with the TWIN option. Refmac5 also found the k,h,-l domain and rejected the other possible domains because they were too small. The Rfactor's are now extremely good: ~14% and the Rfree's are for me acceptable: ~24%. Since I found the difference between R and Rfree somewhat large, I have been playing with the weighting. By using a weight of 0.01, I can bring the Rfactor up to 18%, but the Rfree stays about the same or even gets a little worse. My question: is there a way to bring R and Rfree closer together, or is it related to the twinned data and is it something we have to live with? Best regards, Herman -Ursprüngliche Nachricht- Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von Miller, Mitchell D. Gesendet: Donnerstag, 20. Juni 2013 17:43 An: CCP4BB@JISCMAIL.AC.UK Betreff: Re: [ccp4bb] Twinning problem You are welcome. Let me also for the benefit of others who may search the archives in the future, let me correct two errors below - (typo and a miss-recollection). Specially, I was thinking that phenix.refine was now able to refine multiple twin laws, but according to Nat Echols on the phenix mailing list http://phenix-online.org/pipermail/phenixbb/2013-March/019538.html phenix.refine only handles 1 twin law at this time. (My typo was that and our second structure was 3nuz with twin fractions 0.38, 0.32, 0.16 and 0.14 -- not 2nuz). A useful search for deposited structures mentioning tetartohedral http://www.ebi.ac.uk/pdbe-srv/view/search?search_type=all_texttext=TETARTOHEDRALLY+OR+TETARTOHEDRAL Regards, Mitch -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of herman.schreu...@sanofi.com Sent: Thursday, June 20, 2013 8:04 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] AW: Twinning problem Dear Mitch (and Philip and Phil), It is clear that I should give refmac a go with the non-detwinned F's and just the TWIN command. Thank you for your suggestions, Herman -Ursprüngliche Nachricht- Von: Miller, Mitchell D. [mailto:mmil...@slac.stanford.edu] Gesendet: Donnerstag, 20. Juni 2013 16:18 An: Schreuder, Herman RD/DE Betreff: RE: Twinning problem Hi Herman, Have you considered the possibility of your crystals being tetartohedral twinned. That is more than one of the twin laws may apply to your crystals. E.g. in P32 it is possible to have tetartohedral twinning which would have 4 twin domains - (h,k,l), (k,h,-l), (-h,-k,l) and (-k,-h,-l). Perfect tetartohedral twinning of P3 would merge in P622 and each twin domain would have a faction of 0.25. We have had 2 cases like this (the first 2PRX was before there was support for this type of twinning except for in shelxl and we ended up with refined twin fractions of 0.38, 0.28, 0.19, 0.15 for the deposited crystal and a 2nd crystal that we did not deposit had twin fractions of 0.25, 0.27, 0.17, 0.31). The 2nd case we had was after support for twining (including tetartohedral twinning) was added to refmac (and I think phenix.refine can also handle this). For 2NUZ, it was P32 with refined twin fractions of 0.25, 0.27, 0.17, 0.31. Pietro Roversi wrote a review of tetartohedral twinning for the CCP4 proceedings issues of acta D http://dx.doi.org/10.1107/S0907444912006737 I would try refinement with refmac using the original (non-detwinned F's) with just the TWIN command to see if it ends up keeping twin fractions for all 3 operators (4 domains) -- especially with crystals 1 and 3 which appear to have the largest estimates of the other twin fractions. Regards, Mitch == Mitchell Miller, Ph.D. Joint Center for Structural Genomics Stanford Synchrotron Radiation Lightsource 2575 Sand Hill Rd -- SLAC MS 99 Menlo Park, CA 94025 Phone: 1-650-926-5036 FAX: 1-650-926-3292 -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of herman.schreu...@sanofi.com Sent: Thursday, June 20, 2013 6:47 AM To:
Re: [ccp4bb] AW: Twinning problem - almost solved.
