Re: [ccp4bb] an ambiguous result of molecular replacement
Hi Leonid, Thank you for your valuable suggestion. It is exactly the case. When I tried P21, it works well. The solution is now very clear. Best, Zhiyi On 3/31/12, Leonid Sazanov saza...@mrc-mbu.cam.ac.uk wrote: Hi, we had the same case in apparent C2221, with many similarly shifted Phaser solutions with high scores. The reason was that crystals were actually nearly perfectly twinned in P21, so indexing and processing indicated C2221. Once data was re-processed in P21, Phaser could easily find two distinct solutions - one for each of twin domains, with LLG scores roughly reflecting twin ratios. Similar case is discussed in detail here: http://www.ncbi.nlm.nih.gov/pubmed/15039553
Re: [ccp4bb] an ambiguous result of molecular replacement
When this happens there is usually a serious problem with the data. Have you checked the truncate output for a non-cryst translation vector? It would look as though you have something which is generating a pseudo translation along x of ~ 0.2 Look at the hklview pictures of your data and see if the 0kl 1kl 2kl etc show something funny ? Do the plots indicate twinning? In that case you may have lower symmetry.. Hard to say without seeing data but I think your problem probably pre-dates the MR search! Eleanor On Mar 30 2012, Zhiyi Wei wrote: Dear all, I got a weird solution from Phaser. The background is that, space group C2221, resolution ~4A, in complex with a peptide, and having a apo form structure as the search model. Phaser gave two rotation function peaks with Z 7. But when searching translation function peaks, Phaser gave many high Z score peaks listed below rather than a single solution. These peaks share same fraction YZ but with different X. Most of them pasted the packing validation. The when searching the second copy, each solutions have a single translation peak that showed very high Z score ( 20). I check some of these solutions in Coot, and found that the two copies of each solution has the same relative orientation and each solution shifts several angerstroms in X axis. I also tried C222 and did not get better result than C2221. Any comments or suggestion? Thanks a lot! Best, Zhiyi # (#) Frac X Frac Y Frac Z LLG Z-score Split #Groupraw/top 1 1 0.155 0.436 0.287 +219.80 11.17 0 1 272.58/272.58 2 2 0.350 0.436 0.287 +211.92 10.53 24 1 267.42/267.42 3 3 0.542 0.436 0.287 +211.31 10.48 44 1 266.05/266.05 4 5 0.579 0.436 0.287 +209.66 10.34 40 2 260.14/260.14 5 12 0.267 0.436 0.287 +209.11 10.30 14 2 256.53/256.53 6 4 0.224 0.435 0.288 +208.41 10.24 8 2 261.39/261.39 7 11 0.485 0.436 0.287 +208.28 10.23 40 2 256.95/257.13 8 7 0.191 0.435 0.287 +205.18 9.97 4 2 258.95/258.95 9 15 0.400 0.436 0.287 +201.90 9.70 30 2 254.20/254.20 10 9 0.297 0.437 0.287 +201.79 9.69 17 1 257.75/257.75 11 16 0.449 0.436 0.287 +198.77 9.45 36 1 252.80/252.80 12 17 0.129 0.437 0.287 +195.66 9.19 3 1 252.41/252.41 13 20 0.377 0.436 0.287 +194.95 9.13 27 1 246.37/246.37 14 21 0.422 0.436 0.287 +190.72 8.78 33 1 245.42/245.42 15 19 0.521 0.437 0.287 +190.22 8.74 45 1 246.46/246.46 -- Professor Eleanor Dodson YSNL, Dept of Chemistry University of York Heslington YO10 5YW tel: 00 44 1904 328259 Fax: 00 44 1904 328266
Re: [ccp4bb] an ambiguous result of molecular replacement
Hi, Do you mean that the second molecule is always overlapped with the first, by saying that it shifts several Angstrom along the x axis? If there were a larger translation, then what you're seeing would be consistent with translational NCS (tNCS), but the translation should be large enough to shift the second copy off the first! If you did have tNCS, then the version of Phaser currently distributed with CCP4 would have trouble dealing with it. We have a new version that accounts well for the statistical effects of tNCS. It's available in current releases of Phenix and will soon be available with the upcoming CCP4 release. Alternatively, the version of Molrep in the current CCP4 has its own treatment for tNCS. However, if it's really a small vector, then it's more likely that something else is going on. You could have some kind of lattice translocation disorder. The crystal could be twinned so the real symmetry could be lower, or even some combination of the above. Good luck sorting it out! Best wishes, Randy Read On 30 Mar 2012, at 