Re: [ccp4bb] Map transformation

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CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

Previous message:
Subject: refmac5 and sphericity restraints, 2nd attempt
From: Jan Abendroth jan {- dot -} abendroth {- at -} GMAIL {- dot -} COM
Date: 2010-02-08

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Subject: Re: reforigin on 2FKA
From: "George M {- dot -} Sheldrick" gsheldr {- at -} SHELX {- dot -} UNI-AC {- dot -} GWDG {- dot -} DE
Date: 2010-02-08

Subject: Re: Map transformation
From: Paul Emsley paul {- dot -} emsley {- at -} BIOCH {- dot -} OX {- dot -} AC {- dot -} UK
Date: 2010-02-08

Rana Refaey wrote:
> Hi all,
>
> I am trying to use the transform map command in coot but i am getting the
> following error
> 6:19: In expression (0.9956 -0.08709 -0.03537 ...)::6:19: Wrong type to
> apply: 0.9956
>
> the command that i used was:
> (transform-map 13 (0.9956 -0.08709 -0.03537 -0.08702 -0.9962 0.003531
> -0.03554 -0.0004371 -0.9994) (1.235 1.005 0.1625) (11.6806 -8.6401 -14.960) 10)
>
> i have also added the word list before each group of numbers,
> (transform-map 13 (list 0.9956 -0.08709 -0.03537 -0.08702 -0.9962 0.003531
> -0.03554 -0.0004371 -0.9994) (list 1.235 1.005 0.1625) (list 11.6806 -8.6401
> -14.960) 10)
>
> and i got the following error,
> arguments to transform-map incomprehensible: args: (13 (0.9956 -0.08709
> -0.03537 -0.08702 -0.9962 0.003531 -0.03554 -4.371e-4 -0.9994) (1.235 1.005
> 0.1625) (11.6806 -8.6401 -14.96) 10)
>
> I am not sure what i am doing wrong, could you please point me in the right
> direction ?
>

Dear Rana Refaey,

It seems that the documentation is inconsistent with the functionality
(i.e. there is (was) either an error in the manual or the code, take
your pick).

Your courses of actions are:

1) Tomorrow morning pick up pre-release revision 2790 from here:

http://www.biop.ox.ac.uk/coot/devel/build-info.html

2) right now you can drop in the replacement coot-utils.scm which you
can get from here:

http://coot.googlecode.com/svn/trunk/scheme/coot-utils.scm

3) Alternatively and right now (as JED says) provide the cell and
space-group too:

(transform-map 13 (list 0.9956 -0.08709 -0.03537 -0.08702 -0.9962 0.003531 -0.03554 -0.0004371 -0.9994) (list 1.235 1.005 0.1625) (list 11.6806 -8.6401 -14.960) 10 (show-spacegroup 13) (cell 13))

And as JED also said, you are doing something pretty jolly sophisticated if "Transform map by LSQ" won't do what you want.

Thanks,

Paul.

CCP4bb navigation

CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

Previous message:
Subject: refmac5 and sphericity restraints, 2nd attempt
From: Jan Abendroth jan {- dot -} abendroth {- at -} GMAIL {- dot -} COM
Date: 2010-02-08

Next message:
Subject: Re: reforigin on 2FKA
From: "George M {- dot -} Sheldrick" gsheldr {- at -} SHELX {- dot -} UNI-AC {- dot -} GWDG {- dot -} DE
Date: 2010-02-08