[ccp4bb] aligning structure and generating symetry mates
Dear all, Please guide me on right track in weired confusion. I have model structure(available in pdb) and a structure solved by molecular replacement as a dimer . Our structure does not giving correct tetramer by symmetry mates. Strangely when i am aligning our structure on model structure and generating symmetry mates of our structure to find the correct tetramer from dimer, i am getting the one which i want. Why the structure solved by us give tetramer on aligning with model structure. I do not know weather it is a right way to find the correct oligomeric state of protein or not. So please i reaquest you to suggest me with your valuable advice to overcome with this confusion. Thank you in advance Appu
Re: [ccp4bb] aligning structure and generating symetry mates
I think we need more information. Are the cells and space groups similar What are the transformations which fit your coordinates to the model structure? Have you submitted your coordinates to the PISA server at the EBI - that will suggest possible tetramers? Eleanor On 28 Oct 2012, at 07:31, Appu kumar wrote: Dear all, Please guide me on right track in weired confusion. I have model structure(available in pdb) and a structure solved by molecular replacement as a dimer . Our structure does not giving correct tetramer by symmetry mates. Strangely when i am aligning our structure on model structure and generating symmetry mates of our structure to find the correct tetramer from dimer, i am getting the one which i want. Why the structure solved by us give tetramer on aligning with model structure. I do not know weather it is a right way to find the correct oligomeric state of protein or not. So please i reaquest you to suggest me with your valuable advice to overcome with this confusion. Thank you in advance Appu
Re: [ccp4bb] inflluence of pH for crystallization on protein 3-D structure
Hi Acoot, Here are some examples you can look at: PDB: 1X0I (crystal structure of bacteriorhodopsin (acid blue form) at pH 2) PDB: 1X0K (crystal structure of bacteriorhodopsin at pH 10) PDB: 2W2E (crystal structure of aquaporin at pH 3.5) PDB: 1YMG (crystal structure of aquaporin at pH 10) People are aware of course of the effect of pH on the structure and they always deposit many PDBs when they have different crystal forms/bound molecules, or pHs. The difference sometimes can be large that they will do another publication/study like when getting the different structure at a different pH. I can't remember the details but a virus protein crystal structure was once crystallized at both pH 4 and pH 7 which gave totally unrelated structures. Functional studies are important before the interpretation of the structure. Regards Toufic El Arnaout Membrane Structural and Functional Biology Group Trinity College Dublin On Sun, Oct 28, 2012 at 3:00 AM, Acoot Brett acootbr...@yahoo.com wrote: Dear All, A protein crystal can be got at pH 5 or 8, or a pH with much extreme value. What will be the relatively extreme pH value to get the crystal on the protein structure solved based on the crystal got? I mean usually we regard the physiological pH as 7. If a crystal was got at pH 5, the structure solved may be different from the protein structure at pH 7. But it seems there is rarely analysis on the discrepancy of the protein structures when publishing 3-D structure with the protein crystal got at relatively extreme pH. I am looking forward to getting your comment on it. Cheers, Acoot
Re: [ccp4bb] aligning structure and generating symetry mates
On 28 Oct 2012, at 14:07, Appu kumar wrote: transformation matrix.pptx
Re: [ccp4bb] aligning structure and generating symetry mates
