Re: [ccp4bb] Angle between monomer of a dimer
the angle of rotation is kappa = 160.045deg in this case On 24 Aug 2012, at 04:33, Appu kumar wrote: Sir one more help plz i have the following matrix which one shall i use to calculate the angle. INFO:: coordinates transformed by orthonal matrix: | -0.6927, -0.7191,0.0564| | -0.4828,0.5204,0.7043| | -0.5358,0.4606, -0.7076| ( 76.04,-10.19, 28.64) Rotation - polar (omega,phi,kappa) 69.7525 112.368 160.045 Rotation - euler (alpha,beta,gamma) 85.4221 135.041 40.6865 Translation - Angstroms76.037 -10.1858 28.6373 If you won't mind please tell me how to calculathe angle from this. I am new to this type of problem. Thank you Appu On 24 August 2012 08:52, Appu kumar appu.kum...@gmail.com wrote: Thank you Sir for your kind eply. I will follow your instruction to calculate the angle. On 24 August 2012 00:38, Nikolina Sekulic nikolina.seku...@gmail.com wrote: Dear Appu, I had similar issue once. You can use Coot to overlay two structures and get the rotation matrix a1 a2 a3 b1 b2 b3 c1 c2 c3 from here you can calculate cosine of an angle using formula (a1+b2+c3-1)/2 Good luck, Nikolina Sekulic, PhD postdoctoral fellow University of Pennsylvania On Thu, Aug 23, 2012 at 2:30 PM, Appu kumar appu.kum...@gmail.com wrote: Dear all ccp4 users, I have solved the structure of a protein which is a dimer. On comparison with the other structure from PDB data bank, i found that structure solved by us show a tiltness in monomer-monomer arrangement of a dimer. May you please help me in findng the angle between two monomer. Do i need to calculate the centre of mass of the protein for calcualting the angle between them?. Thanks in advance please help me. Thank you Appu
Re: [ccp4bb] d*trek
Hi It should do. Jim will know for sure. On 23 Aug 2012, at 23:08, jlliu liu wrote: My real questions is: Does d*trek recognize the img file format collected at ALS or APS and process the data? Thanks! On Thu, Aug 23, 2012 at 6:00 PM, jlliu liu jlliu20022...@gmail.com wrote: Do anybody know if d*trek can process data collected from APS? Thanks a lot in advance. Harry -- Dr Harry Powell, MRC Laboratory of Molecular Biology, MRC Centre, Hills Road, Cambridge, CB2 0QH
Re: [ccp4bb] Angle between monomer of a dimer
On 23/08/12 20:08, Nikolina Sekulic wrote: Dear Appu, I had similar issue once. You can use Coot to overlay two structures and get the rotation matrix a1 a2 a3 b1 b2 b3 c1 c2 c3 from here you can calculate cosine of an angle using formula (a1+b2+c3-1)/2 You can if you like, but Coot does it for you also: In the terminal output you find something like: INFO:: Rotation in CCP4 Polar Angles: Polar = (133.961,-95.5736,9.28192) The rotation around the axis is the last number of the triple. Paul.
Re: [ccp4bb] Angle between monomer of a dimer
I believe $CCP4/bin/superpose does the same Eugene On 24 Aug 2012, at 11:44, Paul Emsley wrote: On 23/08/12 20:08, Nikolina Sekulic wrote: Dear Appu, I had similar issue once. You can use Coot to overlay two structures and get the rotation matrix a1 a2 a3 b1 b2 b3 c1 c2 c3 from here you can calculate cosine of an angle using formula (a1+b2+c3-1)/2 You can if you like, but Coot does it for you also: In the terminal output you find something like: INFO:: Rotation in CCP4 Polar Angles: Polar = (133.961,-95.5736,9.28192) The rotation around the axis is the last number of the triple. Paul. -- Scanned by iCritical.
Re: [ccp4bb] d*trek
d*TREK can process single crystal diffraction images from all the common detectors including not only Rigaku detectors, but many different detectors found at synchrotron beamlines around the world such as the APS, ALS, NSLS, CHESS, SLS, ESRF, Diamond, Soleil, PhotonFactory, SPring8, CAMD, Trieste, DESY, AS, LNLS, and you name it. From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Harry Powell [ha...@mrc-lmb.cam.ac.uk] Sent: Friday, August 24, 2012 4:27 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] d*trek Hi It should do. Jim will know for sure. On 23 Aug 2012, at 23:08, jlliu liu wrote: My real questions is: Does d*trek recognize the img file format collected at ALS or APS and process the data? Thanks! On Thu, Aug 23, 2012 at 6:00 PM, jlliu liu jlliu20022...@gmail.commailto:jlliu20022...@gmail.com wrote: Do anybody know if d*trek can process data collected from APS? Thanks a lot in advance. Harry -- Dr Harry Powell, MRC Laboratory of Molecular Biology, MRC Centre, Hills Road, Cambridge, CB2 0QH
[ccp4bb] structural homology
Dear all, i want to do structural homology but i am still beginner , could some one help me to do it.is there are specific programs to do that or should i do it manually ? thank you Amr
Re: [ccp4bb] structural homology
I-tasser or Robetta , modeler and many more Sent from my iPad On Aug 24, 2012, at 22:23, amro selem amro_selem2...@yahoo.commailto:amro_selem2...@yahoo.com wrote: Dear all, i want to do structural homology but i am still beginner , could some one help me to do it.ishttp://it.is there are specific programs to do that or should i do it manually ? thank you Amr
Re: [ccp4bb] structural homology
Adding to the popular suggestions.. Check out the PSI Protein Model Portal (http://www.proteinmodelportal.org/), which allows submission to several servers including I-Tasser and Modeller as well as some informative tutorials on modeling workflow, etc. Also check out some other standalone servers: ProtMod (http://ffas.burnham.org/protmod-cgi/protModHome.pl). 3D-JIGSAW (http://bmm.cancerresearchuk.org/~3djigsaw/) And a list of other sites (http://www.p212121.com/2009/05/10/most-popular-homology-modeling-servers/) -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Bosch, Juergen Sent: Friday, August 24, 2012 1:33 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] structural homology I-tasser or Robetta , modeler and many more Sent from my iPad On Aug 24, 2012, at 22:23, amro selem amro_selem2...@yahoo.com wrote: Dear all, i want to do structural homology but i am still beginner , could some one help me to do it.is there are specific programs to do that or should i do it manually ? thank you Amr
[ccp4bb] Improving microcrystals
Hi everyone, I have been working on a protein for the past year. After a number of trials at crystallizing the protein i have identified conditions for getting spherulites/micro-crystaline material under micro batch method. I have confirmed that the crystalline material is protein, by using Izit-dye test. The condition is 50mM CaCl2, Mes pH 6.5 and 40% PEG 400. I will be happy to get suggestions on improving conditions to obtain single crystals. I have already tried varying a number of parameters like salt, precipitant concentration and buffer pH but that didn't help. Thanks.
[ccp4bb] Off-topic: Duet vectors with C-terminal GST tag
Dear CCP4bb, We would like to co-express proteins under Se-Met conditions for de-novo phasing of a complex. One of the proteins expresses much better with a GST-tag compared with a his-tag. As its binding site is at its N-terminus, we are hoping to co-express it as a C-terminal GST tag recombinant. So far however, we haven't found any commercially available duet vectors with such a tag. We would truly appreciate if anyone knows of the availability of such vectors, or has any suggestions on similar vectors. Thanks so much! Ming
