## [PyMOL] dimerization

 [PyMOL] dimerization From: kanika sharma - 2011-02-26 07:12:43 Attachments: Message as HTML ```Does anyone know how to apply these biometric constraints to generate a dimer of my molecule???? REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 i think first 3 cols represent rotation and last 3 rep translation...But how to do it?? Regards, kanika ```

 [PyMOL] dimerization From: kanika sharma - 2011-02-26 07:12:43 Attachments: Message as HTML ```Does anyone know how to apply these biometric constraints to generate a dimer of my molecule???? REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 i think first 3 cols represent rotation and last 3 rep translation...But how to do it?? Regards, kanika ```
 Re: [PyMOL] dimerization From: Tsjerk Wassenaar - 2011-02-28 07:09:39 Attachments: Message as HTML ```Hi Kanika, Let's say your protein is called 'protein'. Then you can obtain the other unit corresponding to your second biomt operation as: create unit2, protein alter_state 1,unit2,(y,z)=(-y,40.6-z) Note this is a shorthand specific to your case. For a full biomt record (R t), with R being the rotation matrix (first three columns) and t the translation vector (last column), you would have to make the equation reflect the matrix operation Rp+t. Hope it helps, Tsjerk On Feb 28, 2011 6:46 AM, "kanika sharma" wrote: ok, I know that a dimer can be generated from the BIOMT operationon > monomeric unit of protein. > > I have this protein....but its unclear to me how to apply these transformations and what do they represent.... If somebody knows then please let me know...Its really urgent... REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT... REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 40.60000 Best Regards, Kanika ```
 Re: [PyMOL] dimerization From: kanika sharma - 2011-02-28 07:16:38 Attachments: Message as HTML ```Iv applied the foll eq: load 1b8e.pdb, A create B,A alter_state 1,B,(x,y,z)=(x,-y,40.60-z) it should form a dimer of my protein but the object "B" is same as my monomer with no change... i am unable to find the error.. On Mon, Feb 28, 2011 at 12:39 PM, Tsjerk Wassenaar wrote: > Hi Kanika, > > Let's say your protein is called 'protein'. Then you can obtain the other > unit corresponding to your second biomt operation as: > > create unit2, protein > alter_state 1,unit2,(y,z)=(-y,40.6-z) > > Note this is a shorthand specific to your case. For a full biomt record (R > t), with R being the rotation matrix (first three columns) and t the > translation vector (last column), you would have to make the equation > reflect the matrix operation Rp+t. > > > Hope it helps, > > > Tsjerk > > > On Feb 28, 2011 6:46 AM, "kanika sharma" wrote: > > ok, I know that a dimer can be generated from the BIOMT operationon >> monomeric unit of protein. >> >> I have this protein....but its unclear to me how to apply these > transformations and what do they represent.... > > If somebody knows then please let me know...Its really urgent... > > REMARK 350 APPLY THE FOLLOWING TO CHAINS: A > > > REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 > REMARK 350 BIOMT... > REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 40.60000 > > > > Best Regards, > Kanika > > ```
 Re: [PyMOL] dimerization From: Tsjerk Wassenaar - 2011-02-28 07:30:36 ```Hi Kanika, 'b' is a selection keyword. For that reason it doesn't make a good object identifier. Try load 1b8e.pdb, 1b8e_A create 1b8e_B,1b8e_A alter_state 1,1b8e_B,(x,y,z)=(-x,y,33.43-/z) Not that the numbers are different. In 1b8e.pdb I find: REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 33.43000 That's quite different from the record you gave previously. If you want to have good help, especially when it's urgent to you, better do your best in providing correct information and thinking along. Cheers, Tsjerk On Mon, Feb 28, 2011 at 8:16 AM, kanika sharma wrote: > Iv applied the foll eq: > > load 1b8e.pdb, A > create B,A > alter_state 1,B,(x,y,z)=(x,-y,40.60-z) > > it should form a dimer of my protein but the object "B" is same as my > monomer with no change... i am unable to find the error.. > > On Mon, Feb 28, 2011 at 12:39 PM, Tsjerk Wassenaar > wrote: >> >> Hi Kanika, >> >> Let's say your protein is called 'protein'. Then you can obtain the other >> unit corresponding to your second biomt operation as: >> >> create unit2, protein >> alter_state 1,unit2,(y,z)=(-y,40.6-z) >> >> Note this is a shorthand specific to your case. For a full biomt record (R >> t), with R being the rotation matrix (first three columns) and t the >> translation vector (last column), you would have to make the equation >> reflect the matrix operation Rp+t. >> >> Hope it helps, >> >> Tsjerk >> >> On Feb 28, 2011 6:46 AM, "kanika sharma" wrote: >> >>> ok, I know that a dimer can be generated from the BIOMT operationon >>> monomeric unit of protein. >> >> I have this protein....but its unclear to me how to apply these >> transformations and what do they represent.... >> If somebody knows then please let me know...Its really urgent... >> >> REMARK 350 APPLY THE FOLLOWING TO CHAINS: A >> >> >> REMARK 350   BIOMT1   1  1.000000  0.000000  0.000000        0.00000 >>       REMARK 350   BIOMT... >> >> REMARK 350   BIOMT3   2  0.000000  0.000000 -1.000000       40.60000 >> >> >> Best Regards, >> Kanika > > -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group * Groningen Institute for Biomolecular Research and Biotechnology * Zernike Institute for Advanced Materials University of Groningen The Netherlands ```
 Re: [PyMOL] dimerization From: kanika sharma - 2011-02-28 07:57:02 Attachments: Message as HTML ```M really sorry for the wrong information guys...script helped a lot.. If my protein is a dimer...Chain A,B....How can i apply the script here?....i dun know for 2 chains.... Thank you..in advance....apologies for previous mistake... REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 Thank you... On Mon, Feb 28, 2011 at 1:00 PM, Tsjerk Wassenaar wrote: > Hi Kanika, > > 'b' is a selection keyword. For that reason it doesn't make a good > object identifier. Try > > load 1b8e.pdb, 1b8e_A > create 1b8e_B,1b8e_A > alter_state 1,1b8e_B,(x,y,z)=(-x,y,33.43-/z) > > Not that the numbers are different. In 1b8e.pdb I find: > > REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 > REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 > REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 > REMARK 350 BIOMT1 2 -1.000000 0.000000 0.000000 0.00000 > REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 > REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 33.43000 > > That's quite different from the record you gave previously. If you > want to have good help, especially when it's urgent to you, better do > your best in providing correct information and thinking along. > > Cheers, > > Tsjerk > > > On Mon, Feb 28, 2011 at 8:16 AM, kanika sharma > wrote: > > Iv applied the foll eq: > > > > load 1b8e.pdb, A > > create B,A > > alter_state 1,B,(x,y,z)=(x,-y,40.60-z) > > > > it should form a dimer of my protein but the object "B" is same as my > > monomer with no change... i am unable to find the error.. > > > > On Mon, Feb 28, 2011 at 12:39 PM, Tsjerk Wassenaar > > wrote: > >> > >> Hi Kanika, > >> > >> Let's say your protein is called 'protein'. Then you can obtain the > other > >> unit corresponding to your second biomt operation as: > >> > >> create unit2, protein > >> alter_state 1,unit2,(y,z)=(-y,40.6-z) > >> > >> Note this is a shorthand specific to your case. For a full biomt record > (R > >> t), with R being the rotation matrix (first three columns) and t the > >> translation vector (last column), you would have to make the equation > >> reflect the matrix operation Rp+t. > >> > >> Hope it helps, > >> > >> Tsjerk > >> > >> On Feb 28, 2011 6:46 AM, "kanika sharma" wrote: > >> > >>> ok, I know that a dimer can be generated from the BIOMT operationon > >>> monomeric unit of protein. > >> > >> I have this protein....but its unclear to me how to apply these > >> transformations and what do they represent.... > >> If somebody knows then please let me know...Its really urgent... > >> > >> REMARK 350 APPLY THE FOLLOWING TO CHAINS: A > >> > >> > >> REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 > >> REMARK 350 BIOMT... > >> > >> REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 40.60000 > >> > >> > >> Best Regards, > >> Kanika > > > > > > > > -- > Tsjerk A. Wassenaar, Ph.D. > > post-doctoral researcher > Molecular Dynamics Group > * Groningen Institute for Biomolecular Research and Biotechnology > * Zernike Institute for Advanced Materials > University of Groningen > The Netherlands > ```
