Re: [ccp4bb] artificial tetramer
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Hi Fred, this sentence of yours, All pdb's are superposed by a common sequence region, which also will be part of the tetramer interface. probably hides the information which would be necessary for a reasonable answer to your question. If you still are stuck, you might post again with a more detailed description of what you mean. Cheers, Tim On 12/13/2011 07:28 PM, Fred wrote: Dear CCP4bb list, Thank you very much all of you who have answered my post. I'm really sorry if I was unclear. Such operation is so unusual that I could be able to express myself appropriately. From quick reading some replies (James Stroud and Guillaume Ponchel), it seems is possible do build artificial tetramers with Coot. Several problems have been raised like clashes, unusual interfaces and so on. A second step would be to take Coot's rotation and translation matrix and apply it to all pdb's in batch mode with pdbset. All pdb's are superposed by a common sequence region, which also will be part of the tetramer interface. I'll try to make things work. Once more, sorry for any inconvenience and thank you very much. Kind regards, Fred - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.10 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iD8DBQFO6G0aUxlJ7aRr7hoRAlMyAJ9ekKa8oatBgpiNsumGCzJtG1Gu9QCgq5Q7 ZDe36RL5FfSU1usr2p7AZxw= =QHqV -END PGP SIGNATURE-
Re: [ccp4bb] artificial tetramer
Hi Tim, Thanks for your replay. All pdb monomers have the same primary sequence and a perfect matching long helix, which I have used to superpose the coordinates. Such helix is almost straight so that, the idea would be to create a vector along the helix main axis, shift this axis to a some distance (perhaps minimizing clashes) and apply 4-fold rotation. A second step would be to take these into pdbset to make things in batch mode. It sounds simple, but don't know the easiest way/programs to do that. I can do just the basics in Coot. I remember that Xfit had some options to trace vectors inside a cell and give it rotation properties. However, Xfit seems to be frozen and integration with pdbset would be painful. Regards, Fred Em 14-12-2011 07:32, Tim Gruene escreveu: -BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Hi Fred, this sentence of yours, All pdb's are superposed by a common sequence region, which also will be part of the tetramer interface. probably hides the information which would be necessary for a reasonable answer to your question. If you still are stuck, you might post again with a more detailed description of what you mean. Cheers, Tim On 12/13/2011 07:28 PM, Fred wrote: Dear CCP4bb list, Thank you very much all of you who have answered my post. I'm really sorry if I was unclear. Such operation is so unusual that I could be able to express myself appropriately. From quick reading some replies (James Stroud and Guillaume Ponchel), it seems is possible do build artificial tetramers with Coot. Several problems have been raised like clashes, unusual interfaces and so on. A second step would be to take Coot's rotation and translation matrix and apply it to all pdb's in batch mode with pdbset. All pdb's are superposed by a common sequence region, which also will be part of the tetramer interface. I'll try to make things work. Once more, sorry for any inconvenience and thank you very much. Kind regards, Fred - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.10 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iD8DBQFO6G0aUxlJ7aRr7hoRAlMyAJ9ekKa8oatBgpiNsumGCzJtG1Gu9QCgq5Q7 ZDe36RL5FfSU1usr2p7AZxw= =QHqV -END PGP SIGNATURE-
Re: [ccp4bb] artificial tetramer
This sounds as though you will create a 4-helical rod? There are lots of 4-helical bundles but they arenot completely rod like - there is a twist in most I have seen. Maybe you should do secondary structure matching to a suitable 4-helicl bundle, match your helix in turn to each of the bundle helices. Eleanor On 12/14/2011 02:13 PM, Fred wrote: Hi Tim, Thanks for your replay. All pdb monomers have the same primary sequence and a perfect matching long helix, which I have used to superpose the coordinates. Such helix is almost straight so that, the idea would be to create a vector along the helix main axis, shift this axis to a some distance (perhaps minimizing clashes) and apply 4-fold rotation. A second step would be to take these into pdbset to make things in batch mode. It sounds simple, but don't know the easiest way/programs to do that. I can do just the basics in Coot. I remember that Xfit had some options to trace vectors inside a cell and give it rotation properties. However, Xfit seems to be frozen and integration with pdbset would be painful. Regards, Fred Em 14-12-2011 07:32, Tim Gruene escreveu: -BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Hi Fred, this sentence of yours, All pdb's are superposed by a common sequence region, which also will be part of the tetramer interface. probably hides the information which would be necessary for a reasonable answer to your question. If you still are stuck, you might post again with a more detailed description of what you mean. Cheers, Tim On 12/13/2011 07:28 PM, Fred wrote: Dear CCP4bb list, Thank you very much all of you who have answered my post. I'm really sorry if I was