[ccp4bb] Posts available at EMBL-EBI
There are 3 posts available at the European Bioinformatics Institute within the MSD group, the European Partner in the wwPDB Software Engineer: For a 3D Electron Microscopy Project in partnership with the RCSB (Rutgers) and Baylor College Houston http://www-db.embl.de/jss/servlet/de.embl.bk.emblGroups.JobsPage/07118.html Scientific Programmer: To work on a Joint Deposition and processing system in partnership with the wwPDB members http://www-db.embl.de/jss/servlet/de.embl.bk.emblGroups.JobsPage/07117.html Scientific Database Curator: To work on annotating the PDB http://www-db.embl.de/jss/servlet/de.embl.bk.emblGroups.JobsPage/07116.html If you are interested please apply to EMBL using the web site instructions -- Kim HENRICK[EMAIL PROTECTED] ::telephone: +44 (0) 1223 494629
Re: [ccp4bb] CCP4 rotation convention - long comments
Dear all, dear Bernhard, Even when we already had an exchange by mails with Bernhard after he sent his question, I hope it might be useful for many, especially young crystallographers, to follow the problem. Phil Evans writes in acta D57 1355 (2001) on p 1358 section 5.2: the convention used in AMoRe (Navaza, 1994) and other CCP4 programs (Collaborative Computational Project, Number 4, 1994) is to rotate by gamma around z, then by beta around the new y, then by alpha around the new z again, R = Rz(al)Ry(be)Rz(ga) = DOCUMENTAL I tried to find the citation of Navaza about his original definition of alpha, beta, gamma and failed (most of my documentation already left my current office for another place). On the contrary, in his review (2001), Acta Cryst D57, 1367-1372, he CHANGED the names of angles, definitely to avoid confusing, and said : convention by which (phi,theta,psi) denotes a rotation of psi about Z, followed by rotation of theta about the Y axis and finally a rotation of phi about the Z axis, R(phi,theta,psi) = R(phi,Z) R(theta,Y) R(psi,Z) -- AU : It was not precised that here R are rotation matrices that one should multiply by the atomic coordinate vectors in order to get new coordinate values (of course, NEW with respect to the CRYSTAL, or with respect to some other EXTERNAL system of Cartesian coordinates , e.g. another molecule to be superimposed with!) = SOURCE OF CONFUSION == There is a big confusing when describing rotations. The main source of it are the points: WHAT we rotate, in WHICH DIRECTION and - mainly - around WHICH AXES. If you are driving a car, you turn right-left with respect to YOUR CAR and usually do not care the Nord-Sud-Est directions (while modern GPS may show you BOTH views, with respect to your car or with respect to the world axes N-S). The same if you are a pilot of a plane but now you rotate the rigid body (the plane) in 3D. But you may drive with respect to the world axes. Generally speaking, BOTH point of view are completely acceptable; it is a matter of convenience. If you rotate a molecular model inside you crystal, also BOTH conventions are valid. a) you glue coordinate axes to your model and rotate the MODEL with respect to them (you are riding on the model); then of course after you rotate the model around Oz, the molecular Oy has changed its position with respect to your CRYSTAL, and you may rotate around new Oy. b) you have Ox,Oy,Oz fixed, linked to the CRYSTAL, and rotate the MODEL around them, around fixed axes (you are sitting before a screen and rotate you model with respect to it; molecular graphics works in this way, is it?). The NONambiguous answer comes when you give the ROTATION matrices that should be multiplied by the atomic coordinate vectors in order to get new values of atomic coordinates in the crystal. == MATRICES FOR ROTATIONS == Let X,Y,Z be orthogonal axis of the CRYSTAL; X', Y', Z' are axes linked to the model that initially coincide with X,Y,Z, respectively. Let r be a vector standing for atomic coordinates. Rotation, point of view (b). After rotation of the model by alpha about OZ, the coordinates of the atom are R(alpha,OZ) r. The following rotation by beta about OY gives the final coordinates (*)R(beta,OY) R(alpha,OZ) r Rotation, point of view (a). After rotation of hte model by alpha about OZ the coordinates of the atom are R(alpha,OZ) r , but OY' does NOT coincide with OY anymore. A easy way (I do not know better) to describe a rotation around NEW Y, i.e. around OY', is : - rotate it back to the original orientation, thus superimposing OY' and OY - rotate around OY' (now again is the same as OY, so it is easy to describe) - do not forget to recover the orientation obtained previously by R(alpha,OZ). In terms of rotation matrices in the EXTERNAL coordinate system, that you need to apply to atomic coordinates, this gives : [R(alpha,OZ) R(beta,OY) R(-alpha,OZ)] R(alpha,OZ) r = (**)= R(alpha,OZ) R(beta,OY) r - the order has been inverted in comparison with the point of vies (a) - compare with (*) above ! === SUMMARY = Finalizing, b) if the convention is that all rotations are around FIXED axes linked to some external coordinate system, the total rotation matrix for rotation by alpha around OZ, then by beta around OY, then by gamma around OZ is R(gamma,OZ) R(beta,OY) R(alpha,OZ) a) if the convention is that all rotations are around the axes linked to the model and we talk about NEW axes, the total rotation matrix for rotation by alpha around OZ, then by beta around NEW OY, then by gamma around NEW OZ is inverted R(alpha,OZ) R(beta,OY) R(gamma,OZ) == END OF THE STORY I hope this TOO LONG mail (sorry, I failed to make it shorted) makes a useful reminder to
Re: [ccp4bb] CCP4 rotation convention
I just have to write out matrices:
CCP4 rotation matrix:
[R11 R12 R13] [x]
[R21 R22 R23] [y]where x y z are orthogonal coordinates relative
to fixed axes...
