Re: [cctbxbb] 26-fold symm expansion of asu?

Many thanks for your replies. Pavel : by "slow" I meant to (a) apply sym ops to asu and refer results back to unit cell thus obtaining a "full" unit cell (I expect "expand_to_p1()" does this?) (b) translate the cell and (c) find overlap with the 26-brick neighborhood of the starting brick. This should work but seems inefficient. Marat: applying SymOps to the basis vectors seems a great idea. However, it wasn't clear to me how to combine sg SymOps to yield the 26 adjacent bricks. Does the map expansion code do this? On 07/23/2014 12:00 PM, [email protected] wrote:

Send cctbxbb mailing list submissions to [email protected]

To subscribe or unsubscribe via the World Wide Web, visit http://phenix-online.org/mailman/listinfo/cctbxbb or, via email, send a message with subject or body 'help' to [email protected]

You can reach the person managing the list at [email protected]

When replying, please edit your Subject line so it is more specific than "Re: Contents of cctbxbb digest..."

Today's Topics:

1. Re: 26-fold symm expansion of asu? (Pavel Afonine) 2. Re: 26-fold symm expansion of asu? (Mustyakimov, Marat)

----------------------------------------------------------------------

Message: 1 Date: Tue, 22 Jul 2014 18:58:32 -0700 From: Pavel Afonine To: cctbx mailing list Cc: "Mustyakimov, Marat" Subject: Re: [cctbxbb] 26-fold symm expansion of asu? Message-ID: <[email protected]> Content-Type: text/plain; charset=ISO-8859-1; format=flowed

Hi Alastair,

I think I can write a piece of code using cctbx that would do what you want and probably that would be what you call "slow". Could you please explain some more what it is for and why, and may be give some context? Perhaps that helps me to see if we have something similar already available..

For instance we have very efficient code that computes maps in ASU, and also that expands map in ASU into the whole P1 box. This is something Marat wrote recently and is very efficient. May be you can reuse that or at least harvest ideas?

I'm copying to Marat in case he has comments.

Pavel

On 7/21/14, 2:14 PM, Alastair Fyfe wrote:

...

Hi, I'd be grateful for any pointers to clipper or cctbx code that addresses the following: given a "brick" of map grid coordinates that enclose the asu, obtain the 26 symmetry-related "bricks" which contact it. Calculating this by successively generating symmetry mates and testing seems slow; I was wondering whether there was a better way. thank you, Alastair Fyfe UCSC _______________________________________________ cctbxbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/cctbxbb

------------------------------

Message: 2 Date: Wed, 23 Jul 2014 14:01:13 +0000 From: "Mustyakimov, Marat" To: Pavel Afonine Cc: cctbx mailing list Subject: Re: [cctbxbb] 26-fold symm expansion of asu? Message-ID: <[email protected]> Content-Type: text/plain; charset="iso-8859-1"

The fast way to generate symmetry equivalent ASU: Apply symmetry operation to unit vectors: ex = SymOp*(1,0,0), ey=SymOp*(0,1,0) and ez=SymOp*(0,0,1); Then every map point of the symmetry related asu is obtained from the original one: new_ijk = i*ex + j*ey + k*ez where (i,j,k) is the grid point in the original ASU.

Marat Mustyakimov P.O. Box 2008, Bldg. 8600, MS-6475 Oak Ridge National Lab Oak Ridge TN 37831 USA e-mail: [email protected]mailto:[email protected] e-mail: [email protected]mailto:[email protected] Tel: +1-865-253-3924

On Jul 22, 2014, at 9:58 PM, Pavel Afonine mailto:[email protected]> wrote:

Hi Alastair,

I think I can write a piece of code using cctbx that would do what you want and probably that would be what you call "slow". Could you please explain some more what it is for and why, and may be give some context? Perhaps that helps me to see if we have something similar already available..

For instance we have very efficient code that computes maps in ASU, and also that expands map in ASU into the whole P1 box. This is something Marat wrote recently and is very efficient. May be you can reuse that or at least harvest ideas?

I'm copying to Marat in case he has comments.

Pavel

On 7/21/14, 2:14 PM, Alastair Fyfe wrote: Hi, I'd be grateful for any pointers to clipper or cctbx code that addresses the following: given a "brick" of map grid coordinates that enclose the asu, obtain the 26 symmetry-related "bricks" which contact it. Calculating this by successively generating symmetry mates and testing seems slow; I was wondering whether there was a better way. thank you, Alastair Fyfe UCSC _______________________________________________ cctbxbb mailing list [email protected]mailto:[email protected] http://phenix-online.org/mailman/listinfo/cctbxbb

------------------------------

_______________________________________________ cctbxbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/cctbxbb

End of cctbxbb Digest, Vol 64, Issue 2 **************************************