unclear. Such operation is so unusual that I could be able to express myself appropriately. From quick reading some replies (James Stroud and Guillaume Ponchel), it seems is possible do build artificial tetramers with Coot. Several problems have been raised like clashes, unusual interfaces and so on. A second step would be to take Coot's rotation and translation matrix and apply it to all pdb's in batch mode with pdbset. All pdb's are superposed by a common sequence region, which also will be part of the tetramer interface. I'll try to make things work. Once more, sorry for any inconvenience and thank you very much. Kind regards, Fred - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.10 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iD8DBQFO6G0aUxlJ7aRr7hoRAlMyAJ9ekKa8oatBgpiNsumGCzJtG1Gu9QCgq5Q7 ZDe36RL5FfSU1usr2p7AZxw= =QHqV -END PGP SIGNATURE-
Re: [ccp4bb] artificial tetramer
Dear Fred, In this case, I would take one monomer and edit the CRYST1 card of the pdb to have a sufficiently large tetragonal unit cell. Next I would manually align the helix of one monomer with the fourfold axis, e.g. the Z-axis. If you display the unit cell, you will get e.g. the 0,Z,0 axis to guide you. Then I would manually translate the monomer such that it forms a nice tetramer with its symmetry mates and would write out these symmetry mates. Once you have one good tetramer, you can (or have somebody) write a script to superimpose all your other monomers onto this template. My two cents,... Herman -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Fred Sent: Wednesday, December 14, 2011 3:13 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] artificial tetramer Hi Tim, Thanks for your replay. All pdb monomers have the same primary sequence and a perfect matching long helix, which I have used to superpose the coordinates. Such helix is almost straight so that, the idea would be to create a vector along the helix main axis, shift this axis to a some distance (perhaps minimizing clashes) and apply 4-fold rotation. A second step would be to take these into pdbset to make things in batch mode. It sounds simple, but don't know the easiest way/programs to do that. I can do just the basics in Coot. I remember that Xfit had some options to trace vectors inside a cell and give it rotation properties. However, Xfit seems to be frozen and integration with pdbset would be painful. Regards, Fred Em 14-12-2011 07:32, Tim Gruene escreveu: -BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Hi Fred, this sentence of yours, All pdb's are superposed by a common sequence region, which also will be part of the tetramer interface. probably hides the information which would be necessary for a reasonable answer to your question. If you still are stuck, you might post again with a more detailed description of what you mean. Cheers, Tim On 12/13/2011 07:28 PM, Fred wrote: Dear CCP4bb list, Thank you very much all of you who have answered my post. I'm really sorry if I was unclear. Such operation is so unusual that I could be able to express myself appropriately. From quick reading some replies (James Stroud and Guillaume Ponchel), it seems is possible do build artificial tetramers with Coot. Several problems have been raised like clashes, unusual interfaces and so on. A second step would be to take Coot's rotation and translation matrix and apply it to all pdb's in batch mode with pdbset. All pdb's are superposed by a common sequence region, which also will be part of the tetramer interface. I'll try to make things work. Once more, sorry for any inconvenience and thank you very much. Kind regards, Fred - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.10 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iD8DBQFO6G0aUxlJ7aRr7hoRAlMyAJ9ekKa8oatBgpiNsumGCzJtG1Gu9QCgq5Q7 ZDe36RL5FfSU1usr2p7AZxw= =QHqV -END PGP SIGNATURE-
Re: [ccp4bb] artificial tetramer
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Hello Fred, as far as I understand your problem I am not aware of existing programs to carry out the tasks. To automatise the process I would write a program myself which takes the PDB-file and the reside numbers which make that helix as input and: 1) determine the axis of that straight helix (probably by determining the moments of intertia, see e.g. Gruene, T. Sheldrick, G. M. (2011). Acta Cryst. A67, 1-8, section 2.2.1 with x_o the centre of mass. 2) copy the monomer by 3 rotations of 90 degrees about this axis to get the tetramer. 3) move each of the four monomers stepwise perpendicularly to the rotation axis until no more clashes are there (mask the volume of one monomer and check each atom/atom volume whether it falls into that volume. Because of the 4-fold rotation axis you only need to mask one monomer and check against its next and its opposite neighbour). The tricky bit w.r.t automatisation would be to determine the helix axis, unless you already have a list of composing residues for each PDB-file. That's probably nothing I would finish in a week's time, though... Tim On 12/14/2011 03:13 PM, Fred wrote: Hi Tim, Thanks for your replay. All pdb monomers have the same primary sequence and a perfect matching long helix, which I have used to superpose the coordinates. Such helix is almost straight so that, the idea would be to create a vector along the helix main