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 <ksharma...@gmail.com> 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 <tsje...@gmail.com>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 <ksharma...@gmail.com> >> 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 <tsje...@gmail.com> >> > 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" <ksharma...@gmail.com> 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 >> > >
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