Hmm - once you have transformed your co-ordinates by that matrix which is non-crystallographic they are no longer aligned in your unit cell, so you can't apply your symmetry operators to them . I don't think what you are doing is valid, but to be sure I would need to know more about the 2 structures Eleanor On 28 Oct 2012, at 14:07, Appu kumar wrote: The space group and unit cells in two pdb are different. In model.pdb it is, 64.386 69.508 116.859 90.00 90.00 90.00 P 21 21 21 and in our str it is 46.921 105.301 47.751 90.00 103.26 90.00 P 1 21 1 on aligning both the structure in coot, the resulting transformation matrix is attached with this mail. As both Arka Chakraborty and Eleanor Dodson suggested me to do PISA, I did but i am not getting the correct tetramer arrangement which i am getting on aligning the our strcture on model structure first and then genrating the symmetry mates of our structure and then finally filtering the right tetramer. My question is, generating the tetramer after aligning the structure, is a right way to find the tetramer. PDB PISA is not suggesting me the right assembly for tetramer. I making the tetramer in different way which is not straightforward. I am first allowing my structure to rotate and translate on model structure and the generating the symmetry mates for finding the tetramer. I have got the right tetramer too but i am not sure the way i did is right or wrong. On 28 October 2012 16:41, Eleanor Dodson eleanor.dod...@york.ac.uk wrote: I think we need more information. Are the cells and space groups similar What are the transformations which fit your coordinates to the model structure? Have you submitted your coordinates to the PISA server at the EBI - that will suggest possible tetramers? Eleanor On 28 Oct 2012, at 07:31, Appu kumar wrote: Dear all, Please guide me on right track in weired confusion. I have model structure(available in pdb) and a structure solved by molecular replacement as a dimer . Our structure does not giving correct tetramer by symmetry mates. Strangely when i am aligning our structure on model structure and generating symmetry mates of our structure to find the correct tetramer from dimer, i am getting the one which i want. Why the structure solved by us give tetramer on aligning with model structure. I do not know weather it is a right way to find the correct oligomeric state of protein or not. So please i reaquest you to suggest me with your valuable advice to overcome with this confusion. Thank you in advance Appu transformation matrix.pptx
Re: [ccp4bb] aligning structure and generating symetry mates
Appu kumar wrote: Dear all, Please guide me on right track in weired confusion. I have model structure(available in pdb) and a structure solved by molecular replacement as a dimer . Our structure does not giving correct tetramer by symmetry mates. Strangely when i am aligning our structure on model structure and generating symmetry mates of our structure to find the correct tetramer from dimer, i am getting the one which i want. Why the structure solved by us give tetramer on aligning with model structure. I do not know weather it is a right way to find the correct oligomeric state of protein or not. So please i reaquest you to suggest me with your valuable advice to overcome with this confusion. Thank you in advance Appu After transforming your solution dimer back to the position in the structure from which you got the model, then applying NCS gives the proper tetramer? Is this using the cell and spacegroup of the original model, or your cell and space group? If the former, then it is not surprising but it doesn't tell you anything about the arrangement in your new structure.
Re: [ccp4bb] adding some user-defined graphical objects in a PDB file (and displaying them)
Hi Francois, instead of addressing the problem from the PDB side, you could take a look at the embed feature in Pymol. It allows embedding structural information into a special command script. It ties you down to PyMol, but on the other hand you don't need to worry about extending the PDB format. HTH Carsten Save the following as B_spectrum.p1m (needs to be .p1m, does not work as .pml) embed atomline, pdb ATOM 1 C1 INH I 1 0.000 0.000 0.000 1.00 1.00 IC ATOM 2 C2 INH I 1 0.500 0.000 0.000 1.00 10.00 IC ATOM 3 C3 INH I 1 1.000 0.000 0.000 1.00 20.00 IC ATOM 4 C4 INH I 1 1.500 0.000 0.000 1.00 30.00 IC ATOM 5 C5 INH I 1 2.000 0.000 0.000 1.00 40.00 IC ATOM 6 C6 INH I 1 2.500 0.000 0.000 1.00 50.00 IC ATOM 7 C7 INH I 1 3.000 0.000 0.000 1.00 60.00 IC ATOM 8 C8 INH I 1 3.500 0.000 0.000 1.00 70.00 IC ATOM 9 C9 INH I 1 4.000 0.000 0.000 1.00 80.00 IC ATOM 10 C10 INH I 1 4.500 0.000 0.000 1.00 90.00 IC ATOM 11 C11 INH I 1 5.000 0.000 0.000 1.00100.00 IC END embed end load_embedded atomline hide lines, atomline show spheres, atomline set sphere_scale, 0.1 spectrum b, palette=rainbow, minimum=-10, maximum=110,selection=atomline and elem C