axis, shift this axis to a some distance (perhaps minimizing clashes) and apply 4-fold rotation. A second step would be to take these into pdbset to make things in batch mode. It sounds simple, but don't know the easiest way/programs to do that. I can do just the basics in Coot. I remember that Xfit had some options to trace vectors inside a cell and give it rotation properties. However, Xfit seems to be frozen and integration with pdbset would be painful. Regards, Fred Em 14-12-2011 07:32, Tim Gruene escreveu: Hi Fred, this sentence of yours, All pdb's are superposed by a common sequence region, which also will be part of the tetramer interface. probably hides the information which would be necessary for a reasonable answer to your question. If you still are stuck, you might post again with a more detailed description of what you mean. Cheers, Tim On 12/13/2011 07:28 PM, Fred wrote: Dear CCP4bb list, Thank you very much all of you who have answered my post. I'm really sorry if I was unclear. Such operation is so unusual that I could be able to express myself appropriately. From quick reading some replies (James Stroud and Guillaume Ponchel), it seems is possible do build artificial tetramers with Coot. Several problems have been raised like clashes, unusual interfaces and so on. A second step would be to take Coot's rotation and translation matrix and apply it to all pdb's in batch mode with pdbset. All pdb's are superposed by a common sequence region, which also will be part of the tetramer interface. I'll try to make things work. Once more, sorry for any inconvenience and thank you very much. Kind regards, Fred -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.10 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iD8DBQFO6LusUxlJ7aRr7hoRAk5QAJ0ewv3ZjLRSU9fF1c2xBDDypcLX6ACg5+2P X01grlPsYcSeWZbQWIVtXD0= =Fse5 -END PGP SIGNATURE-
Re: [ccp4bb] artificial tetramer
An old old trick for getting a straight helix along a crystal axis using the GUI. Run the Amore TABLING step - it is part of the GUI with the helix as your model. (See molecular replacement - amore suite.) Amore calculates the ppl axes and will align it along the Z axis .. Thank you Jorge.. Eleanor On 12/14/2011 03:07 PM, Tim Gruene wrote: -BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Hello Fred, as far as I understand your problem I am not aware of existing programs to carry out the tasks. To automatise the process I would write a program myself which takes the PDB-file and the reside numbers which make that helix as input and: 1) determine the axis of that straight helix (probably by determining the moments of intertia, see e.g. Gruene, T. Sheldrick, G. M. (2011). Acta Cryst. A67, 1-8, section 2.2.1 with x_o the centre of mass. 2) copy the monomer by 3 rotations of 90 degrees about this axis to get the tetramer. 3) move each of the four monomers stepwise perpendicularly to the rotation axis until no more clashes are there (mask the volume of one monomer and check each atom/atom volume whether it falls into that volume. Because of the 4-fold rotation axis you only need to mask one monomer and check against its next and its opposite neighbour). The tricky bit w.r.t automatisation would be to determine the helix axis, unless you already have a list of composing residues for each PDB-file. That's probably nothing I would finish in a week's time, though... Tim On 12/14/2011 03:13 PM, Fred wrote: Hi Tim, Thanks for your replay. All pdb monomers have the same primary sequence and a perfect matching long helix, which I have used to superpose the coordinates. Such helix is almost straight so that, the idea would be to create a vector along the helix main axis, shift this axis to a some distance (perhaps minimizing clashes) and apply 4-fold rotation. A second step would be to take these into pdbset to make things in batch mode. It sounds simple, but don't know the easiest way/programs to do that. I can do just the basics in Coot. I remember that Xfit had some options to trace vectors inside a cell and give it rotation properties. However, Xfit seems to be frozen and integration with pdbset would be painful. Regards, Fred Em 14-12-2011 07:32, Tim Gruene escreveu: Hi Fred, this sentence of yours, All pdb's are superposed by a common sequence region, which also will be part of the tetramer interface. probably hides the information which would be necessary for a reasonable answer to your question. If you still are stuck, you might post again with a more detailed description of what you mean. Cheers, Tim On 12/13/2011 07:28 PM, Fred wrote: Dear CCP4bb list, Thank you very much all of you who have answered my post. I'm really sorry if I was unclear. Such operation is so unusual that I could be able to express myself appropriately. From quick reading some replies (James Stroud and Guillaume Ponchel), it seems is possible do build artificial tetramers with Coot. Several problems have been raised like clashes, unusual interfaces and so on. A second step would be to take Coot's rotation and translation matrix and apply it to all pdb's in batch mode with pdbset. All pdb's are superposed by a common sequence region, which also will be part of the tetramer interface. I'll try to make things work. Once more, sorry for any inconvenience and thank you very much. Kind regards, Fred -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.10 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iD8DBQFO6LusUxlJ7aRr7hoRAk5QAJ0ewv3ZjLRSU9fF1c2xBDDypcLX6ACg5+2P X01grlPsYcSeWZbQWIVtXD0= =Fse5 -END PGP SIGNATURE-
