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From: kanika sharma <ksharma997@gm...>  20110226 07:12:43
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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 
From: Tsjerk Wassenaar <tsjerkw@gm...>  20110228 07:09:39
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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,40.6z) 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" <ksharma997@...> 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 
From: kanika sharma <ksharma997@gm...>  20110228 07:16:38
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Iv applied the foll eq: load 1b8e.pdb, A create B,A alter_state 1,B,(x,y,z)=(x,y,40.60z) 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 <tsjerkw@...>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,40.6z) > > 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" <ksharma997@...> 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 > > 
From: Tsjerk Wassenaar <tsjerkw@gm...>  20110228 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 <ksharma997@...> wrote: > Iv applied the foll eq: > > load 1b8e.pdb, A > create B,A > alter_state 1,B,(x,y,z)=(x,y,40.60z) > > 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 <tsjerkw@...> > 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,40.6z) >> >> 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" <ksharma997@...> 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. postdoctoral researcher Molecular Dynamics Group * Groningen Institute for Biomolecular Research and Biotechnology * Zernike Institute for Advanced Materials University of Groningen The Netherlands 
From: kanika sharma <ksharma997@gm...>  20110228 07:57:02
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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 <tsjerkw@...> 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 <ksharma997@...> > wrote: > > Iv applied the foll eq: > > > > load 1b8e.pdb, A > > create B,A > > alter_state 1,B,(x,y,z)=(x,y,40.60z) > > > > 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 <tsjerkw@...> > > 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,40.6z) > >> > >> 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" <ksharma997@...> 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. > > postdoctoral researcher > Molecular Dynamics Group > * Groningen Institute for Biomolecular Research and Biotechnology > * Zernike Institute for Advanced Materials > University of Groningen > The Netherlands > 
From: kanika sharma <ksharma997@gm...>  20110228 11:08:49
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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 <ksharma997@...> 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 <tsjerkw@...>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 <ksharma997@...> >> wrote: >> > Iv applied the foll eq: >> > >> > load 1b8e.pdb, A >> > create B,A >> > alter_state 1,B,(x,y,z)=(x,y,40.60z) >> > >> > 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 <tsjerkw@...> >> > 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,40.6z) >> >> >> >> 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" <ksharma997@...> 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. >> >> postdoctoral researcher >> Molecular Dynamics Group >> * Groningen Institute for Biomolecular Research and Biotechnology >> * Zernike Institute for Advanced Materials >> University of Groningen >> The Netherlands >> > > 
From: Tsjerk Wassenaar <tsjerkw@gm...>  20110226 09:03:33
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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" <ksharma997@...> 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 RealTime 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/splunkdev2dev _______________________________________________ PyMOLusers mailing list (PyMOLusers@...) Info Page: https://lists.sourceforge.net/lists/listinfo/pymolusers Archives: http://www.mailarchive.com/pymolusers@... 
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