Re: [ccp4bb] Self rotation function
Yes - Prasun - I think self rotation functions are a validation tool rather than a preliminary piece of evidence.. Sometimes it helps to know one expects a trimer or a 13 fold axis or some such but in this case they can help tell you you have the right solution - once you have it! All the best Eleanor PS - how clear is the spacegroup determination - a helical search model can be a bit ambiguous.. On Sat, 22 May 2021 at 21:11, Ian Tickle wrote: > > Hi Eleanor > > According to the peak search the 3 highest peaks on the chi=180 section > are at: > > | 390.00 -52.26 180.000.49 | > | 490.00 -73.73 180.000.47 | > | 590.00 -66.55 180.000.44 | > > > plus a lot of lower peaks on that section which are clearly in the noise. > However eyeballing that contoured section that's clearly not right: there > are no clear peaks at those positions and I bet the ones above would vanish > with higher contour levels. > > The highest peaks are elsewhere on the contoured chi=180 section, i.e. due > to the 3 crystallographic 2-folds at: > >900 180 (2_x) >90 90 180 (2_y) > 00 180 (2_z) > > The other peaks in the peak search could be similarly in error: it would > probably work better with a noise threshold. I would have more confidence > in the results if I saw the contoured sections for myself ! > > A peak on the chi=90 section doesn't necessarily imply a 4-fold axis (i.e. > a closed group). It could simply be 2 (or even 3) subunits related by a 90 > deg. rotation (i.e. not a closed group). A 4-fold axis gives rise to > multiple overlapping peaks on the chi=90 and chi=180 sections (so the peak > heights would be greater). > > Cheers > > -- Ian > > On Sat, 22 May 2021 at 18:14, Eleanor Dodson > wrote: > >> Ian - I read the log file - agree, you cant get much from the pictures.. >> But the peak heat of the translation vector is 50% od the origin - ie >> pretty strong.. >> And ditto for the rotation angles - all 50% of origin too >> But of course any set of rotation angles does not have to generate a >> closed rotation system - they could be relating distant monomers.. >> Cheers Eleanor >> >> >> >> On Sat, 22 May 2021 at 17:50, Ian Tickle wrote: >> >>> >>> Hi Eleanor >>> >>> On Sat, 22 May 2021 at 14:55, Eleanor Dodson < >>> 176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk> wrote: >>> And several strong rotations 180 0 90. - ie a 4 fold round the c axis? 0 0 60 - ie a 6 fold round the c axis? >>> >>> How can you tell that from the meagre information provided by MOLREP? >>> An NCS point group doesn't have to be a crystallographic one: it could be >>> 5-fold, 7-fold, 19-fold or indeed anything-fold and we're not given the >>> relevant sections to make a decision on that. MOLREP has an option to >>> choose a different angle for the 60 deg. section, but to sample the chi >>> angle at 5 deg. intervals would require running 32 jobs! It's much easier >>> to run POLARRFN once and get all the sections in one job. >>> >>> Also NCS doesn't even have to form a closed group, i.e. assuming there >>> are 2 subunits they don't have to be related by a 180 deg rotation (or 90 >>> deg for 4 subunits, or 60 deg for 6). It could be any angle of rotation >>> relating 2 (or more) subunits. >>> >>> Then numerous two folds in the a b plane. >>> >>> Isn't that just noise because MOLREP has used a contour level that's >>> much too low? If you raise the contour levels that noise will disappear, >>> and maybe the c axis rotations as well (though I doubt that: the c axis >>> peaks look quite strong). I couldn't see how to change the contour levels >>> in MOLREP: again POLARRFN allows you to do that. >>> >>> Cheers >>> >>> -- Ian >>> >>> To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
Re: [ccp4bb] Self rotation function