Re: [ccp4bb] artificial tetramer
I've done this sort of thing (but different) using the Clipper libraries in C++. I found it easier to write short programs to do specific tasks rather than try to write generic all-purpose tools Phil On 14 Dec 2011, at 15:07, Tim Gruene wrote: -BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Hello Fred, as far as I understand your problem I am not aware of existing programs to carry out the tasks. To automatise the process I would write a program myself which takes the PDB-file and the reside numbers which make that helix as input and: 1) determine the axis of that straight helix (probably by determining the moments of intertia, see e.g. Gruene, T. Sheldrick, G. M. (2011). Acta Cryst. A67, 1-8, section 2.2.1 with x_o the centre of mass. 2) copy the monomer by 3 rotations of 90 degrees about this axis to get the tetramer. 3) move each of the four monomers stepwise perpendicularly to the rotation axis until no more clashes are there (mask the volume of one monomer and check each atom/atom volume whether it falls into that volume. Because of the 4-fold rotation axis you only need to mask one monomer and check against its next and its opposite neighbour). The tricky bit w.r.t automatisation would be to determine the helix axis, unless you already have a list of composing residues for each PDB-file. That's probably nothing I would finish in a week's time, though... Tim On 12/14/2011 03:13 PM, Fred wrote: Hi Tim, Thanks for your replay. All pdb monomers have the same primary sequence and a perfect matching long helix, which I have used to superpose the coordinates. Such helix is almost straight so that, the idea would be to create a vector along the helix main axis, shift this axis to a some distance (perhaps minimizing clashes) and apply 4-fold rotation. A second step would be to take these into pdbset to make things in batch mode. It sounds simple, but don't know the easiest way/programs to do that. I can do just the basics in Coot. I remember that Xfit had some options to trace vectors inside a cell and give it rotation properties. However, Xfit seems to be frozen and integration with pdbset would be painful. Regards, Fred Em 14-12-2011 07:32, Tim Gruene escreveu: Hi Fred, this sentence of yours, All pdb's are superposed by a common sequence region, which also will be part of the tetramer interface. probably hides the information which would be necessary for a reasonable answer to your question. If you still are stuck, you might post again with a more detailed description of what you mean. Cheers, Tim On 12/13/2011 07:28 PM, Fred wrote: Dear CCP4bb list, Thank you very much all of you who have answered my post. I'm really sorry if I was unclear. Such operation is so unusual that I could be able to express myself appropriately. From quick reading some replies (James Stroud and Guillaume Ponchel), it seems is possible do build artificial tetramers with Coot. Several problems have been raised like clashes, unusual interfaces and so on. A second step would be to take Coot's rotation and translation matrix and apply it to all pdb's in batch mode with pdbset. All pdb's are superposed by a common sequence region, which also will be part of the tetramer interface. I'll try to make things work. Once more, sorry for any inconvenience and thank you very much. Kind regards, Fred -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.10 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iD8DBQFO6LusUxlJ7aRr7hoRAk5QAJ0ewv3ZjLRSU9fF1c2xBDDypcLX6ACg5+2P X01grlPsYcSeWZbQWIVtXD0= =Fse5 -END PGP SIGNATURE-
Re: [ccp4bb] artificial tetramer
I am a bit puzzled - do you know the direction of the rotation axis which can be converted to polar phi/psi angles, a mid point you want to rotate about, and the distance of the centre of mass of your molecule from that point, from which you could find the tranlation shift? If so I could design a script for pdbset rotat polar phi psi 90 tran tx1 ty1 tz1 Then rotat polar phi psi 180 tran tx2 ty2 tz2 And rotat polar phi psi -90 tran tx3 ty3 tz3 You would have to reassemble the tetramer from the 4 copies. Eleanor On 12/12/2011 07:49 PM, Fred wrote: Hi List, I would like to build an artificial tetramer from a monomer PBD file. All that I have is the coordinates it self with CRYST/CELL information cards. The artificial 4-fold axis has an arbitrary orientation into the cell. I mean, its not parallel to any crystallographic axis and have to be at a certain distance of the molecule. This sounds conceptually simple, but I would like to do that in batch mode for hundreds of PDB's. Could someone, please, tell me the easiest way/program to do that? Thanks in advance, Fred
Re: [ccp4bb] artificial tetramer