[R31 R32 R33] [z]
represents a rotation of ccordinates by first gamma then beta then alpha
as Phil says:
[R11 R12 R13]
[R21 R22 R23]== [R_alpha_about Z0] {R_beta_about_Y1] [
R_gamma_about_Z2]
[R31 R32 R33]
If you consider axes Xo Y0 Z0 :
[X0 Y0 Zo] [R11 R12 R13]
[R21 R22 R23]
[R31 R32 R33]
the matrix rotatates the axes by first alpha, then beta then gamma.
Many programs dont make it clear what they are using the rotation to
describe..
Bernhard Rupp wrote:
Dear programmers -
Phil Evans writes in acta D57 1355 (2001) on p 1358 section 5.2:
the convention used in AMoRe (Navaza, 1994)
and other CCP4 programs (Collaborative Computational
Project, Number 4, 1994) is to rotate by gamma around z, then by beta
around the new y, then by alpha around the new z again,
R = Rz(al)Ry(be)Rz(ga)
This seems correct, as the first rotation is applied first to
vector x, then the second to the new one, etc, thus
x' = (Rz(al)(Ry(be)(Rz(ga)x)))
In J.Appl.Cryst. 30 402-410 (1977) in the convrot description,
Sascha Uzhumtsev lists in table one for (Navaza 1994):
alpha about Z, beta about Y and gamma about new Z
and gives the *same* resulting rotation
Rz(al)Ry(be)Rz(ga)
This seems to be a contradiction I cannot resolve?
Thx, br
-
Bernhard Rupp
001 (925) 209-7429
+43 (676) 571-0536
[EMAIL PROTECTED]
[EMAIL PROTECTED]
http://www.ruppweb.org/
-
People can be divided in three classes:
The few who make things happen
The many who watch things happen
And the overwhelming majority
who have no idea what is happening.
-
Re: [ccp4bb] CCP4 rotation convention
Hi folks I hate to say this but I think everyone here has got it wrong to some degree (including myself - and I hereby retract my previous e-mail and issue the correction below!). If you don't believe me then read digest Jorge Navaza's article Rotation functions in Int. Tab. Vol. F (sect 13.2, p. 269), particularly sections 13.2.2 and Appendix A13.2.1.1. Phil's article in Acta D57 1355-1359 (2001), i.e. the 2001 S/W proceedings, states: ... the convention used in AMoRe (Navaza, 1994) and other CCP4 programs (Collaborative Computational Project, Number 4, 1994) is to rotate by gamma around z, then by beta around the new y, then by alpha around the new z again, R = Rz'(a).Ry'(b).Rz(g) Compare this with Jorge's equation 13.2.2.3 which he explicitly states applies to rotations about fixed axes, not rotated axes (but using my notation): R = Rz(a).Ry(b).Rz(g) i.e. first by gamma about z, then by beta about the *fixed* y axis, then by alpha about the *fixed* z axis. The same formula cannot apply to both rotations about fixed and rotated axes at the same time! Looking at Jorge's equation 13.2.2.1 it's plain that the correct version involving rotated axes is (again substituting my own notation which should be obvious): R = Rz'(g).Ry'(b).Rz(a) i.e. the correct statement is that the rotation is generated by rotating first by alpha about z, then by beta about the rotated y axis (y'), then by gamma about the rotated z axis (z'). Of course it may well be that Phil's equation is based on an older version of Jorge's analysis perhaps using a different convention in his Acta Cryst. (1994), A50, 157-163 paper, but unfortunately I don't have online access to AC(A) to check it out, maybe someone who has access could do so. In fact it's quite obvious looking at the individual matrices Rz(a) Ry(b) at the bottom of page 1358 in Phil's paper that they must apply to fixed not rotating axes, because if say the Ry(b) matrix were for rotation about the rotated y axis, it would have to be a function of gamma: applying the Rz(g) matrix as given in the paper first to the y-axis vector (0,1,0) gives the rotated y-axis vector (-sin(g),cos(g),0). Similarly if the Rz(a) matrix represented rotation about the rotated z axis it would have to be a function of both beta gamma and plainly it's not. This all goes to show that a) even the experts sometimes get it wrong particularly where matrix algebra is concerned, and b) you should avoid the concept of rotating about rotated axes like the plague! -- Ian -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Bernhard Rupp Sent: 12 August 2007 20:37 To: CCP4BB@JISCMAIL.AC.UK Subject: CCP4 rotation convention Dear programmers - Phil Evans writes in acta D57 1355 (2001) on p 1358 section 5.2: the convention used in AMoRe (Navaza, 1994) and other CCP4 programs (Collaborative Computational Project, Number 4, 1994) is to rotate by gamma around z, then by beta around the new y, then by alpha around the new z again, R = Rz(al)Ry(be)Rz(ga) This seems correct, as the first rotation is applied first to vector x, then the second to the new one, etc, thus x' = (Rz(al)(Ry(be)(Rz(ga)x))) In J.Appl.Cryst. 