Re: [ccp4bb] adding some user-defined graphical objects in a PDB file (and displaying them)
On 10/27/2012 05:32 AM, Pete Meyer wrote: Just out of curiosity, why use PDB format instead of converting PDB into a format readable by a more general 3d graphics program and combining with your cube/sphere/line segment there? I want to interact with the scene. Rotate, view, zoom, change protein representation, etc. So, if I go for some pymol-supported format, I will do all my visual inspection in pymol. Pete Francois Berenger wrote: Hello, For some new project, I'd like to be able to generate things and store them in PDB format. For example, a triangle, a line segment, a square, a cube, a sphere, an arrow, etc. Being able to change the color and line width would be nice. Is there some official recommended way of doing this? Is there some software able to read and display such graphical annotations of PDB files? I'll also need the format description in that case. I want to be able to process a PDB file and store the result of my processing in the same PDB file as some kind of annotation. My current way of doing this is to discretize my objects as H atoms in some other output PDB file, but that's just a temporary workaround. My current search got me this: http://www.cgl.ucsf.edu/eccc1/ So, maybe there is some support for what I am looking for into Chimera. Thanks a lot for your suggestions, Francois.
Re: [ccp4bb] adding some user-defined graphical objects in a PDB file (and displaying them)
For those interested, I think I'll go for Chimera and its support for .bild files. And that will be the end of this not so much xtal-related topic. ;) Sorry for the noise. Regards, F. On 10/29/2012 09:47 AM, Francois Berenger wrote: On 10/27/2012 05:32 AM, Pete Meyer wrote: Just out of curiosity, why use PDB format instead of converting PDB into a format readable by a more general 3d graphics program and combining with your cube/sphere/line segment there? I want to interact with the scene. Rotate, view, zoom, change protein representation, etc. So, if I go for some pymol-supported format, I will do all my visual inspection in pymol. Pete Francois Berenger wrote: Hello, For some new project, I'd like to be able to generate things and store them in PDB format. For example, a triangle, a line segment, a square, a cube, a sphere, an arrow, etc. Being able to change the color and line width would be nice. Is there some official recommended way of doing this? Is there some software able to read and display such graphical annotations of PDB files? I'll also need the format description in that case. I want to be able to process a PDB file and store the result of my processing in the same PDB file as some kind of annotation. My current way of doing this is to discretize my objects as H atoms in some other output PDB file, but that's just a temporary workaround. My current search got me this: http://www.cgl.ucsf.edu/eccc1/ So, maybe there is some support for what I am looking for into Chimera. Thanks a lot for your suggestions, Francois. .color white .dot 0 0 0 .color red .vector 0 0 0 20 0 0 .dot 20 0 0 .color green .vector 0 0 0 0 20 0 .dot 0 20 0 .color blue .vector 0 0 0 0 0 20 .dot 0 0 20 .color 44 .arrow 1 1 1 5 5 5 .arrow 1 1 2 8 6 9 .arrow 1 2 1 10 10 4 .arrow 2 1 1 -2 7 10 .color 22 .polygon 20 0 0 0 20 0 0 0 20 .color 5 .marker 20 20 20 .dr -20 0 0 .v 20 20 20 20 0 20 .dr 0 20 -20 .v 20 20 20 20 20 0 .dr -20 0 20 .dr 20 -20 0 .color 12 .sphere 10 10 10 3 .color 10 .arrow 19 19 19 12 12 12 0.2 1.0 .color 53 .cylinder 14 -5 14 14 0 14 2 open .sphere 14 -5 14 2 .sphere 14 0 14 2
[ccp4bb] Mosaicity and anomalous signal