Do you mean just any tetramer? If so, Why not use an existing one - eg haemoglobin.. Eleanor On 12/12/2011 09:42 PM, Fred wrote: I only want to produce an artificial tetramer. Em 12-12-2011 19:41, Jacob Keller escreveu: Can you clarify your reason for doing this? JPK On Mon, Dec 12, 2011 at 3:36 PM, Fredccp4bb.l...@gmail.com wrote: Hi James, In my first post arbitrary orientation into the cell only means not parallel to any crystallographic axis, which would simplify things very much. I want to apply the 4-fold axis to the protein coordinates. If I have a cell and therefore an origin, I can take a point at any distance of the origin, pass a vector/axis through it and take the 3 others molecules by symmetry. That's trivial, given the point, the orientation and the property of the rotation. Don't know which program to use. Regards, Fred Em 12-12-2011 19:18, James Stroud escreveu: This is not trivial. Assuming an arbitrary origin, the simplest 4-fold symmetry operation (4-fold rotation) has 5 free parameters (translation along the symmetry axis is irrelevant). The biggest problem is determining the values for these parameters. For example, once you apply the symmetry, your molecule may clash with its symmetry mates or not even contact them. And even if you solve this latter problem automatically (which is not trivial because of irregularity), that leaves a net of 3 parameters describing the orientation of the protomer. James On Dec 12, 2011, at 1:34 PM, Fred wrote: Hi Tim, Thanks for your message and sorry if I wasn't clear. I don't have neither the axis orientation nor the rotation matrix. I would like to create them but don't know how and which program to use. Theoretically a have to create a axis (vector) at some distance of the molecule into the cell and give it the 4-fold propriety. Quite simple, but don't which program to use. Regards, Fred Em 12-12-2011 18:23, Tim Gruene escreveu: -BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Hello Fred, if you know the rotation matrix, you can use pdbset with its 'rotate' keyword. It is not clear to me whether or not you have the rotation matrix or how you define rotation. Cheers, Tim On 12/12/2011 08:49 PM, Fred wrote: Hi List, I would like to build an artificial tetramer from a monomer PBD file. All that I have is the coordinates it self with CRYST/CELL information cards. The artificial 4-fold axis has an arbitrary orientation into the cell. I mean, its not parallel to any crystallographic axis and have to be at a certain distance of the molecule. This sounds conceptually simple, but I would like to do that in batch mode for hundreds of PDB's. Could someone, please, tell me the easiest way/program to do that? Thanks in advance, Fred - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.10 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iD8DBQFO5mKwUxlJ7aRr7hoRAsyuAKDfnH50sG/EuKiFz7tCzgTUtnZrdQCg3zSn cqs8GHOu5M3JQahA/CofR1k= =tDUj -END PGP SIGNATURE-
Re: [ccp4bb] artificial tetramer
Dear CCP4bb list, Thank you very much all of you who have answered my post. I'm really sorry if I was unclear. Such operation is so unusual that I could be able to express myself appropriately. From quick reading some replies (James Stroud and Guillaume Ponchel), it seems is possible do build artificial tetramers with Coot. Several problems have been raised like clashes, unusual interfaces and so on. A second step would be to take Coot's rotation and translation matrix and apply it to all pdb's in batch mode with pdbset. All pdb's are superposed by a common sequence region, which also will be part of the tetramer interface. I'll try to make things work. Once more, sorry for any inconvenience and thank you very much. Kind regards, Fred
Re: [ccp4bb] artificial tetramer
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Hello Fred, if you know the rotation matrix, you can use pdbset with its 'rotate' keyword. It is not clear to me whether or not you have the rotation matrix or how you define rotation. Cheers, Tim On 12/12/2011 08:49 PM, Fred wrote: Hi List, I would like to build an artificial tetramer from a monomer PBD file. All that I have is the coordinates it self with CRYST/CELL information cards. The artificial 4-fold axis has an arbitrary orientation into the cell. I mean, its not parallel to any crystallographic axis and have to be at a certain distance of the molecule. This sounds conceptually simple, but I would like to do that in batch mode for hundreds of PDB's. Could someone, please, tell me the easiest way/program to do that? Thanks in advance, Fred - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.10 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iD8DBQFO5mKwUxlJ7aRr7hoRAsyuAKDfnH50sG/EuKiFz7tCzgTUtnZrdQCg3zSn cqs8GHOu5M3JQahA/CofR1k= =tDUj -END PGP SIGNATURE-
Re: [ccp4bb] artificial tetramer
Hi Tim, Thanks for your message and sorry if I wasn't clear. I don't have neither the axis orientation nor the rotation matrix. I would like to create them but don't know how and which program to use. Theoretically a have to create a axis (vector) at some distance of the molecule into the cell and give it the 4-fold propriety. Quite simple, but don't which program to use. Regards, Fred Em 12-12-2011 18:23, Tim Gruene escreveu: -BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Hello Fred, if you know the rotation matrix, you can use pdbset with its 'rotate' keyword. It is not clear to me whether or not you have the rotation matrix or how you define rotation. Cheers, Tim On 12/12/2011 08:49 PM, Fred wrote: Hi List, I would like to build an artificial tetramer from a monomer PBD file. All that I have is the coordinates it self with CRYST/CELL information cards. The artificial 4-fold axis has an arbitrary orientation into the cell. I mean, its not parallel to any crystallographic axis and have to be at a certain distance of the molecule. This sounds conceptually simple, but I would like to do that in batch mode for hundreds of PDB's. Could someone, please, tell me the easiest way/program to do that? Thanks in advance, Fred - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.10 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iD8DBQFO5mKwUxlJ7aRr7hoRAsyuAKDfnH50sG/EuKiFz7tCzgTUtnZrdQCg3zSn cqs8GHOu5M3JQahA/CofR1k= =tDUj -END PGP SIGNATURE-