05:22, Zhiyi Wei wrote: Dear all, I got a weird solution from Phaser. The background is that, space group C2221, resolution ~4A, in complex with a peptide, and having a apo form structure as the search model. Phaser gave two rotation function peaks with Z 7. But when searching translation function peaks, Phaser gave many high Z score peaks listed below rather than a single solution. These peaks share same fraction YZ but with different X. Most of them pasted the packing validation. The when searching the second copy, each solutions have a single translation peak that showed very high Z score ( 20). I check some of these solutions in Coot, and found that the two copies of each solution has the same relative orientation and each solution shifts several angerstroms in X axis. I also tried C222 and did not get better result than C2221. Any comments or suggestion? Thanks a lot! Best, Zhiyi # (#) Frac X Frac Y Frac Z LLG Z-score Split #Groupraw/top 1 1 0.155 0.436 0.287 +219.80 11.17 0 1 272.58/272.58 2 2 0.350 0.436 0.287 +211.92 10.5324 1 267.42/267.42 3 3 0.542 0.436 0.287 +211.31 10.4844 1 266.05/266.05 4 5 0.579 0.436 0.287 +209.66 10.3440 2 260.14/260.14 5 12 0.267 0.436 0.287 +209.11 10.3014 2 256.53/256.53 6 4 0.224 0.435 0.288 +208.41 10.24 8 2 261.39/261.39 7 11 0.485 0.436 0.287 +208.28 10.2340 2 256.95/257.13 8 7 0.191 0.435 0.287 +205.189.97 4 2 258.95/258.95 9 15 0.400 0.436 0.287 +201.909.7030 2 254.20/254.20 109 0.297 0.437 0.287 +201.799.6917 1 257.75/257.75 1116 0.449 0.436 0.287 +198.779.4536 1 252.80/252.80 1217 0.129 0.437 0.287 +195.669.19 3 1 252.41/252.41 1320 0.377 0.436 0.287 +194.959.1327 1 246.37/246.37 1421 0.422 0.436 0.287 +190.728.7833 1 245.42/245.42 1519 0.521 0.437 0.287 +190.228.7445 1 246.46/246.46 -- Randy J. Read Department of Haematology, University of Cambridge Cambridge Institute for Medical Research Tel: + 44 1223 336500 Wellcome Trust/MRC Building Fax: + 44 1223 336827 Hills RoadE-mail: rj...@cam.ac.uk Cambridge CB2 0XY, U.K. www-structmed.cimr.cam.ac.uk
Re: [ccp4bb] an ambiguous result of molecular replacement
Hi, we had the same case in apparent C2221, with many similarly shifted Phaser solutions with high scores. The reason was that crystals were actually nearly perfectly twinned in P21, so indexing and processing indicated C2221. Once data was re-processed in P21, Phaser could easily find two distinct solutions - one for each of twin domains, with LLG scores roughly reflecting twin ratios. Similar case is discussed in detail here: http://www.ncbi.nlm.nih.gov/pubmed/15039553
[ccp4bb] an ambiguous result of molecular replacement
Dear all, I got a weird solution from Phaser. The background is that, space group C2221, resolution ~4A, in complex with a peptide, and having a apo form structure as the search model. Phaser gave two rotation function peaks with Z 7. But when searching translation function peaks, Phaser gave many high Z score peaks listed below rather than a single solution. These peaks share same fraction YZ but with different X. Most of them pasted the packing validation. The when searching the second copy, each solutions have a single translation peak that showed very high Z score ( 20). I check some of these solutions in Coot, and found that the two copies of each solution has the same relative orientation and each solution shifts several angerstroms in X axis. I also tried C222 and did not get better result than C2221. Any comments or suggestion? Thanks a lot! Best, Zhiyi # (#) Frac X Frac Y Frac Z LLG Z-score Split #Groupraw/top 1 1 0.155 0.436 0.287 +219.80 11.17 0 1 272.58/272.58 2 2 0.350 0.436 0.287 +211.92 10.5324 1 267.42/267.42 3 3 0.542 0.436 0.287 +211.31 10.4844 1 266.05/266.05 4 5 0.579 0.436 0.287 +209.66 10.3440 2 260.14/260.14 5 12 0.267 0.436 0.287 +209.11 10.3014 2 256.53/256.53 6 4 0.224 0.435 0.288 +208.41 10.24 8 2 261.39/261.39 7 11 0.485 0.436 0.287 +208.28 10.2340 2 256.95/257.13 8 7 0.191 0.435 0.287 +205.189.97 4 2 258.95/258.95 9 15 0.400 0.436 0.287 +201.909.7030 2 254.20/254.20 109 0.297 0.437 0.287 +201.799.6917 1 257.75/257.75 1116 0.449 0.436 0.287 +198.779.4536 1 252.80/252.80 1217 0.129 0.437 0.287 +195.669.19 3 1 252.41/252.41 1320 0.377 0.436 0.287 +194.959.1327 1 246.37/246.37 1421 0.422 0.436 0.287 +190.728.7833 1 245.42/245.42 1519 0.521 0.437 0.287 +190.228.7445 1 246.46/246.46
