[ccp4bb] AW: [ccp4bb] XDS, refinement not converge
Hi Charles, This message usually means that refinement of cell parameters and distance blows up, e.g. huge cell dimensions and a huge distance. That is probably the reason behind the suggested method to fix the distance in IDXREF. However, I suspect that your error occurred in the INTEGRATE stage. I checked the XDS manual, and there is also a “REFINE(INTEGRATE)=” keyword. If your error occurred in the INTEGRATE stage, I would try this keyword with the same parameters as for the “REFINE(IDXREF)=” keyword. By the way, so far I got away with this problem by using a different (better) crystal, but next time I encounter this problem, I will try it as well! Good luck and let me know if it worked, Herman Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von CPMAS Chen Gesendet: Donnerstag, 18. September 2014 22:44 An: CCP4BB@JISCMAIL.AC.UK Betreff: [ccp4bb] XDS, refinement not converge Hi, there, I saw some warning info during XDS data processing, !!! WARNING !!! REFINEMENT DID NOT CONVERGE LAST CORRECTION SHIFT WAS 6.1E-02 (should be 1.0E-03) I have tries the suggested method, REFINE(IDXREF)=CELL BEAM ORIENTATION AXIS ! DISTANCE This warning is still there. Are there other options I can try to make this converge? Thanks! Charles -- *** Charles Chen Research Associate University of Pittsburgh School of Medicine Department of Anesthesiology **
[ccp4bb] Opportunities at Diamond's XFEL Hub
Dear All, I would like to draw your attention to two job vacancies at Diamond Light Source to develop the XFEL Hub (http://www.diamond.ac.uk/Science/Integrated-facilities/UK-XFEL-Hub.html) based at Diamond. Software Scientist /Senior Software Scientist for diffraction methods http://www.diamond.ac.uk/Careers/Vacancies/All/DIA0960_TH.html Senior scientist to lead XFEL and Synchrotron Sample environment and delivery developments http://www.diamond.ac.uk/Careers/Vacancies/All/DIA0961_TH.html Best regards, Gwyndaf -- This e-mail and any attachments may contain confidential, copyright and or privileged material, and are for the use of the intended addressee only. If you are not the intended addressee or an authorised recipient of the addressee please notify us of receipt by returning the e-mail and do not use, copy, retain, distribute or disclose the information in or attached to the e-mail. Any opinions expressed within this e-mail are those of the individual and not necessarily of Diamond Light Source Ltd. Diamond Light Source Ltd. cannot guarantee that this e-mail or any attachments are free from viruses and we cannot accept liability for any damage which you may sustain as a result of software viruses which may be transmitted in or with the message. Diamond Light Source Limited (company no. 4375679). Registered in England and Wales with its registered office at Diamond House, Harwell Science and Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom
[ccp4bb] Phaser MR problem
Dear CCP4 members, Recently I have collected native data at 3.3 A resolution. The structure of the protein should have two domains. The structure of c terminal domain from homologous (30 seq similarity) is known. I took n terminal domain from another homologous protein. I ran the phaser using these two ensembles and got the following solutions. # [No title given] SOLU SET RFZ=3.9 TFZ=14.3 PAK=4 LLG=144 TFZ==10.5 RFZ=2.4 TFZ=11.9 PAK=9 LLG=259 TFZ==7.0 RFZ=4.0 TFZ=4.5 PAK=24 LLG=207 TFZ==7.4 SOLU SPAC I 41 3 2 SOLU 6DIM ENSE ensemble1 EULER 43.364 14.638 271.356 FRAC 0.81509 0.22245 0.92422 BFAC -7.23070 SOLU 6DIM ENSE ensemble2 EULER 173.495 55.758 234.557 FRAC 1.25797 -0.71934 0.10135 BFAC 1.81823 SOLU 6DIM ENSE ensemble2 EULER 351.235 68.606 254.802 FRAC 0.64931 0.81795 0.27592 BFAC 5.82534 SOLU ENSE ensemble1 VRMS 1.157 SOLU ENSE ensemble2 VRMS 1.540 SOLU SET RFZ=3.9 TFZ=14.3 PAK=4 LLG=144 TFZ==10.5 RFZ=2.4 TFZ=11.9 PAK=9 LLG=259 TFZ==7.0 RFZ=2.7 TFZ=4.7 PAK=19 LLG=202 SOLU SPAC I 41 3 2 SOLU 6DIM ENSE ensemble1 EULER 43.364 14.638 271.356 FRAC 0.81509 0.22245 0.92422 BFAC -7.23070 SOLU 6DIM ENSE ensemble2 EULER 173.495 55.758 234.557 FRAC 1.25797 -0.71934 0.10135 BFAC 1.81823 SOLU 6DIM ENSE ensemble2 EULER 41.452 118.850 315.630 FRAC 0.61025 0.05816 1.60902 BFAC 5.47988 SOLU ENSE ensemble1 VRMS 1.157 SOLU ENSE ensemble2 VRMS 1.540 The TFZ score 14.3 suggests a solution. Then I did refinement using Ploy Ala phaser model. The R values are 0.590/0.62. I use the map to build the model in Buccaneer but it did not build anything. Is the pahser solution correct? Why are the R values so high despite the good TFZ score? Any suggestions are greatly appreciated. Thank you Veerendra Note: This message may contain confidential information. If this Email/Fax has been sent to you by mistake, please notify the sender and delete it immediately. Thank you.