Dear Folks, I have collected 360 image anomalous data in home source and integrated using automar. These images that show the mosaicity value is 0.05. But, mosaicity value 0.073 has shown when i integrated the 1-180 images data. Why 180 image data mosaicity value is higher than 360 image? and anomalous signal value of 180 image data is also higher than 360 image data. Please make me clear in this part. Thanks in advance With regards B. Vijay
Re: [ccp4bb] Mosaicity and anomalous signal
180 better than 360 is because you killed your crystal. Over exposure is a common thread to solving a structure. Jürgen On Oct 28, 2012, at 10:25 PM, Vijayakumar.B wrote: Dear Folks, I have collected 360 image anomalous data in home source and integrated using automar. These images that show the mosaicity value is 0.05. But, mosaicity value 0.073 has shown when i integrated the 1-180 images data. Why 180 image data mosaicity value is higher than 360 image? and anomalous signal value of 180 image data is also higher than 360 image data. Please make me clear in this part. Thanks in advance With regards B. Vijay .. Jürgen Bosch Johns Hopkins University Bloomberg School of Public Health Department of Biochemistry Molecular Biology Johns Hopkins Malaria Research Institute 615 North Wolfe Street, W8708 Baltimore, MD 21205 Office: +1-410-614-4742 Lab: +1-410-614-4894 Fax: +1-410-955-2926 http://lupo.jhsph.edu
Re: [ccp4bb] How to start my XDS journey after HKL2000?
Here, I show some information about my data and input files of XDS. Wavelength (A) 1. Raster size (mm) 0.10240 (default) Raster size (mm) 0.10240 (default) Film width (mm) 209.72 (default) Film length (mm) 209.72 (default) Record length (pixels) 2048 (default) Number of records 2048 (default) Top limit of useful data 0. (default) Left limit of useful data 0. (default) spots rejected when pixel overflow at value : 65500.0 pixels rejected at value: 0 Oscillation starts at 0. Oscillation range 1. Lattice type: primitive Orientation axis 1 (vertical plane) 1*h 0*k 0*l (default) Orientation axis 2 (spindle) 0*h 0*k 1*l (default) Mosaicity 0.3 CrysZ (beam) axis 0. (default) CrysY (vertical) axis 0. (default) CrysX (spindle) axis 0. (default) unit cell parameters not entered Detector (mis)orientation angles: CassZ (beam) axis 0. CassY (vertical) axis 0. CassX (spindle) axis 0. Detector 2 theta 0. Detector rotation 90.000 (default) Flat detector (default) Detector to crystal distance 166.20 X beam104.80 Y beam105.10 Beam polarization 0.99000 Detector absorption 100.00 (default) Air absorption length 860.00 (default) Crossfire y 0. Crossfire x 0. Crossfire xy 0. Horizontal box size 3.6864 Vertical box size3.6864 2012/10/29 Zhijie Li zhijie...@utoronto.ca: BTW, did you supply XDS with correct beamline/detector information in your input file? Have you compared these information with your HKL2000 site file? If you show us the input file and the HKL2000 site file it might be helpful. -- From: Chang Qing robie0...@gmail.com Sent: Monday, October 29, 2012 12:06 AM To: Zhijie Li zhijie...@utoronto.ca Subject: Re: [ccp4bb] How to start my XDS journey after HKL2000? There were no obvious error messages after XDS. Just, the result of space group was wrong. I can not solve structure through wrong space group. Quality of data is very good. I thought I could get correct result even parameters were in default as recommended in tutorial. I was confused so much. 2012/10/29 Zhijie Li zhijie...@utoronto.ca: You had better also include some error message. -- From: Chang Qing robie0...@gmail.com Sent: Sunday, October 28, 2012 10:40 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] How to start my XDS journey after HKL2000? Hi all Now, I am studying XDS. I have 2 sets of data, which can correctly treated by HKL2000 and the results are very good. I followed the tutorial of XDS, but got wrong space group. Inputing the correct space group was helpless. Results of pointless were also wrong, and I can not pass scala. Can someone give me some recommendation? Thanks. Chang XDS.INP Description: Binary data