At your resolution that seems to me a reasonable gap between R and Rfree? Eleanor On 21 Jun 2013, at 12:28, herman.schreu...@sanofi.com wrote: Dear Bulletin Board, After some headbanging (Refmac5 had helpfully created gap records for all insertions and deletions present in the structure), I got refmac5 running with the TWIN option. Refmac5 also found the k,h,-l domain and rejected the other possible domains because they were too small. The Rfactor's are now extremely good: ~14% and the Rfree's are for me acceptable: ~24%. Since I found the difference between R and Rfree somewhat large, I have been playing with the weighting. By using a weight of 0.01, I can bring the Rfactor up to 18%, but the Rfree stays about the same or even gets a little worse. My question: is there a way to bring R and Rfree closer together, or is it related to the twinned data and is it something we have to live with? Best regards, Herman -Ursprüngliche Nachricht- Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von Miller, Mitchell D. Gesendet: Donnerstag, 20. Juni 2013 17:43 An: CCP4BB@JISCMAIL.AC.UK Betreff: Re: [ccp4bb] Twinning problem You are welcome. Let me also for the benefit of others who may search the archives in the future, let me correct two errors below - (typo and a miss-recollection). Specially, I was thinking that phenix.refine was now able to refine multiple twin laws, but according to Nat Echols on the phenix mailing list http://phenix-online.org/pipermail/phenixbb/2013-March/019538.html phenix.refine only handles 1 twin law at this time. (My typo was that and our second structure was 3nuz with twin fractions 0.38, 0.32, 0.16 and 0.14 -- not 2nuz). A useful search for deposited structures mentioning tetartohedral http://www.ebi.ac.uk/pdbe-srv/view/search?search_type=all_texttext=TETARTOHEDRALLY+OR+TETARTOHEDRAL Regards, Mitch -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of herman.schreu...@sanofi.com Sent: Thursday, June 20, 2013 8:04 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] AW: Twinning problem Dear Mitch (and Philip and Phil), It is clear that I should give refmac a go with the non-detwinned F's and just the TWIN command. Thank you for your suggestions, Herman -Ursprüngliche Nachricht- Von: Miller, Mitchell D. [mailto:mmil...@slac.stanford.edu] Gesendet: Donnerstag, 20. Juni 2013 16:18 An: Schreuder, Herman RD/DE Betreff: RE: Twinning problem Hi Herman, Have you considered the possibility of your crystals being tetartohedral twinned. That is more than one of the twin laws may apply to your crystals. E.g. in P32 it is possible to have tetartohedral twinning which would have 4 twin domains - (h,k,l), (k,h,-l), (-h,-k,l) and (-k,-h,-l). Perfect tetartohedral twinning of P3 would merge in P622 and each twin domain would have a faction of 0.25. We have had 2 cases like this (the first 2PRX was before there was support for this type of twinning except for in shelxl and we ended up with refined twin fractions of 0.38, 0.28, 0.19, 0.15 for the deposited crystal and a 2nd crystal that we did not deposit had twin fractions of 0.25, 0.27, 0.17, 0.31). The 2nd case we had was after support for twining (including tetartohedral twinning) was added to refmac (and I think phenix.refine can also handle this). For 2NUZ, it was P32 with refined twin fractions of 0.25, 0.27, 0.17, 0.31. Pietro Roversi wrote a review of tetartohedral twinning for the CCP4 proceedings issues of acta D http://dx.doi.org/10.1107/S0907444912006737 I would try refinement with refmac using the original (non-detwinned F's) with just the TWIN command to see if it ends up keeping twin fractions for all 3 operators (4 domains) -- especially with crystals 1 and 3 which appear to have the largest estimates of the other twin fractions. Regards, Mitch == Mitchell Miller, Ph.D. Joint Center for Structural Genomics Stanford Synchrotron Radiation Lightsource 2575 Sand Hill Rd -- SLAC MS 99 Menlo Park, CA 94025 Phone: 1-650-926-5036 FAX: 1-650-926-3292 -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of herman.schreu...@sanofi.com Sent: Thursday, June 20, 2013 6:47 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Twinning problem Dear Bulletin Board, Prodded by pdb annotators, which are very hesitant to accept coordinate files when their Rfactor does not correspond with our Rfactor, I had a look again into some old data sets, which I suspect are twinned. Below are the results of some twinning tests with the Detwin program (top value: all reflections, lower value: reflections Nsig*obs (whatever that may mean). The space group is P32, the resolution is 2.3 - 2.6 Å and data are reasonable
Re: [ccp4bb] AW: Twinning problem - almost solved.