Hi Eleanor According to the peak search the 3 highest peaks on the chi=180 section are at: | 390.00 -52.26 180.000.49 | | 490.00 -73.73 180.000.47 | | 590.00 -66.55 180.000.44 | plus a lot of lower peaks on that section which are clearly in the noise. However eyeballing that contoured section that's clearly not right: there are no clear peaks at those positions and I bet the ones above would vanish with higher contour levels. The highest peaks are elsewhere on the contoured chi=180 section, i.e. due to the 3 crystallographic 2-folds at: 900 180 (2_x) 90 90 180 (2_y) 00 180 (2_z) The other peaks in the peak search could be similarly in error: it would probably work better with a noise threshold. I would have more confidence in the results if I saw the contoured sections for myself ! A peak on the chi=90 section doesn't necessarily imply a 4-fold axis (i.e. a closed group). It could simply be 2 (or even 3) subunits related by a 90 deg. rotation (i.e. not a closed group). A 4-fold axis gives rise to multiple overlapping peaks on the chi=90 and chi=180 sections (so the peak heights would be greater). Cheers -- Ian On Sat, 22 May 2021 at 18:14, Eleanor Dodson wrote: > Ian - I read the log file - agree, you cant get much from the pictures.. > But the peak heat of the translation vector is 50% od the origin - ie > pretty strong.. > And ditto for the rotation angles - all 50% of origin too > But of course any set of rotation angles does not have to generate a > closed rotation system - they could be relating distant monomers.. > Cheers Eleanor > > > > On Sat, 22 May 2021 at 17:50, Ian Tickle wrote: > >> >> Hi Eleanor >> >> On Sat, 22 May 2021 at 14:55, Eleanor Dodson < >> 176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk> wrote: >> >>> And several strong rotations >>> 180 0 90. - ie a 4 fold round the c axis? >>> 0 0 60 - ie a 6 fold round the c axis? >>> >> >> How can you tell that from the meagre information provided by MOLREP? An >> NCS point group doesn't have to be a crystallographic one: it could be >> 5-fold, 7-fold, 19-fold or indeed anything-fold and we're not given the >> relevant sections to make a decision on that. MOLREP has an option to >> choose a different angle for the 60 deg. section, but to sample the chi >> angle at 5 deg. intervals would require running 32 jobs! It's much easier >> to run POLARRFN once and get all the sections in one job. >> >> Also NCS doesn't even have to form a closed group, i.e. assuming there >> are 2 subunits they don't have to be related by a 180 deg rotation (or 90 >> deg for 4 subunits, or 60 deg for 6). It could be any angle of rotation >> relating 2 (or more) subunits. >> >> Then numerous two folds in the a b plane. >>> >> >> Isn't that just noise because MOLREP has used a contour level that's much >> too low? If you raise the contour levels that noise will disappear, and >> maybe the c axis rotations as well (though I doubt that: the c axis peaks >> look quite strong). I couldn't see how to change the contour levels in >> MOLREP: again POLARRFN allows you to do that. >> >> Cheers >> >> -- Ian >> >> To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
Re: [ccp4bb] Self rotation function
Ian - I read the log file - agree, you cant get much from the pictures.. But the peak heat of the translation vector is 50% od the origin - ie pretty strong.. And ditto for the rotation angles - all 50% of origin too But of course any set of rotation angles does not have to generate a closed rotation system - they could be relating distant monomers.. Cheers Eleanor On Sat, 22 May 2021 at 17:50, Ian Tickle wrote: > > Hi Eleanor > > On Sat, 22 May 2021 at 14:55, Eleanor Dodson < > 176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk> wrote: > >> And several strong rotations >> 180 0 90. - ie a 4 fold round the c axis? >> 0 0 60 - ie a 6 fold round the c axis? >> > > How can you tell that from the meagre information provided by MOLREP? An > NCS point group doesn't have to be a crystallographic one: it could be > 5-fold, 7-fold, 19-fold or indeed anything-fold and we're not given the > relevant sections to make a decision on that. MOLREP has an option to > choose a different angle for the 60 deg. section, but to sample the chi > angle at 5 deg. intervals would require running 32 jobs! It's much easier > to run POLARRFN once and get all the sections in one job. > > Also NCS doesn't even have to form a closed group, i.e. assuming there are > 2 subunits they don't have to be related by a 180 deg rotation (or 90 deg > for 4 subunits, or 60 deg for 6). It could be any angle of rotation > relating 2 (or more) subunits. > > Then numerous two folds in the a b plane. >> > > Isn't that just noise because MOLREP has used a contour level that's much > too low? If you raise the contour levels that noise will disappear, and > maybe the c axis rotations as well (though I doubt that: the c axis peaks > look quite strong). I couldn't see how to change the contour levels in > MOLREP: again POLARRFN allows you to do that. > > Cheers > > -- Ian > > To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