[ccp4bb] AW: Phaser MR problem
Dear Veerendra, Based on the very limited information you give, it is hard to figure out what really is the problem. However, here are some comments: -Molecules in the asymmetric unit: If e.g. there are two molecules in the asu and you searched only for one, you might get good phaser statistics and bad R-factors. In the phaser log file there is an estimate how many molecules phaser would expect in the asu. -Correct space group: Depending on your phaser job, phaser might decide that the true space group is different from the space group used during data processing. If you did not change the space group of your input mtz to the one found by phaser, refinement might have been done with the wrong space group, resulting in catastrophic Rfactors. -Other problems like twinning. Good luck! Herman -Ursprüngliche Nachricht- Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von Veerendra KUMAR (IMCB) Gesendet: Freitag, 19. September 2014 11:34 An: CCP4BB@JISCMAIL.AC.UK Betreff: [ccp4bb] Phaser MR problem Dear CCP4 members, Recently I have collected native data at 3.3 A resolution. The structure of the protein should have two domains. The structure of c terminal domain from homologous (30 seq similarity) is known. I took n terminal domain from another homologous protein. I ran the phaser using these two ensembles and got the following solutions. # [No title given] SOLU SET RFZ=3.9 TFZ=14.3 PAK=4 LLG=144 TFZ==10.5 RFZ=2.4 TFZ=11.9 PAK=9 LLG=259 TFZ==7.0 RFZ=4.0 TFZ=4.5 PAK=24 LLG=207 TFZ==7.4 SOLU SPAC I 41 3 2 SOLU 6DIM ENSE ensemble1 EULER 43.364 14.638 271.356 FRAC 0.81509 0.22245 0.92422 BFAC -7.23070 SOLU 6DIM ENSE ensemble2 EULER 173.495 55.758 234.557 FRAC 1.25797 -0.71934 0.10135 BFAC 1.81823 SOLU 6DIM ENSE ensemble2 EULER 351.235 68.606 254.802 FRAC 0.64931 0.81795 0.27592 BFAC 5.82534 SOLU ENSE ensemble1 VRMS 1.157 SOLU ENSE ensemble2 VRMS 1.540 SOLU SET RFZ=3.9 TFZ=14.3 PAK=4 LLG=144 TFZ==10.5 RFZ=2.4 TFZ=11.9 PAK=9 LLG=259 TFZ==7.0 RFZ=2.7 TFZ=4.7 PAK=19 LLG=202 SOLU SPAC I 41 3 2 SOLU 6DIM ENSE ensemble1 EULER 43.364 14.638 271.356 FRAC 0.81509 0.22245 0.92422 BFAC -7.23070 SOLU 6DIM ENSE ensemble2 EULER 173.495 55.758 234.557 FRAC 1.25797 -0.71934 0.10135 BFAC 1.81823 SOLU 6DIM ENSE ensemble2 EULER 41.452 118.850 315.630 FRAC 0.61025 0.05816 1.60902 BFAC 5.47988 SOLU ENSE ensemble1 VRMS 1.157 SOLU ENSE ensemble2 VRMS 1.540 The TFZ score 14.3 suggests a solution. Then I did refinement using Ploy Ala phaser model. The R values are 0.590/0.62. I use the map to build the model in Buccaneer but it did not build anything. Is the pahser solution correct? Why are the R values so high despite the good TFZ score? Any suggestions are greatly appreciated. Thank you Veerendra Note: This message may contain confidential information. If this Email/Fax has been sent to you by mistake, please notify the sender and delete it immediately. Thank you.
[ccp4bb] Inhibitor screen
Dear All, Sorry for off topic e-mail. I have two structures of the same protein one in apo form and other in substrate bound form. The substrate bound structure shows 20 degree movement with respect to one domain. I want to screen the inhibitor for that. Can anyone tell me if any company makes a mixture of inhibitors (inhibitor cocktails) so that I can co-crystallize my protein with it. -- WITH REGARDS Rohit Kumar Singh Lab. no. 430, P.I. Dr. S. Gourinath, School of Life Sciences, Jawaharlal Nehru University New Delhi -110067
[ccp4bb] software or server to validate ligand density
Dear All, I have collected a diffraction dataset from a crystal soaked in a solution containing the ligand of interest. After refining a few cycles, I can see some density in the active site pocket, but not so clear to model the ligand unambiguously. Is any tool available to validate whether the ligand is actually there or not ? The Twilight server appears to be for PDB files that have already been deposited. thanks and regards, Ansuman Biswas, dept. of Physics, Indian Institute of science
Re: [ccp4bb] software or server to validate ligand density
hmm - crystallographically difficult. The usual way is to make a dictionary file from the chemical information about the ligand. try to build something obeying the chemical restraints into the density - refine those coordinates and validate them. Eleanor On 19 September 2014 22:06, ansuman biswas bubai_...@yahoo.co.in wrote: Dear All, I have collected a diffraction dataset from a crystal soaked in a solution containing the ligand of interest. After refining a few cycles, I can see some density in the active site pocket, but not so clear to model the ligand unambiguously. Is any tool available to validate whether the ligand is actually there or not ? The Twilight server appears to be for PDB files that have already been deposited. thanks and regards, Ansuman Biswas, dept. of Physics, Indian Institute of science
[ccp4bb] calculation of active site area
Dear all Please tell me the names of good servers / tools which calculate the size and surface area of the active site pocket of a protein.. -- Regards Faisal School of Life Sciences JNU
