[cctbxbb] 26-fold symm expansion of asu?

[Alastair Fyfe]

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, cctbxbb-request at phenix-online.org wrote:
> Send cctbxbb mailing list submissions to
> 	cctbxbb at phenix-online.org
>
> 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
> 	cctbxbb-request at phenix-online.org
>
> You can reach the person managing the list at
> 	cctbxbb-owner at phenix-online.org
>
> 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 <pafonine at lbl.gov>
> To: cctbx mailing list <cctbxbb at phenix-online.org>
> Cc: "Mustyakimov, Marat" <mustyakimovm at ornl.gov>
> Subject: Re: [cctbxbb] 26-fold symm expansion of asu?
> Message-ID: <53CF16C8.5040504 at lbl.gov>
> 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
>> cctbxbb at phenix-online.org
>> http://phenix-online.org/mailman/listinfo/cctbxbb
>
>
> ------------------------------
>
> Message: 2
> Date: Wed, 23 Jul 2014 14:01:13 +0000
> From: "Mustyakimov, Marat" <mustyakimovm at ornl.gov>
> To: Pavel Afonine <pafonine at lbl.gov>
> Cc: cctbx mailing list <cctbxbb at phenix-online.org>
> Subject: Re: [cctbxbb] 26-fold symm expansion of asu?
> Message-ID: <9457BEEC-4821-4BBB-8D91-E903AAFAE7F0 at ornl.gov>
> 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: mustyakimovm at ornl.gov<mailto:mustyakimovm at ornl.gov>
> e-mail: marat.mustyakimov at gmail.com<mailto:marat.mustyakimov at gmail.com>
> Tel: +1-865-253-3924
>
> On Jul 22, 2014, at 9:58 PM, Pavel Afonine <pafonine at lbl.gov<mailto:pafonine at lbl.gov>> 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
> cctbxbb at phenix-online.org<mailto:cctbxbb at phenix-online.org>
> http://phenix-online.org/mailman/listinfo/cctbxbb
>
>
>
>
> ------------------------------
>
> _______________________________________________
> cctbxbb mailing list
> cctbxbb at phenix-online.org
> http://phenix-online.org/mailman/listinfo/cctbxbb
>
>
> End of cctbxbb Digest, Vol 64, Issue 2
> **************************************