Re: [ccp4bb] Self rotation function
Hi Eleanor On Sat, 22 May 2021 at 14:55, Eleanor Dodson < 176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk> wrote: > And several strong rotations > 180 0 90. - ie a 4 fold round the c axis? > 0 0 60 - ie a 6 fold round the c axis? > How can you tell that from the meagre information provided by MOLREP? An NCS point group doesn't have to be a crystallographic one: it could be 5-fold, 7-fold, 19-fold or indeed anything-fold and we're not given the relevant sections to make a decision on that. MOLREP has an option to choose a different angle for the 60 deg. section, but to sample the chi angle at 5 deg. intervals would require running 32 jobs! It's much easier to run POLARRFN once and get all the sections in one job. Also NCS doesn't even have to form a closed group, i.e. assuming there are 2 subunits they don't have to be related by a 180 deg rotation (or 90 deg for 4 subunits, or 60 deg for 6). It could be any angle of rotation relating 2 (or more) subunits. Then numerous two folds in the a b plane. > Isn't that just noise because MOLREP has used a contour level that's much too low? If you raise the contour levels that noise will disappear, and maybe the c axis rotations as well (though I doubt that: the c axis peaks look quite strong). I couldn't see how to change the contour levels in MOLREP: again POLARRFN allows you to do that. Cheers -- Ian To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
Re: [ccp4bb] SELF-ROTATION FUNCTION FROM MOLREP
Dear CCP4 Users, In Phenix.xtriage and phaser, the analyses of the Patterson function reveals a significant off-origin peak that is 23.25 % of the origin peak, indicating pseudo translational symmetry at frac. cord. vector 0.0000.5000.022 . It did not indicate any twinng. Data is good with resolution upto 2.8A. The cell dimension in P21 SG is 57.877, 63.321, 108.028, 90, 89.987, 90 and in P222 SG is 57.805, 63.266, 108.053, 90, 90, 90. We can say cell dimension align well in in P21 and P222 SG. For MR template, about 75% of domain1, we have solved in our lab and remaining 25% is available from pdb with 30% sequence identity. It is a transcription factor with ligand bindng domain and DNA binding domain. I tried finding MR solution but does not gave satisfaction result. The Rwork and Rfree stalls around 47% and 53% respectively. Is there any possiblity to guess the no of molecules present in ASU from self-rotation function? If we can then we will be sure of whether it is full length of truncated one. Thank you Monica On 11/18/13, Eleanor Dodson wrote: > First Q - how good is your data - is there no possibility of twinning > or any other distraction? > > Second Q - To compare those results properly we need to know how the > P2 and the P222 cell align - are the cell dimensions more or less the > same? > > But the 2 plots you attach (and the list above) show both very strong > 222 symmetry so the most likely assumption is that the pointgroup is > P222. > > The next peak down the list is only 0.13 for one and 0.17 for the > other pointgroup, which only borders on significance.. > But this doesnt really prove anything - for example, if there is a > flexible linker the 2 domains of each molecule may be in different > relative orientations . Do you have any MR search model for the 2 > domains? I would search with them and see what they predict - on the > whole self rotation functions are most comprehensible AFTER the > structure is solved! > > Eleanor > > > On 18 November 2013 09:58, Monica Mittal wrote: >> Dear CCp4 users, >> May anyone help me in interpreting the >> self-rotation function from molrep. Data can be indexed,scaled equally >> well in P21 and P222. This protein has two domain linked by a long >> flexible linker and get cleaved during crystallization. After >> crystallizing it in many condition, i believed