 Re: [PyMOL] dimerization From: kanika sharma - 2011-02-28 11:08:49 Attachments: Message as HTML ```this is an identity matrix so will not make any change,i think....but the file says so... can any one help me...!! Regards, Kanika On Mon, Feb 28, 2011 at 1:26 PM, kanika sharma wrote: > M really sorry for the wrong information guys...script helped a lot.. > > If my protein is a dimer...Chain A,B....How can i apply the script > here?....i dun know for 2 chains.... > > Thank you..in advance....apologies for previous mistake... > > REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B > > REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 > > REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 > > REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 > Thank you... > > > > On Mon, Feb 28, 2011 at 1:00 PM, Tsjerk Wassenaar wrote: > >> Hi Kanika, >> >> 'b' is a selection keyword. For that reason it doesn't make a good >> object identifier. Try >> >> load 1b8e.pdb, 1b8e_A >> create 1b8e_B,1b8e_A >> alter_state 1,1b8e_B,(x,y,z)=(-x,y,33.43-/z) >> >> Not that the numbers are different. In 1b8e.pdb I find: >> >> REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 >> REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 >> REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 >> REMARK 350 BIOMT1 2 -1.000000 0.000000 0.000000 0.00000 >> REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 >> REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 33.43000 >> >> That's quite different from the record you gave previously. If you >> want to have good help, especially when it's urgent to you, better do >> your best in providing correct information and thinking along. >> >> Cheers, >> >> Tsjerk >> >> >> On Mon, Feb 28, 2011 at 8:16 AM, kanika sharma >> wrote: >> > Iv applied the foll eq: >> > >> > load 1b8e.pdb, A >> > create B,A >> > alter_state 1,B,(x,y,z)=(x,-y,40.60-z) >> > >> > it should form a dimer of my protein but the object "B" is same as my >> > monomer with no change... i am unable to find the error.. >> > >> > On Mon, Feb 28, 2011 at 12:39 PM, Tsjerk Wassenaar >> > wrote: >> >> >> >> Hi Kanika, >> >> >> >> Let's say your protein is called 'protein'. Then you can obtain the >> other >> >> unit corresponding to your second biomt operation as: >> >> >> >> create unit2, protein >> >> alter_state 1,unit2,(y,z)=(-y,40.6-z) >> >> >> >> Note this is a shorthand specific to your case. For a full biomt record >> (R >> >> t), with R being the rotation matrix (first three columns) and t the >> >> translation vector (last column), you would have to make the equation >> >> reflect the matrix operation Rp+t. >> >> >> >> Hope it helps, >> >> >> >> Tsjerk >> >> >> >> On Feb 28, 2011 6:46 AM, "kanika sharma" wrote: >> >> >> >>> ok, I know that a dimer can be generated from the BIOMT operationon >> >>> monomeric unit of protein. >> >> >> >> I have this protein....but its unclear to me how to apply these >> >> transformations and what do they represent.... >> >> If somebody knows then please let me know...Its really urgent... >> >> >> >> REMARK 350 APPLY THE FOLLOWING TO CHAINS: A >> >> >> >> >> >> REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 >> >> REMARK 350 BIOMT... >> >> >> >> REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 40.60000 >> >> >> >> >> >> Best Regards, >> >> Kanika >> > >> > >> >> >> >> -- >> Tsjerk A. Wassenaar, Ph.D. >> >> post-doctoral researcher >> Molecular Dynamics Group >> * Groningen Institute for Biomolecular Research and Biotechnology >> * Zernike Institute for Advanced Materials >> University of Groningen >> The Netherlands >> > > ```
 Re: [PyMOL] dimerization From: Tsjerk Wassenaar - 2011-02-26 09:03:33 Attachments: Message as HTML ```Hi Kanika, You're right about the columns for translation and rotation. But since in your case it's an identity matrix, it's not going to help you achieve your goal. Cheers, Tsjerk On Feb 26, 2011 8:14 AM, "kanika sharma" wrote: Does anyone know how to apply these biometric constraints to generate a dimer of my molecule???? REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 i think first 3 cols represent rotation and last 3 rep translation...But how to do it?? Regards, kanika ------------------------------------------------------------------------------ Free Software Download: Index, Search & Analyze Logs and other IT data in Real-Time with Splunk. Collect, index and harness all the fast moving IT data generated by your applications, servers and devices whether physical, virtual or in the cloud. Deliver compliance at lower cost and gain new business insights. http://p.sf.net/sfu/splunk-dev2dev _______________________________________________ PyMOL-users mailing list (PyMOL-users@...) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@... ```