Re: [ccp4bb] artificial tetramer
at few Angstrons of the protein. Em 12-12-2011 19:01, Jacob Keller escreveu: How do you know where to put the axis? JPK On Mon, Dec 12, 2011 at 2:34 PM, Fredccp4bb.l...@gmail.com wrote: Hi Tim, Thanks for your message and sorry if I wasn't clear. I don't have neither the axis orientation nor the rotation matrix. I would like to create them but don't know how and which program to use. Theoretically a have to create a axis (vector) at some distance of the molecule into the cell and give it the 4-fold propriety. Quite simple, but don't which program to use. Regards, Fred Em 12-12-2011 18:23, Tim Gruene escreveu: -BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Hello Fred, if you know the rotation matrix, you can use pdbset with its 'rotate' keyword. It is not clear to me whether or not you have the rotation matrix or how you define rotation. Cheers, Tim On 12/12/2011 08:49 PM, Fred wrote: Hi List, I would like to build an artificial tetramer from a monomer PBD file. All that I have is the coordinates it self with CRYST/CELL information cards. The artificial 4-fold axis has an arbitrary orientation into the cell. I mean, its not parallel to any crystallographic axis and have to be at a certain distance of the molecule. This sounds conceptually simple, but I would like to do that in batch mode for hundreds of PDB's. Could someone, please, tell me the easiest way/program to do that? Thanks in advance, Fred - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.10 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iD8DBQFO5mKwUxlJ7aRr7hoRAsyuAKDfnH50sG/EuKiFz7tCzgTUtnZrdQCg3zSn cqs8GHOu5M3JQahA/CofR1k= =tDUj -END PGP SIGNATURE-
Re: [ccp4bb] artificial tetramer
This is not trivial. Assuming an arbitrary origin, the simplest 4-fold symmetry operation (4-fold rotation) has 5 free parameters (translation along the symmetry axis is irrelevant). The biggest problem is determining the values for these parameters. For example, once you apply the symmetry, your molecule may clash with its symmetry mates or not even contact them. And even if you solve this latter problem automatically (which is not trivial because of irregularity), that leaves a net of 3 parameters describing the orientation of the protomer. James On Dec 12, 2011, at 1:34 PM, Fred wrote: Hi Tim, Thanks for your message and sorry if I wasn't clear. I don't have neither the axis orientation nor the rotation matrix. I would like to create them but don't know how and which program to use. Theoretically a have to create a axis (vector) at some distance of the molecule into the cell and give it the 4-fold propriety. Quite simple, but don't which program to use. Regards, Fred Em 12-12-2011 18:23, Tim Gruene escreveu: -BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Hello Fred, if you know the rotation matrix, you can use pdbset with its 'rotate' keyword. It is not clear to me whether or not you have the rotation matrix or how you define rotation. Cheers, Tim On 12/12/2011 08:49 PM, Fred wrote: Hi List, I would like to build an artificial tetramer from a monomer PBD file. All that I have is the coordinates it self with CRYST/CELL information cards. The artificial 4-fold axis has an arbitrary orientation into the cell. I mean, its not parallel to any crystallographic axis and have to be at a certain distance of the molecule. This sounds conceptually simple, but I would like to do that in batch mode for hundreds of PDB's. Could someone, please, tell me the easiest way/program to do that? Thanks in advance, Fred - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.10 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iD8DBQFO5mKwUxlJ7aRr7hoRAsyuAKDfnH50sG/EuKiFz7tCzgTUtnZrdQCg3zSn cqs8GHOu5M3JQahA/CofR1k= =tDUj -END PGP SIGNATURE-
Re: [ccp4bb] artificial tetramer
Hi James, In my first post arbitrary orientation into the cell only means not parallel to any crystallographic axis, which would simplify things very much. I want to apply the 4-fold axis to the protein coordinates. If I have a cell and therefore an origin, I can take a point at any distance of the origin, pass a vector/axis through it and take the 3 others molecules by symmetry. That's trivial, given the point, the orientation and the property of the rotation. Don't know which program to use. Regards, Fred Em 12-12-2011 19:18, James Stroud escreveu: This is not trivial. Assuming an arbitrary origin, the simplest 4-fold symmetry operation (4-fold rotation) has 5 free parameters (translation along the symmetry axis is irrelevant). The biggest problem is determining the values for these parameters. For example, once you apply the symmetry, your molecule may clash with its symmetry mates or not even contact them. And even if you solve this latter