that i found new >> condition where it may be full length. May anyone please suggest me by >> looking at the self-rotation function, how many molecule exist in ASU. >> Matthews coefficient suggest that there would be 2 copy of full >> length protein or four of truncated protein in P21 space group. For >> your interpretation, please find attached images of rotation function >> around K=180 >> Molrep self rotation peaks are >> >> P21 space group >> >> theta phi chi P(i)/P(0)| >> +--+ >> | 1 0.000.000.001.00 | >> | 290.00 -0.00 180.000.79 | >> | 335.78 -0.00 180.000.17 | >> | 490.00 -170.05 180.000.17 | >> | 558.71 180.00 180.000.14 | >> | 6 108.34 180.00 180.000.14 | >> | 7 117.39 180.00 180.000.13 | >> | 890.00 90.00 108.540.13 | >> | 990.00 -90.00 108.540.13 | >> | 10 144.50 -0.00 180.000.13 | >> | 1137.57 25.59 179.980.12 | >> | 12 148.100.00 180.000.12 | >> | 13 121.736.36 179.620.11 | >> | 1463.31 -42.27 180.000.11 | >> | 1590.00 90.00 162.290.11 | >> | 1690.00 -90.00 162.290.11 | >> | 1771.12 136.88 180.000.10 | >> | 1899.17 -180.00 180.000.10 | >> | 19 144.80 -161.87 180.000.10 | >> | 2090.00 -138.24 180.000.10 | >> | 2182.27 -76.45 180.000.10 | >> | 2290.00 90.00 115.940.10 | >> | 2390.00 -90.00 115.940.10 | >> | 24 159.16 27.07 180.000.10 | >> | 2595.08 -35.92 179.840.10 | >> | 26 113.86 -139.44 179.540.10 | >> | 2790.23 -0.00 89.320.10 | >> | 2820.18 -156.63 179.980.10 | >> | 29 116.90 -40.40 179.500.10 | >> | 3063.12 139.60 179.500.10 >> >> >> P222 space group >> >> theta phi chi P(i)/P(0)| >> +--+ >> | 1 0.000.000.001.00 | >> | 290.00 -21.41 180.000.13 | >> | 3 125.320.00 180.000.13 | >> | 4 151.18 -90.00 180.000.12 | >> | 590.00 -180.00 90.000.12 | >> | 6 141.32 26.82 180.000.12 | >> | 790.00 -42.59 180.000.11 | >> | 8 127.22 -25.21 180.000.11 | >> | 937.04 -14.48 180.00
Re: [ccp4bb] SELF-ROTATION FUNCTION FROM MOLREP
First Q - how good is your data - is there no possibility of twinning or any other distraction? Second Q - To compare those results properly we need to know how the P2 and the P222 cell align - are the cell dimensions more or less the same? But the 2 plots you attach (and the list above) show both very strong 222 symmetry so the most likely assumption is that the pointgroup is P222. The next peak down the list is only 0.13 for one and 0.17 for the other pointgroup, which only borders on significance.. But this doesnt really prove anything - for example, if there is a flexible linker the 2 domains of each molecule may be in different relative orientations . Do you have any MR search model for the 2 domains? I would search with them and see what they predict - on the whole self rotation functions are most comprehensible AFTER the structure is solved! Eleanor On 18 November 2013 09:58, Monica Mittal wrote: > Dear CCp4 users, > May anyone help me in interpreting the > self-rotation function from molrep. Data can be indexed,scaled equally > well in P21 and P222. This protein has two domain linked by a long > flexible linker and get cleaved during crystallization. After > crystallizing it in many condition, i believed that i found new > condition where it may be full length. May anyone please suggest me by > looking at the self-rotation function, how many molecule exist in ASU. > Matthews coefficient suggest that there would be 2 copy of full > length protein or four of truncated protein in P21 space group. For > your interpretation, please find attached images of rotation function > around K=180 > Molrep self rotation peaks are > > P21 space group > > theta phi chi P(i)/P(0)| > +--+ > | 1 0.000.000.001.00 | > | 290.00 -0.00 180.000.79 | > | 335.78 -0.00 180.000.17 | > | 490.00 -170.05 180.000.17 | > | 558.71 180.00 180.000.14 | > | 6 108.34 180.00 180.000.14 | > | 7 117.39 180.00 180.000.13 | > | 890.00 90.00 108.540.13 | > | 990.00 -90.00 108.540.13 | > | 10 144.50 -0.00 180.000.13 | > | 1137.57 25.59 179.980.12 | > | 12 148.100.00 180.000.12 | > | 13 121.736.36 179.620.11 | > | 1463.31 -42.27 180.000.11 | > | 1590.00 90.00 162.290.11 | > | 1690.00 -90.00 162.290.11 | > | 1771.12 136.88 180.000.10 | > | 1899.17 -180.00 180.000.10 | > | 19 144.80 -161.87 180.000.10 | > | 2090.00 -138.24 180.000.10 | > | 2182.27 -76.45 180.000.10 | > | 2290.00 90.00 115.940.10 | > | 2390.00 -90.00 115.940.10 | > | 24 159.16 27.07 180.000.10 | > | 2595.08 -35.92 179.840.10 | > | 26 113.86 -139.44 179.540.10 | > | 2790.23 -0.00 89.320.10 | > | 2820.18 -156.63 179.980.10 | > | 29 116.90 -40.40 179.500.10 | > | 3063.12 139.60 179.500.10 > > > P222 space group > > theta phi chi P(i)/P(0)| > +--+ > | 1 0.000.000.001.00 | > | 290.00 -21.41 180.000.13 | > | 3 125.320.00 180.000.13 | > | 4 151.18 -90.00 180.000.12 | > | 590.00 -180.00 90.000.12 | > | 6 141.32 26.82 180.000.12 | > | 790.00 -42.59 180.000.11 | > | 8 127.22 -25.21 180.000.11 | > | 937.04 -14.48 180.000.11 | > | 1059.17 -129.14 180.000.10 | > | 1156.66 -174.09 180.000.09 | > | 1240.85 144.82 180.000.09 | > | 1354.16 -167.88 180.000.09 | > | 14 109.29 -61.09 180.000.09 | > | 15 123.12 -84.90 180.000.09 | > | 1664.66 -93.79 180.000.09 | > | 17 113.09 108.59 179.890.09 | > | 1893.84 37.37 179.940.08 | > | 1990.00 -33.41 180.000.08 | > | 20 131.95 90.00 90.750.08 | > | 2153.78 -144.59 180.000.08 | > | 2249.15 -43.11 180.000.08 | > | 2362.98 -56.60 180.000.08 | > | 2461.97 138.06 179.910.08 | > | 2596.77 59.47 179.900.08 | > | 26 118.74 40.91 179.850.07 | > | 27 100.14 57.97 179.860.07 | > | 2859.74 -139.98 180.000.07 | > | 2958.97 -141.14 180.000.07 | > | 30 103.38 59.92 179.810.07 > > Many Thanks in advance for your kind help. > THANK YOU
Re: [ccp4bb] Self rotation function and translation peak
Well - translation peaks are listed in the data processing log file - look for the word translation. If there is an off-origin peak > 25% of the origin you probably have two 9or more) molecules in similar orientations but displaced from each other. Self rotation peaks are listed in various programs. Do you have an example - it is easier to comment on a particular result rather than try to describe general ones. Eleanor On 5 Jul 2013, at 23:27, Faisal Tarique wrote: > Dear All > In case we have more than one molecule per asymmetric unit, how to look for > the results of the self-rotation function calculation and translation peak in > the native patterson. > > > -- > Regards > > Faisal > School of Life Sciences > JNU
Re: [ccp4bb] Self rotation function interpretation
Emma, You need to provide more information. Luckily, I222 is orthorhombic, so a* is along a, b* is along b, and c* is along c. This makes things so much easier to interpret. I hope the plotting conventions you used are typical: b along +y (North pole), a along +x (to the right), and c perpendicular to the page. Let us also assume that you have contours at every 10% of the origin peak height. If so, my quick assessment is that there is not much. At each of the crystallographic axes in the chi=180 map, you see an origin peak arising from the crystallographic 2-fold symmetry; the mirror symmetry is expected with orthorhombic space groups. At ~45 degrees in the ac-plane there is a small peak that is ~40% of the origin peak. An interpretation is that there may be 2-fold NCS, with the axis ~45 away from the crystallographic a- and c-axes, but the noise across the map is kind of high. However, without more details about how you set the SRF up (data completeness, resolution, etc.), matthew's coefficient, and what you expect to see, little more can be done. Good luck, Michael R. Michael Garavito, Ph.D. Professor of Biochemistry & Molecular Biology 603 Wilson Rd., Rm. 513 Michigan State University East Lansing, MI 48824-1319 Office: (517) 355-9724 Lab: (517) 353-9125 FAX: (517) 353-9334Email: rmgarav...@gmail.com On Feb 9, 2013, at 11:00 PM, Emma Littlejohn wrote: > Hi all, > > I have generated a self rotation function using MOLREP for a low res data set > which indexed in space group I222 (attached). I am hoping it may provide some > information on the oligomeric state of the protein. I am new to analysing SF > and was wondering if anyone can help with the interpretation or has any tips > that might be able to help me shed some light on what the SF is revealing? > > Thanks in advance. > Emma > > >
Re: [ccp4bb] Self rotation function interpretation
