can any one help me...!!

Regards,

Kanika

On Mon, Feb 28, 2011 at 1:26 PM, kanika sharma <ksharma997@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, BREMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000Thank you...On Mon, Feb 28, 2011 at 1:00 PM, Tsjerk Wassenaar <tsjerkw@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 BIOMT2 1 0.000000 1.000000 0.000000 0.00000

REMARK 350 BIOMT1 1 1.000000 0.000000 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@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 <tsjerkw@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" <ksharma997@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