30 402-410 (1977) in the convrot description, Sascha Uzhumtsev lists in table one for (Navaza 1994): alpha about Z, beta about Y and gamma about new Z and gives the *same* resulting rotation Rz(al)Ry(be)Rz(ga) This seems to be a contradiction I cannot resolve? Thx, br - Bernhard Rupp 001 (925) 209-7429 +43 (676) 571-0536 [EMAIL PROTECTED] [EMAIL PROTECTED] http://www.ruppweb.org/ - People can be divided in three classes: The few who make things happen The many who watch things happen And the overwhelming majority who have no idea what is happening. - Disclaimer This communication is confidential and may contain privileged information intended solely for the named addressee(s). It may not be used or disclosed except for the purpose for which it has been sent. If you are not the intended recipient you must not review, use, disclose, copy, distribute or take any action in reliance upon it. If you have received this communication in error, please notify Astex Therapeutics Ltd by emailing [EMAIL PROTECTED] and destroy all copies of the message and any attached documents. Astex Therapeutics Ltd monitors, controls and protects all its messaging traffic in compliance with its corporate email policy. The Company accepts no liability or responsibility for any onward transmission or use of emails and attachments having left the Astex Therapeutics domain. Unless expressly stated, opinions in this message are those of the individual sender and not of Astex
Re: [ccp4bb] CCP4 rotation convention
Just my own amount of salt in the Rotation function soup... I just want to try defending the poor little Euler angles. First, Euler invented them... Yes ! Second, only Euler angles yield a very nice interpretation of Rot Funct symmetry in terms of space group. See the two venerable papers: Tollin, Main Rossmann, Acta Cryst 20 (1966) 404 and Narasinga, Jih Hartsuck, Acta Cryst A36(1980) 878 Third, only Euler angles yield a very practical and intuitive thing, namely it does not matter rotating by (alpha, beta,gamma) in the usual way, or first, prerotating by gamma around Z (but without rotating any axes !) and then making the alpha rotation around Z (rotating now the axes) followed by the beta rotation around the new Y. This is most easily seen with a cylinder that one rotates in the two ways. Last, the inverse rotation matrix of the Euler matrix defined by (alpha, beta, gamma) is just the Euler matrix defined by (-gamma, -beta, -alpha). Ian, isn't worth the effort ? Philippe Dumas IBMC-CNRS, UPR9002 15, rue René Descartes 67084 Strasbourg cedex tel: +33 (0)3 88 41 70 02 [EMAIL PROTECTED] -Message d'origine- De : CCP4 bulletin board [mailto:[EMAIL PROTECTED] la part de Ian Tickle Envoyé : Monday, August 13, 2007 8:11 PM À : CCP4BB@JISCMAIL.AC.UK Objet : Re: [ccp4bb] CCP4 rotation convention Hi folks I hate to say this but I think everyone here has got it wrong to some degree (including myself - and I hereby retract my previous e-mail and issue the correction below!). If you don't believe me then read digest Jorge Navaza's article Rotation functions in Int. Tab. Vol. F (sect 13.2, p. 269), particularly sections 13.2.2 and Appendix A13.2.1.1. Phil's article in Acta D57 1355-1359 (2001), i.e. the 2001 S/W proceedings, states: ... the convention used in AMoRe (Navaza, 1994) and other CCP4 programs (Collaborative Computational Project, Number 4, 1994) is to rotate by gamma around z, then by beta around the new y, then by alpha around the new z again, R = Rz'(a).Ry'(b).Rz(g) Compare this with Jorge's equation 13.2.2.3 which he explicitly states applies to rotations about fixed axes, not rotated axes (but using my notation): R = Rz(a).Ry(b).Rz(g) i.e. first by gamma about z, then by beta about the *fixed* y axis, then by alpha about the *fixed* z axis. The same formula cannot apply to both