Did you perform Matthews analysis? It should give you some indications on the number of monomers in the asymmetric unit. Can you send the list of peaks? It should be a file with .tab extension. Cheers Fulvio Saccoccia Dept. of Biochemical Sciences Sapienza University of Rome Il 10/02/2013 05:00, Emma Littlejohn ha scritto: Hi all, I have generated a self rotation function using MOLREP for a low res data set which indexed in space group I222 (attached). I am hoping it may provide some information on the oligomeric state of the protein. I am new to analysing SF and was wondering if anyone can help with the interpretation or has any tips that might be able to help me shed some light on what the SF is revealing? Thanks in advance. Emma
Re: [ccp4bb] self rotation function
On 06/03/2011 02:01 PM, Careina Edgooms wrote: Dear ccp4 members I have question about how to interpret polarrfn log. I wish to know if my crystal display NCS. I am not sure how to interpret the file. I see it have two peak, one is origin and the other is not that high to me. I have attach copy of the file. If someone could assist me to understand the file it would be appreciated. best Careina Well - a peak of 29% of the origin is reasonably significant at 2A resolution. This indicates a non-crystallographic 2-fold axis in the a-b plane ( the multiple solutions are all symmetry equivalents..) omega phikappa Peak 7 1 1 0.00.0 285.329.5 180.0 180.0 74.7 1 2 0.0 180.0 254.729.5 90.0 142.7 180.0 . How many molecules do you expect in the asymmetric unit. Eleanor
Re: [ccp4bb] self rotation function
Hi Careina 30% of the origin peak is fairly respectable. You could probably make it higher by varying the high res cutoff. You have 2 Ang: it may be that the NCS doesn't extend to that resolution, so making it a bit lower might improve the signal/noise ratio. It would be nice to see the plot of the kappa=180 section, but from the log file it's clear you have a lot of NCS 2-folds in the ab plane (kappa=180, omega=90), so my guess would be a 222 tetramer aligned with an NCS 2-fold parallel to the c axis. If so this should give you an translational NCS peak somewhere in the z=1/2 Harker section of the native Patterson. From the solvent content how many molecules in the a.u. do you expect? Cheers -- Ian On Fri, Jun 3, 2011 at 2:01 PM, Careina Edgooms wrote: > Dear ccp4 members > > I have question about how to interpret polarrfn log. I wish to know if my > crystal display NCS. I am not sure how to interpret the file. I see it have > two peak, one is origin and the other is not that high to me. I have attach > copy of the file. If someone could assist me to understand the file it would > be appreciated. > > best > Careina >
Re: [ccp4bb] Self Rotation function - NCS
You need to tell us the spacegroup for us to be very helpful... And I often find the molrep plots less useful than the list of peaks and all the symmetry equivalents.. (It has a weird name - *rf or *doc I think) But I guess all the variant are in point group P222? There are the 3 expected 2 folds on the Chi=180 section plus one other which is presumed an non-crystallographic 2 fold Then there seems to be a non-cryst 4 fold showing up on the section chi=90 However that doesnt tell you whether your 4 molecules are arranged as a tetramer or as 2 dimers.Do you have a model and if so does that form a multimer? In fact if you have a model it is usually simpler to solve the MR then use the self-rotation as verification of your solution. The program PISA, available at the ebi http://www.ebi.ac.uk/msd-srv/prot_int/pistart.html or from CCP4 will analyse a structure and suggest what multimer is most likely. Then you can see if the suggested non-cryst of the solution agrees with the self rotation function.. The project B one is more interesting - again one needs to know the space group but there are obviously 8 2 folds - try plotting the chi = 45 section or looking at the list of peaks, and you should see a strong 8 fold axis.. Eleanor Paul Lindblom wrote: Hello everyone, I have a little problem concerning the self rotation function. I hope I´m not asking to much, but I am not sure how to interprete the images I get from the calculation with molrep. I calculated the self rotation map for 4 variants with each 4 molecules in the ASU and one map for another project (most likely 8 molecules/ASU) I see the peaks, but how do I see, if there is NCS? The images are attached. Thanks a lot, P.