Hi Herman, Tighter restraints typically close the gap between R and R-free. This does not mean one should just tighten the restraints to satisfy one's own (or a referee's) idea of what the gap should be. I don't think there is a clear target of how large or small the gap should be. If you optimize the restraints to get the best (free) likelihood, you usually get a reasonable R gap without explicitly optimizing it. Cheers, Robbie -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Eleanor Dodson Sent: Friday, June 21, 2013 14:21 To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] AW: Twinning problem - almost solved. At your resolution that seems to me a reasonable gap between R and Rfree? Eleanor On 21 Jun 2013, at 12:28, herman.schreu...@sanofi.com wrote: Dear Bulletin Board, After some headbanging (Refmac5 had helpfully created gap records for all insertions and deletions present in the structure), I got refmac5 running with the TWIN option. Refmac5 also found the k,h,-l domain and rejected the other possible domains because they were too small. The Rfactor's are now extremely good: ~14% and the Rfree's are for me acceptable: ~24%. Since I found the difference between R and Rfree somewhat large, I have been playing with the weighting. By using a weight of 0.01, I can bring the Rfactor up to 18%, but the Rfree stays about the same or even gets a little worse. My question: is there a way to bring R and Rfree closer together, or is it related to the twinned data and is it something we have to live with? Best regards, Herman -Ursprüngliche Nachricht- Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von Miller, Mitchell D. Gesendet: Donnerstag, 20. Juni 2013 17:43 An: CCP4BB@JISCMAIL.AC.UK Betreff: Re: [ccp4bb] Twinning problem You are welcome. Let me also for the benefit of others who may search the archives in the future, let me correct two errors below - (typo and a miss- recollection). Specially, I was thinking that phenix.refine was now able to refine multiple twin laws, but according to Nat Echols on the phenix mailing list http://phenix-online.org/pipermail/phenixbb/2013-March/019538.html phenix.refine only handles 1 twin law at this time. (My typo was that and our second structure was 3nuz with twin fractions 0.38, 0.32, 0.16 and 0.14 -- not 2nuz). A useful search for deposited structures mentioning tetartohedral http://www.ebi.ac.uk/pdbe- srv/view/search?search_type=all_texttext=TETARTOHEDRALLY+OR+TETAR TOHEDRAL Regards, Mitch -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of herman.schreu...@sanofi.com Sent: Thursday, June 20, 2013 8:04 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] AW: Twinning problem Dear Mitch (and Philip and Phil), It is clear that I should give refmac a go with the non-detwinned F's and just the TWIN command. Thank you for your suggestions, Herman -Ursprüngliche Nachricht- Von: Miller, Mitchell D. [mailto:mmil...@slac.stanford.edu] Gesendet: Donnerstag, 20. Juni 2013 16:18 An: Schreuder, Herman RD/DE Betreff: RE: Twinning problem Hi Herman, Have you considered the possibility of your crystals being tetartohedral twinned. That is more than one of the twin laws may apply to your crystals. E.g. in P32 it is possible to have tetartohedral twinning which would have 4 twin domains - (h,k,l), (k,h,-l), (-h,-k,l) and (-k,-h,-l). Perfect tetartohedral twinning of P3 would merge in P622 and each twin domain would have a faction of 0.25. We have had 2 cases like this (the first 2PRX was before there was support for this type of twinning except for in shelxl and we ended up with refined twin fractions of 0.38, 0.28, 0.19, 0.15 for the deposited crystal and a 2nd crystal that we did not deposit had twin fractions of 0.25, 0.27, 0.17, 0.31). The 2nd case we had was after support for twining (including tetartohedral twinning) was added to refmac (and I think phenix.refine can also handle this). For 2NUZ, it was P32 with refined twin fractions of 0.25, 0.27, 0.17, 0.31. Pietro Roversi wrote a review of tetartohedral twinning for the CCP4 proceedings issues of acta D http://dx.doi.org/10.1107/S0907444912006737 I would try refinement with refmac using the original (non-detwinned F's) with just the TWIN command to see if it ends up keeping twin fractions for all 3 operators (4 domains) -- especially with crystals 1 and 3 which appear to have the largest estimates of the other twin fractions. Regards, Mitch == Mitchell Miller, Ph.D. Joint Center for Structural Genomics Stanford Synchrotron Radiation Lightsource 2575 Sand Hill Rd -- SLAC MS 99 Menlo Park, CA 94025 Phone: 1-650-926-5036 FAX: 1-650-926-3292 -Original Message
[ccp4bb] AW: [ccp4bb] AW: Twinning problem - almost solved.