problem automatically (which is not trivial because of irregularity), that leaves a net of 3 parameters describing the orientation of the protomer. James On Dec 12, 2011, at 1:34 PM, Fred wrote: Hi Tim, Thanks for your message and sorry if I wasn't clear. I don't have neither the axis orientation nor the rotation matrix. I would like to create them but don't know how and which program to use. Theoretically a have to create a axis (vector) at some distance of the molecule into the cell and give it the 4-fold propriety. Quite simple, but don't which program to use. Regards, Fred Em 12-12-2011 18:23, Tim Gruene escreveu: -BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Hello Fred, if you know the rotation matrix, you can use pdbset with its 'rotate' keyword. It is not clear to me whether or not you have the rotation matrix or how you define rotation. Cheers, Tim On 12/12/2011 08:49 PM, Fred wrote: Hi List, I would like to build an artificial tetramer from a monomer PBD file. All that I have is the coordinates it self with CRYST/CELL information cards. The artificial 4-fold axis has an arbitrary orientation into the cell. I mean, its not parallel to any crystallographic axis and have to be at a certain distance of the molecule. This sounds conceptually simple, but I would like to do that in batch mode for hundreds of PDB's. Could someone, please, tell me the easiest way/program to do that? Thanks in advance, Fred - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.10 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iD8DBQFO5mKwUxlJ7aRr7hoRAsyuAKDfnH50sG/EuKiFz7tCzgTUtnZrdQCg3zSn cqs8GHOu5M3JQahA/CofR1k= =tDUj -END PGP SIGNATURE-
Re: [ccp4bb] artificial tetramer
Can you clarify your reason for doing this? JPK On Mon, Dec 12, 2011 at 3:36 PM, Fred ccp4bb.l...@gmail.com wrote: Hi James, In my first post arbitrary orientation into the cell only means not parallel to any crystallographic axis, which would simplify things very much. I want to apply the 4-fold axis to the protein coordinates. If I have a cell and therefore an origin, I can take a point at any distance of the origin, pass a vector/axis through it and take the 3 others molecules by symmetry. That's trivial, given the point, the orientation and the property of the rotation. Don't know which program to use. Regards, Fred Em 12-12-2011 19:18, James Stroud escreveu: This is not trivial. Assuming an arbitrary origin, the simplest 4-fold symmetry operation (4-fold rotation) has 5 free parameters (translation along the symmetry axis is irrelevant). The biggest problem is determining the values for these parameters. For example, once you apply the symmetry, your molecule may clash with its symmetry mates or not even contact them. And even if you solve this latter problem automatically (which is not trivial because of irregularity), that leaves a net of 3 parameters describing the orientation of the protomer. James On Dec 12, 2011, at 1:34 PM, Fred wrote: Hi Tim, Thanks for your message and sorry if I wasn't clear. I don't have neither the axis orientation nor the rotation matrix. I would like to create them but don't know how and which program to use. Theoretically a have to create a axis (vector) at some distance of the molecule into the cell and give it the 4-fold propriety. Quite simple, but don't which program to use. Regards, Fred Em 12-12-2011 18:23, Tim Gruene escreveu: -BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Hello Fred, if you know the rotation matrix, you can use pdbset with its 'rotate' keyword. It is not clear to me whether or not you have the rotation matrix or how you define rotation. Cheers, Tim On 12/12/2011 08:49 PM, Fred wrote: Hi List, I would like to build an artificial tetramer from a monomer PBD file. All that I have is the coordinates it self with CRYST/CELL information cards. The artificial 4-fold axis has an arbitrary orientation into the cell. I mean, its not parallel to any crystallographic axis and have to be at a certain distance of the molecule. This sounds conceptually simple, but I would like to do that in batch mode for hundreds of PDB's. Could someone, please, tell me the easiest way/program to do that? Thanks in advance, Fred - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.10 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iD8DBQFO5mKwUxlJ7aRr7hoRAsyuAKDfnH50sG/EuKiFz7tCzgTUtnZrdQCg3zSn cqs8GHOu5M3JQahA/CofR1k= =tDUj -END PGP SIGNATURE- -- *** Jacob Pearson Keller Northwestern University Medical Scientist Training Program email: j-kell...@northwestern.edu ***
Re: [ccp4bb] artificial tetramer