rotations about fixed and rotated axes at the same time! Looking at Jorge's equation 13.2.2.1 it's plain that the correct version involving rotated axes is (again substituting my own notation which should be obvious): R = Rz'(g).Ry'(b).Rz(a) i.e. the correct statement is that the rotation is generated by rotating first by alpha about z, then by beta about the rotated y axis (y'), then by gamma about the rotated z axis (z'). Of course it may well be that Phil's equation is based on an older version of Jorge's analysis perhaps using a different convention in his Acta Cryst. (1994), A50, 157-163 paper, but unfortunately I don't have online access to AC(A) to check it out, maybe someone who has access could do so. In fact it's quite obvious looking at the individual matrices Rz(a) Ry(b) at the bottom of page 1358 in Phil's paper that they must apply to fixed not rotating axes, because if say the Ry(b) matrix were for rotation about the rotated y axis, it would have to be a function of gamma: applying the Rz(g) matrix as given in the paper first to the y-axis vector (0,1,0) gives the rotated y-axis vector (-sin(g),cos(g),0). Similarly if the Rz(a) matrix represented rotation about the rotated z axis it would have to be a function of both beta gamma and plainly it's not. This all goes to show that a) even the experts sometimes get it wrong particularly where matrix algebra is concerned, and b) you should avoid the concept of rotating about rotated axes like the plague! -- Ian -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Bernhard Rupp Sent: 12 August 2007 20:37 To: CCP4BB@JISCMAIL.AC.UK Subject: CCP4 rotation convention Dear programmers - Phil Evans writes in acta D57 1355 (2001) on p 1358 section 5.2: the convention used in AMoRe (Navaza, 1994) and other CCP4 programs (Collaborative Computational Project, Number 4, 1994) is to rotate by gamma around z, then by beta around the new y, then by alpha around the new z again, R = Rz(al)Ry(be)Rz(ga) This seems correct, as the first rotation is applied first to vector x, then the second to the new one, etc, thus x' = (Rz(al)(Ry(be)(Rz(ga)x))) In J.Appl.Cryst. 30 402-410 (1977) in the convrot description, Sascha Uzhumtsev lists in table one for (Navaza 1994): alpha about Z, beta about Y and gamma about new Z and gives the *same* resulting rotation Rz(al)Ry(be)Rz(ga) This seems to be a contradiction I cannot resolve? Thx, br - Bernhard Rupp 001 (925) 209-7429 +43 (676) 571-0536 [EMAIL
Re: [ccp4bb] domains missing
Hi, Did you do rigid body refinement or regular minimization? If over half your structure is missing, anything besides rigid body refinement will probably just bias the phases toward nothing in the rest of the asymmetric unit. I've had correct molrep solutions with R-factors that high, so there is hope. But depending on how you refined your partial model, you could have a completely wrong solution with that R-factor as well. How sure are you that your solution is really correct? If you take the rigid-body-refined-only model (to minimize phase bias), and delete something you know should be well-ordered (a fat side chain if you've got good data, a helix if you've got lousy data), then make an Fo-Fc map, does it reappear? If not, forget all the statistics and start over with your searches. If yes, can you see any sign of the other domains in that map, that solvent modification might help bring up from the land of noise? Phoebe Rice At 02:38 PM 8/13/2007, you wrote: Hi, ccp4 community, I am solving my protein (300 aa) structure using molecular replacement. The space group is P622. There is only one molecule in the ASU. The protein is supported to have three domains. We have solved the domain 1 (120aa) structure; therefore we tried to use it as a model to solve the new structure. MolRep and Phaser can find the domain 1. We refined the model and the R and Rfree factor was around 50%. When we used Coot to see the model and map, we found that the other two domains are missing. In the map, there is a big 'hole' and little extra density (with 6-fold) inside. It is a big surprise to us. Is there any possibility that R is around 50 if the other two domains are missing? Any suggests to figure out what happen to my structure? Thanks a lot! Mousheng Wu --- Phoebe A. Rice Assoc. Prof., Dept. of Biochemistry Molecular Biology The University of Chicago phone 773 834 1723 fax 773 702 0439 http://bmb.bsd.uchicago.edu/index.html http://www.nasa.gov/mission_pages/cassini/multimedia/pia06064.html