Hi Robbie, That is what I tried. The Rfactor got a lot worse (14%-18%) and the Rfree got a little worse (by 0.1-0.2%). My feeling is that that is not the right approach. Roger Rowlett suggested to give PDB_REDO a try. Maybe you have some instructions available how to get a local version? Best, Herman -Ursprüngliche Nachricht- Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von Robbie Joosten Gesendet: Freitag, 21. Juni 2013 16:21 An: CCP4BB@JISCMAIL.AC.UK Betreff: Re: [ccp4bb] AW: Twinning problem - almost solved. Hi Herman, Tighter restraints typically close the gap between R and R-free. This does not mean one should just tighten the restraints to satisfy one's own (or a referee's) idea of what the gap should be. I don't think there is a clear target of how large or small the gap should be. If you optimize the restraints to get the best (free) likelihood, you usually get a reasonable R gap without explicitly optimizing it. Cheers, Robbie -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Eleanor Dodson Sent: Friday, June 21, 2013 14:21 To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] AW: Twinning problem - almost solved. At your resolution that seems to me a reasonable gap between R and Rfree? Eleanor On 21 Jun 2013, at 12:28, herman.schreu...@sanofi.com wrote: Dear Bulletin Board, After some headbanging (Refmac5 had helpfully created gap records for all insertions and deletions present in the structure), I got refmac5 running with the TWIN option. Refmac5 also found the k,h,-l domain and rejected the other possible domains because they were too small. The Rfactor's are now extremely good: ~14% and the Rfree's are for me acceptable: ~24%. Since I found the difference between R and Rfree somewhat large, I have been playing with the weighting. By using a weight of 0.01, I can bring the Rfactor up to 18%, but the Rfree stays about the same or even gets a little worse. My question: is there a way to bring R and Rfree closer together, or is it related to the twinned data and is it something we have to live with? Best regards, Herman -Ursprüngliche Nachricht- Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von Miller, Mitchell D. Gesendet: Donnerstag, 20. Juni 2013 17:43 An: CCP4BB@JISCMAIL.AC.UK Betreff: Re: [ccp4bb] Twinning problem You are welcome. Let me also for the benefit of others who may search the archives in the future, let me correct two errors below - (typo and a miss- recollection). Specially, I was thinking that phenix.refine was now able to refine multiple twin laws, but according to Nat Echols on the phenix mailing list http://phenix-online.org/pipermail/phenixbb/2013-March/019538.html phenix.refine only handles 1 twin law at this time. (My typo was that and our second structure was 3nuz with twin fractions 0.38, 0.32, 0.16 and 0.14 -- not 2nuz). A useful search for deposited structures mentioning tetartohedral http://www.ebi.ac.uk/pdbe- srv/view/search?search_type=all_texttext=TETARTOHEDRALLY+OR+TETAR TOHEDRAL Regards, Mitch -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of herman.schreu...@sanofi.com Sent: Thursday, June 20, 2013 8:04 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] AW: Twinning problem Dear Mitch (and Philip and Phil), It is clear that I should give refmac a go with the non-detwinned F's and just the TWIN command. Thank you for your suggestions, Herman -Ursprüngliche Nachricht- Von: Miller, Mitchell D. [mailto:mmil...@slac.stanford.edu] Gesendet: Donnerstag, 20. Juni 2013 16:18 An: Schreuder, Herman RD/DE Betreff: RE: Twinning problem Hi Herman, Have you considered the possibility of your crystals being tetartohedral twinned. That is more than one of the twin laws may apply to your crystals. E.g. in P32 it is possible to have tetartohedral twinning which would have 4 twin domains - (h,k,l), (k,h,-l), (-h,-k,l) and (-k,-h,-l). Perfect tetartohedral twinning of P3 would merge in P622 and each twin domain would have a faction of 0.25. We have had 2 cases like this (the first 2PRX was before there was support for this type of twinning except for in shelxl and we ended up with refined twin fractions of 0.38, 0.28, 0.19, 0.15 for the deposited crystal and a 2nd crystal that we did not deposit had twin fractions of 0.25, 0.27, 0.17, 0.31). The 2nd case we had was after support for twining (including tetartohedral twinning) was added to refmac (and I think phenix.refine can also handle this). For 2NUZ, it was P32 with refined twin fractions of 0.25, 0.27, 0.17, 0.31. Pietro Roversi wrote a review of tetartohedral twinning for the CCP4 proceedings issues of acta D http://dx.doi.org/10.1107
Re: [ccp4bb] AW: [ccp4bb] AW: Twinning problem - almost solved.