I only want to produce an artificial tetramer. Em 12-12-2011 19:41, Jacob Keller escreveu: Can you clarify your reason for doing this? JPK On Mon, Dec 12, 2011 at 3:36 PM, Fredccp4bb.l...@gmail.com wrote: Hi James, In my first post arbitrary orientation into the cell only means not parallel to any crystallographic axis, which would simplify things very much. I want to apply the 4-fold axis to the protein coordinates. If I have a cell and therefore an origin, I can take a point at any distance of the origin, pass a vector/axis through it and take the 3 others molecules by symmetry. That's trivial, given the point, the orientation and the property of the rotation. Don't know which program to use. Regards, Fred Em 12-12-2011 19:18, James Stroud escreveu: This is not trivial. Assuming an arbitrary origin, the simplest 4-fold symmetry operation (4-fold rotation) has 5 free parameters (translation along the symmetry axis is irrelevant). The biggest problem is determining the values for these parameters. For example, once you apply the symmetry, your molecule may clash with its symmetry mates or not even contact them. And even if you solve this latter problem automatically (which is not trivial because of irregularity), that leaves a net of 3 parameters describing the orientation of the protomer. James On Dec 12, 2011, at 1:34 PM, Fred wrote: Hi Tim, Thanks for your message and sorry if I wasn't clear. I don't have neither the axis orientation nor the rotation matrix. I would like to create them but don't know how and which program to use. Theoretically a have to create a axis (vector) at some distance of the molecule into the cell and give it the 4-fold propriety. Quite simple, but don't which program to use. Regards, Fred Em 12-12-2011 18:23, Tim Gruene escreveu: -BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Hello Fred, if you know the rotation matrix, you can use pdbset with its 'rotate' keyword. It is not clear to me whether or not you have the rotation matrix or how you define rotation. Cheers, Tim On 12/12/2011 08:49 PM, Fred wrote: Hi List, I would like to build an artificial tetramer from a monomer PBD file. All that I have is the coordinates it self with CRYST/CELL information cards. The artificial 4-fold axis has an arbitrary orientation into the cell. I mean, its not parallel to any crystallographic axis and have to be at a certain distance of the molecule. This sounds conceptually simple, but I would like to do that in batch mode for hundreds of PDB's. Could someone, please, tell me the easiest way/program to do that? Thanks in advance, Fred - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.10 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iD8DBQFO5mKwUxlJ7aRr7hoRAsyuAKDfnH50sG/EuKiFz7tCzgTUtnZrdQCg3zSn cqs8GHOu5M3JQahA/CofR1k= =tDUj -END PGP SIGNATURE-
Re: [ccp4bb] artificial tetramer
Coot can do this using the Rubik's Cube principle: transform to some state where the operation can be performed, perform the operation, then transform back. So, in coot, I would (1) rotate the molecule to the appropriate orientation (2) move to the appropriate place in the unit cell (3) change the symmetry to P4 (3) apply P4 symmetry (4) change the symmetry back to whatever (5) move the tetramer back to the appropriate place in the unit cell (6) rotate the molecule back Then, your original molecule will be in the original place surrounded by it's symmetry mates. James On Dec 12, 2011, at 2:36 PM, Fred wrote: Hi James, In my first post arbitrary orientation into the cell only means not parallel to any crystallographic axis, which would simplify things very much. I want to apply the 4-fold axis to the protein coordinates. If I have a cell and therefore an origin, I can take a point at any distance of the origin, pass a vector/axis through it and take the 3 others molecules by symmetry. That's trivial, given the point, the orientation and the property of the rotation. Don't know which program to use. Regards, Fred Em 12-12-2011 19:18, James Stroud escreveu: This is not trivial. Assuming an arbitrary origin, the simplest 4-fold symmetry operation (4-fold rotation) has 5 free parameters (translation along the symmetry axis is irrelevant). The biggest problem is determining the values for these parameters. For example, once you apply the symmetry, your molecule may clash with its symmetry mates or not even contact them. And even if you solve this latter problem automatically (which is not trivial because of irregularity), that leaves a net of 3 parameters describing the orientation of the protomer. James On Dec 12, 2011, at 1:34 PM, Fred wrote: Hi Tim, Thanks for your message and sorry if I wasn't clear. I don't have neither the axis orientation nor the rotation matrix. I would like to create them but don't know how and which program to use. Theoretically a have to create a axis (vector) at some distance of the molecule into the cell and give it the 4-fold propriety. Quite simple, but don't which program to use. Regards, Fred Em 12-12-2011 18:23, Tim Gruene escreveu: -BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Hello Fred, if you know the rotation matrix, you can use pdbset with its 'rotate' keyword. It is not clear to me whether or not you have the rotation matrix or how you define rotation. Cheers, Tim On 12/12/2011 08:49 PM, Fred wrote: Hi List, I would like to build an artificial tetramer from a monomer PBD file. All that I have is the coordinates it self with CRYST/CELL information cards. The artificial 4-fold axis has an arbitrary orientation into the cell. I mean, its not parallel to any crystallographic axis and have to be at a certain distance of the molecule. This sounds conceptually simple, but I would like to do that in batch mode for hundreds of PDB's. Could someone, please, tell me the easiest way/program to do that? Thanks in advance, Fred - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.10 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iD8DBQFO5mKwUxlJ7aRr7hoRAsyuAKDfnH50sG/EuKiFz7tCzgTUtnZrdQCg3zSn cqs8GHOu5M3JQahA/CofR1k= =tDUj -END PGP SIGNATURE-
