Re: [ccp4bb] relative domain motion calculation...
Hi Mintu You can use Chimera to calculate rotation angel. http://www.cgl.ucsf.edu/chimera/videodoc/AlignDomains/ Veerendra On 21/4/15 3:39 PM, Mintu Chandra mi...@iiserb.ac.in wrote: Dear All, I am working with a protein containing tandem domains, connected with 3-4 residue linker. I want to calculate the relative motion/orientation of one domain with respect to the hinge region as well as with respect to the other domain. Both the domains have very less seq. identity (20%). Please suggest some web server to calculate the same. Thanks, Mintu 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] 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.