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear Herman, a large gap between R and Rfree might indicate a horrible geometry of your structure, especially if R increased by lowering the matrix weight in refmac. Or, to put it the other way round: it is easy to achieve a low R-value by screwing up the geometry of your model. Did you run the PDB file through molprobity? My guess is with the R=14% model you get a very red chart... Best, Tim On 06/21/2013 04:45 PM, herman.schreu...@sanofi.com wrote: Hi Robbie, That is what I tried. The Rfactor got a lot worse (14%-18%) and the Rfree got a little worse (by 0.1-0.2%). My feeling is that that is not the right approach. Roger Rowlett suggested to give PDB_REDO a try. Maybe you have some instructions available how to get a local version? Best, Herman -Ursprüngliche Nachricht- Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von Robbie Joosten Gesendet: Freitag, 21. Juni 2013 16:21 An: CCP4BB@JISCMAIL.AC.UK Betreff: Re: [ccp4bb] AW: Twinning problem - almost solved. Hi Herman, Tighter restraints typically close the gap between R and R-free. This does not mean one should just tighten the restraints to satisfy one's own (or a referee's) idea of what the gap should be. I don't think there is a clear target of how large or small the gap should be. If you optimize the restraints to get the best (free) likelihood, you usually get a reasonable R gap without explicitly optimizing it. Cheers, Robbie -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Eleanor Dodson Sent: Friday, June 21, 2013 14:21 To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] AW: Twinning problem - almost solved. At your resolution that seems to me a reasonable gap between R and Rfree? Eleanor On 21 Jun 2013, at 12:28, herman.schreu...@sanofi.com wrote: Dear Bulletin Board, After some headbanging (Refmac5 had helpfully created gap records for all insertions and deletions present in the structure), I got refmac5 running with the TWIN option. Refmac5 also found the k,h,-l domain and rejected the other possible domains because they were too small. The Rfactor's are now extremely good: ~14% and the Rfree's are for me acceptable: ~24%. Since I found the difference between R and Rfree somewhat large, I have been playing with the weighting. By using a weight of 0.01, I can bring the Rfactor up to 18%, but the Rfree stays about the same or even gets a little worse. My question: is there a way to bring R and Rfree closer together, or is it related to the twinned data and is it something we have to live with? Best regards, Herman -Ursprüngliche Nachricht- Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von Miller, Mitchell D. Gesendet: Donnerstag, 20. Juni 2013 17:43 An: CCP4BB@JISCMAIL.AC.UK Betreff: Re: [ccp4bb] Twinning problem You are welcome. Let me also for the benefit of others who may search the archives in the future, let me correct two errors below - (typo and a miss- recollection). Specially, I was thinking that phenix.refine was now able to refine multiple twin laws, but according to Nat Echols on the phenix mailing list http://phenix-online.org/pipermail/phenixbb/2013-March/019538.html phenix.refine only handles 1 twin law at this time. (My typo was that and our second structure was 3nuz with twin fractions 0.38, 0.32, 0.16 and 0.14 -- not 2nuz). A useful search for deposited structures mentioning tetartohedral http://www.ebi.ac.uk/pdbe- srv/view/search?search_type=all_texttext=TETARTOHEDRALLY+OR+TETAR TOHEDRAL Regards, Mitch -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of herman.schreu...@sanofi.com Sent: Thursday, June 20, 2013 8:04 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] AW: Twinning problem Dear Mitch (and Philip and Phil), It is clear that I should give refmac a go with the non-detwinned F's and just the TWIN command. Thank you for your suggestions, Herman -Ursprüngliche Nachricht- Von: Miller, Mitchell D. [mailto:mmil...@slac.stanford.edu] Gesendet: Donnerstag, 20. Juni 2013 16:18 An: Schreuder, Herman RD/DE Betreff: RE: Twinning problem Hi Herman, Have you considered the possibility of your crystals being tetartohedral twinned. That is more than one of the twin laws may apply to your crystals. E.g. in P32 it is possible to have tetartohedral twinning which would have 4 twin domains - (h,k,l), (k,h,-l), (-h,-k,l) and (-k,-h,-l). Perfect tetartohedral twinning of P3 would merge in P622 and each twin domain would have a faction of 0.25. We have had 2 cases like this (the first 2PRX was before there was support for this type of twinning except for in shelxl and we ended up with refined twin fractions of 0.38, 0.28, 0.19, 0.15 for the deposited crystal
[ccp4bb] AW: [ccp4bb] AW: [ccp4bb] AW: Twinning problem - almost solved.