Re: [ccp4bb] Self rotation function calculation
Dear All, Thank you very much for the reply and suggesions regarding my self rotation function calculation. Really I appreciate who are all responded me regarding my query. Now I got some idea about my structure in the assymetric unit. Thanking you once again. Sincerely yours, Sampath On Thu, Nov 20, 2008 at 11:18 PM, Sampath Natarajan <[EMAIL PROTECTED]>wrote: > Dear All, > > I have a problem in analyze the self rotation function. My crystal is > belongs to C2 space group. According to Mathews calculation, this crystal > shows 7 or 8 molecules in the asymmetric unit. But I couldn't conclude the > number molecules in the A.U. So I calculated the self rotation function > using the program MOLREF. But Still I am not able to interpret the results > using that. Here I'm attaching the figures which I calculated the self > rotation function with different chi angles. Could anyone help me to find > the symmetry of molecules in the A.U? It will be great helping me to solve > the structure. > > Thanking you, > > Sincerely > > Sampath > > >
Re: [ccp4bb] Self rotation function calculation
Hi Sampath, Looks to me like you might have a hexamer with 32 symmetry in asymmetric unit. Ben (I think if you were in the wrong space-group and the 3 fold was crystallographic the peak height on the chi =120 section would be higher?) "Sampath Natarajan" <[EMAIL PROTECTED]> Sent by: "CCP4 bulletin board" 21-Nov-2008 07:18 Please respond to "Sampath Natarajan" <[EMAIL PROTECTED]> To CCP4BB@JISCMAIL.AC.UK cc Subject [ccp4bb] Self rotation function calculation Dear All, I have a problem in analyze the self rotation function. My crystal is belongs to C2 space group. According to Mathews calculation, this crystal shows 7 or 8 molecules in the asymmetric unit. But I couldn't conclude the number molecules in the A.U. So I calculated the self rotation function using the program MOLREF. But Still I am not able to interpret the results using that. Here I'm attaching the figures which I calculated the self rotation function with different chi angles. Could anyone help me to find the symmetry of molecules in the A.U? It will be great helping me to solve the structure. Thanking you, Sincerely Sampath [attachment "self rotation1.png" deleted by Benjamin D Bax/PharmRD/GSK] [attachment "self rotation2.png" deleted by Benjamin D Bax/PharmRD/GSK] --- This e-mail was sent by GlaxoSmithKline Services Unlimited (registered in England and Wales No. 1047315), which is a member of the GlaxoSmithKline group of companies. The registered address of GlaxoSmithKline Services Unlimited is 980 Great West Road, Brentford, Middlesex TW8 9GS. ---
Re: [ccp4bb] Self rotation function calculation
Hi Sympath, Did you try to change the default "Search radius"? To my understanding MOLREP estimats the search radius somehow from the volume of the asymmetric unit and not from the expected radius of the monomer (you don't give the program the number of expected molecules). The signal of the SRF could be much better if you try several search radii in the expected dimension for a monomer/(dimer). In a special case with 6 monomers in the asu (SG P21) where the default SRF was hard to interprete it gave nice peaks when the search radius was adapted. Best wishes, Karsten Sampath Natarajan wrote: Dear All, I have a problem in analyze the self rotation function. My crystal is belongs to C2 space group. According to Mathews calculation, this crystal shows 7 or 8 molecules in the asymmetric unit. But I couldn't conclude the number molecules in the A.U. So I calculated the self rotation function using the program MOLREF. But Still I am not able to interpret the results using that. Here I'm attaching the figures which I calculated the self rotation function with different chi angles. Could anyone help me to find the symmetry of molecules in the A.U? It will be great helping me to solve the structure. Thanking you, Sincerely Sampath
Re: [ccp4bb] Self rotation function calculation