Re: [ccp4bb] CCP4 rotation convention
How about this (may be way off base): Any transformation can be seen either as moving of the coordinates in a fixed coordinate system, or as a change of coordinates and expressing the position of the same object with respect to the new coordinates. In molecular replacement it is convenient to think of it as a change in coordinates, with the old coordinates being along the old cell axes (or some orthogonalization of them) and the new coordinates along the new cell. gamma is rotation about z in the old cell, beta is the nose-down you do before plopping it into the new cell, and alpha is rotation about the z axis in the new cell. Take a physical example: My MR model is a proper dimer with its dimer 2-fold along Z. Lets drive it over into the new cell according to rotation function results. I see there are two equal results with gamma differing by 180. That's because my model has two-fold symmetry about z (old z, that is). I pick either gamma, rotate about my models axis that much, then rotate about x by beta (but mind you, x doesn't pass through my model the way it used to- this is new x. Now I assume I am in the new coordinate system and rotate about z again- only this time z is not along my dimer axis. The new cell has 3-fold crystallograhic symmetry about z, so I see the rotsol alpha is 3-fold degenerate. Rotation about z is mathematically rotation about z, whether it be the old z or new z, i.e. the matrix has a special simple form like cos sin 0 -sin cos 0 0 01 Otherwise there would be no point in factoring single matrix into three equally general matrices. Ed
Re: [ccp4bb] extra density on Cysteine
Hi, They're likely both BME adducts, just in the first case the CH2CH2OH portion is way more disordered. Artem _ From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of [EMAIL PROTECTED] Sent: Monday, August 13, 2007 9:59 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] extra density on Cysteine Dear all, I am refining a 2.0A structure. I found that there were some extra density on two cysteines, even though I have added 5mM BME in the protein buffer. I am wondering whether the first one (Cys292) is a bme and the second one is an oxidized cysteine. Any suggestion? I attached the images for your reference. thanks Regards _ Xu Ting ,Ph.D 10 Biopolis Road Singapore 138670 Fax: +65 6722 2916 Phone: +65 6722 2980
Re: [ccp4bb] CCP4 rotation convention
Someone should design a device like a compass gimbal with an extra ring for teaching euler's angles, patent it (Gnu hardware license- world demand is probably 100 pieces), and persuade Hampton research or MitEGen to manufacture it. The device (picture at (http://sb20.lbl.gov/berry/Euler2.gif), but I'm no artist) consists of 3 concentric rings: The outer ring is mounted by external studs in an F-shaped support so it can rotate about a vertical diameter (alpha, new Z). One of the bearings has a brass disk with degree marks etched and an indicator on the ring reads alpha angle. The central ring is connected to the outer ring by by horizontal bearings, allowing it to rotate about a horizontal diameter. Likewise a brass disk indicates the beta angle. The innermost ring is connected to the central ring by vertical bearings, allowing it to rotate about a vertical axis (when beta and alpha are zero). An indicator read gamma. Inside the inner ring is suspended an asymmetric object like a pointing hand or arrow painted red on one side and green on the other. Also wire axes indicating x,y,z direction in the original crystal. The F-shaped mounting bracket would have x,y,z direction in the target crystal indicated (and they would be the same when alpha, beta, and gamma are zero, i.e. the rings are coplanar). Playing with this would take some of the abstractness out of Euler angles. It would also let the student resolve for herself the apparent contradiction that all orientations can be reached by the inner object, despite the fact that two of the rotations are (initially) coaxial. Ed