Dear Tim, I normally do not use Refmac, so I have no idea what to expect and what would be a good weight. I will do the molprobity test, but I do not expect major problems. This is a MR structure with a high resolution search model with 100% sequence identity. A few amino acids may have problems, but the overall structure should be ok. E.g. Refmac lists an RMSD bonds of 0.008 Å and an RMDS bond angles of 1.3°. Anyway, if the structure turns out to be really bad, I will get punished by the PDB annotators with lots of REMARK 500 records! Best, Herman -Ursprüngliche Nachricht- Von: Tim Gruene [mailto:t...@shelx.uni-ac.gwdg.de] Gesendet: Freitag, 21. Juni 2013 17:30 An: Schreuder, Herman RD/DE Cc: CCP4BB@JISCMAIL.AC.UK Betreff: Re: [ccp4bb] AW: [ccp4bb] AW: Twinning problem - almost solved. -BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear Herman, a large gap between R and Rfree might indicate a horrible geometry of your structure, especially if R increased by lowering the matrix weight in refmac. Or, to put it the other way round: it is easy to achieve a low R-value by screwing up the geometry of your model. Did you run the PDB file through molprobity? My guess is with the R=14% model you get a very red chart... Best, Tim On 06/21/2013 04:45 PM, herman.schreu...@sanofi.com wrote: Hi Robbie, That is what I tried. The Rfactor got a lot worse (14%-18%) and the Rfree got a little worse (by 0.1-0.2%). My feeling is that that is not the right approach. Roger Rowlett suggested to give PDB_REDO a try. Maybe you have some instructions available how to get a local version? Best, Herman -Ursprüngliche Nachricht- Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von Robbie Joosten Gesendet: Freitag, 21. Juni 2013 16:21 An: CCP4BB@JISCMAIL.AC.UK Betreff: Re: [ccp4bb] AW: Twinning problem - almost solved. Hi Herman, Tighter restraints typically close the gap between R and R-free. This does not mean one should just tighten the restraints to satisfy one's own (or a referee's) idea of what the gap should be. I don't think there is a clear target of how large or small the gap should be. If you optimize the restraints to get the best (free) likelihood, you usually get a reasonable R gap without explicitly optimizing it. Cheers, Robbie -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Eleanor Dodson Sent: Friday, June 21, 2013 14:21 To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] AW: Twinning problem - almost solved. At your resolution that seems to me a reasonable gap between R and Rfree? Eleanor On 21 Jun 2013, at 12:28, herman.schreu...@sanofi.com wrote: Dear Bulletin Board, After some headbanging (Refmac5 had helpfully created gap records for all insertions and deletions present in the structure), I got refmac5 running with the TWIN option. Refmac5 also found the k,h,-l domain and rejected the other possible domains because they were too small. The Rfactor's are now extremely good: ~14% and the Rfree's are for me acceptable: ~24%. Since I found the difference between R and Rfree somewhat large, I have been playing with the weighting. By using a weight of 0.01, I can bring the Rfactor up to 18%, but the Rfree stays about the same or even gets a little worse. My question: is there a way to bring R and Rfree closer together, or is it related to the twinned data and is it something we have to live with? Best regards, Herman -Ursprüngliche Nachricht- Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von Miller, Mitchell D. Gesendet: Donnerstag, 20. Juni 2013 17:43 An: CCP4BB@JISCMAIL.AC.UK Betreff: Re: [ccp4bb] Twinning problem You are welcome. Let me also for the benefit of others who may search the archives in the future, let me correct two errors below - (typo and a miss- recollection). Specially, I was thinking that phenix.refine was now able to refine multiple twin laws, but according to Nat Echols on the phenix mailing list http://phenix-online.org/pipermail/phenixbb/2013-March/019538.html phenix.refine only handles 1 twin law at this time. (My typo was that and our second structure was 3nuz with twin fractions 0.38, 0.32, 0.16 and 0.14 -- not 2nuz). A useful search for deposited structures mentioning tetartohedral http://www.ebi.ac.uk/pdbe- srv/view/search?search_type=all_texttext=TETARTOHEDRALLY+OR+TETAR TOHEDRAL Regards, Mitch -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of herman.schreu...@sanofi.com Sent: Thursday, June 20, 2013 8:04 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] AW: Twinning problem Dear Mitch (and Philip and Phil), It is clear that I should give refmac a go with the non-detwinned F's and just the TWIN command. Thank you for your suggestions, Herman