It is hard to say without the program output as well, and information about the unit cell. However it seems that you have a three fold axis at 120 degrees to the C2 2fold axis, and 3 other NCS 2-folds perpendicular that 3 fold. It is possible your space group is really H32 - run your data (either as unmerged mtz or unmerged sca file) into pointless and see if it suggests reindexing the C2 data as H32. Eleanor Sampath Natarajan wrote: Dear All, I have a problem in analyze the self rotation function. My crystal is belongs to C2 space group. According to Mathews calculation, this crystal shows 7 or 8 molecules in the asymmetric unit. But I couldn't conclude the number molecules in the A.U. So I calculated the self rotation function using the program MOLREF. But Still I am not able to interpret the results using that. Here I'm attaching the figures which I calculated the self rotation function with different chi angles. Could anyone help me to find the symmetry of molecules in the A.U? It will be great helping me to solve the structure. Thanking you, Sincerely Sampath
Re: [ccp4bb] Self rotation function calculation
Hi Sampath, We had a very similar case, an octamer (422 symmetry) in C2 space group. What saved us for solving the structure (and by the way interpreting the self-rotation function !!) was a low resolution electron microscopy envelope (silver stain and cryo-EM) that gave us the organisation of the octamer. Sure, the condition is that the content of the asymetric unit corresponds to what you have in solution. I would bet you have 6 or 9 molecules in the asymmetric unit corresponding to very low or very solvent content. Good luck, Claudine > Dear All, > > I have a problem in analyze the self rotation function. My crystal is > belongs to C2 space group. According to Mathews calculation, this crystal > shows 7 or 8 molecules in the asymmetric unit. But I couldn't conclude the > number molecules in the A.U. So I calculated the self rotation function > using the program MOLREF. But Still I am not able to interpret the results > using that. Here I'm attaching the figures which I calculated the self > rotation function with different chi angles. Could anyone help me to find > the symmetry of molecules in the A.U? It will be great helping me to solve > the structure. > > Thanking you, > > Sincerely > > Sampath > * ATTENTION : NOUVELLE ADRESSE MAIL : [EMAIL PROTECTED] * Pr Claudine MAYER Université Paris Diderot - Paris 7 *
Re: [ccp4bb] Self rotation function and figures
U Sam wrote: Hi, I am using a native data of 2 angstrom and C2 space group, final R-merge is 0.059. I processed data using HKL2000. I highly appreciate suggestion how can I generate self-rotation function, get figures and save that in required format. Thanks, Sam _ Don't get caught with egg on your face. Play chicktionary! http://club.live.com/chicktionary.aspx?icid=chick_wlhmtextlink1_feb Hallo Sam, Molrep included in CCP4 -suite is an example which calculate self-rotation functions and will give you *.ps-files. best reagrds, georg
[ccp4bb] [Fwd: Re: [ccp4bb]: self rotation function matrix & NCS matrix]
Hi Eleanor and others: This is a little too late to follow up on this thread. But here is a similar question concerning MR and self-rotation. Without going into the translational part of MR, is it possible to tell the orientation of a 2-fold axis directly from the cross-rotation peaks? e.g. I have 2 top peaks from the cross-rotation function. There is also a strong 2-fold axis shown in self-rotation (kappa=180). Persumbaly then the two cross-rotation peaks are related by this 2-fold axis. From the angles of the two cross-rotation peaks, can I already tell the direction of the 2-fold axis? Regards, Weikai > ÍúÍú wrote: > >> I calculated the self-rotation function matrix with POLARRFN (named >> 1), and also got the molecular replacement solution with phaser, and >> used CNS's get_ncs_matrices to acquire the NCS matrix (named 2). >> Now what I wanted to do is to compare the results of 1 and 2. Are they >> the same or not, or which self-rotation function matrix is the right >> one of true NCS. Could you give me some suggestions? >> By the way, if I have got one molecule's PDB, and the rotation >> function matrix, are there any softwares on acquiring the other >> molecule's PDB? Many thanks > > > > POLARRFN will give you ALL symmetry equivalent rotations for your point > group. > > Only one of these will relate your molecule A to B, and its inverse > should relate B to A. Both will be listed in the POLARRFN output, plus > probably many others depending on your point group.. > > I do not know the CNS convention now but it certainly used to be > different from the CCP4 one. > > Hwever if you use he GUI > cordinarte utilities > superpose molecules > > select superpose by numbered residues > > then match A to B the log file will give you the ALPHA BETA GAMMA and > the polar angles nt e same convention as POLARRFN. > > Eleanor > >
