Re: [ccp4bb] Regarding symmetry notion in coot
On 06/21/2018 03:34 PM, John Berrisford wrote:
From a PDB deposition point of view, I echo Paul’s comment. If possible,
please move your molecule closer to the origin. It helps with the curation
process and is easier for users of your entry as some software struggles with
such extreme transformations.
Regards
John
Now that we've all read the manual :),
Since the origin shift in question here is always integral: { 1 0 1 }
It seems this is not about _where_ in the unit cell, but in _which_ unit cell.
As I understand it the symop: -X, Y+1/2, Z + (0 -1 1)
is what would work if you were in the first cell { 0 0 0 }
So you need to
Take the current coordinate X =x,y,z
subtract the origin translation O = { 1 0 1 },
apply the symop S = -X, Y+1/2, Z + (0 -1 1) = -X,Y,Z +(0,-1/2,1)
add back the origin translation O
something like X' = S(X-O) + O
which could take three runs of pdbset.
But you could really work out an operator that would do it in one run:
the symop S consists of a rotation and translation
S(x) = M(x) + T
S(X-O) = M(X-O) +T
S(X-O) = M(X) - M(O) +T
X' = S(X-O) + O = M(X) - M(O) + T + O
In the example given, M = -X,Y,Z; T = (0,-1/2,1); O = (1 0 1)
M(O) = -1,0,1
-M(O) = 1,0,-1
add T gives 1,-1/2,0
add O gives 2,-1/2,1
so the operator should be
-X+2,Y-1/2,Z+1
or something like that, which you could use in pdbset.
Matrix inverts along x, coordinates are way positive in x, result way negative,
need to add 2 unit cell translations to position it adjacent to orig
coordinates
Would something like that work?
*From:*CCP4 bulletin board *On Behalf Of *Paul Emsley
*Sent:* 21 June 2018 17:30
*To:* CCP4BB@JISCMAIL.AC.UK
*Subject:* Re: [ccp4bb] Regarding symmetry notion in coot
On 20/06/18 20:49, Anurag Misra wrote:
What is the meaning of the last field — the one in curly brackets -- that
describes the symmetry transformation of a given molecule in coot?
See Section 4.11 of Coot User Manual: "Symmetry"
For example, for
a given X Y Z, coot displays the symmetry transformation of an equivalent
position as " -X, Y+1/2, Z + (0 -1 1) & { 1 0 1 }”.
Can the symmetry molecule be written like bellow by summing respective
values?
In the general case, no. Move your molecule closer to the origin - so that the
pre-translation is (0,0,0) - then coot will report "conventional" symmetry.
Regards,
Paul.
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Re: [ccp4bb] Regarding symmetry notion in coot
And so does MOLREP.. Phaser too please? E And Paul - yes; please cut and paste.. E On 21 June 2018 at 20:00, George Sheldrick wrote: > For small molecules, programs such as SHELXT move the structure to be as > near as possible to the center of the unit-cell, not the origin. Failure to > do so may cause a 'checkCIF alert'. > > George > > > On 06/21/2018 09:34 PM, John Berrisford wrote: > > From a PDB deposition point of view, I echo Paul’s comment. If possible, > please move your molecule closer to the origin. It helps with the curation > process and is easier for users of your entry as some software struggles > with such extreme transformations. > > > > Regards > > > > John > > > > -- > Prof. George M. Sheldrick FRS > Dept. Structural Chemistry, > University of Goettingen, > Tammannstr. 4, > D37077 Goettingen, Germany > Tel: +49-551-39-33021 or +49-5594-227312 > > > > -- > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 > To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
Re: [ccp4bb] Regarding symmetry notion in coot
For small molecules, programs such as SHELXT move the structure to be as near as possible to the center of the unit-cell, not the origin. Failure to do so may cause a 'checkCIF alert'. George On 06/21/2018 09:34 PM, John Berrisford wrote: From a PDB deposition point of view, I echo Paul’s comment. If possible, please move your molecule closer to the origin. It helps with the curation process and is easier for users of your entry as some software struggles with such extreme transformations. Regards John -- Prof. George M. Sheldrick FRS Dept. Structural Chemistry, University of Goettingen, Tammannstr. 4, D37077 Goettingen, Germany Tel: +49-551-39-33021 or +49-5594-227312 To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
Re: [ccp4bb] Regarding symmetry notion in coot
>From a PDB deposition point of view, I echo Paul’s comment. If possible,
>please move your molecule closer to the origin. It helps with the curation
>process and is easier for users of your entry as some software struggles with
>such extreme transformations.
Regards
John
From: CCP4 bulletin board On Behalf Of Paul Emsley
Sent: 21 June 2018 17:30
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Regarding symmetry notion in coot
On 20/06/18 20:49, Anurag Misra wrote:
What is the meaning of the last field — the one in curly brackets -- that
describes the symmetry transformation of a given molecule in coot?
See Section 4.11 of Coot User Manual: "Symmetry"
For example, for
a given X Y Z, coot displays the symmetry transformation of an equivalent
position as " -X, Y+1/2, Z + (0 -1 1) & { 1 0 1 }”.
Can the symmetry molecule be written like bellow by summing respective values?
In the general case, no. Move your molecule closer to the origin - so that the
pre-translation is (0,0,0) - then coot will report "conventional" symmetry.
Regards,
Paul.
_
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Re: [ccp4bb] Regarding symmetry notion in coot
On 21/06/18 18:36, Eleanor Dodson wrote: > Paul - where and what is the definition of this line?? > > Dear Eleanor, It is not clear to me how I should answer other than cutting and pasting Section 4.11 "Symmetry" of the manual. Is that what you want me to do? Regards, Paul. To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
Re: [ccp4bb] Regarding symmetry notion in coot
Paul - where and what is the definition of this line??
eleanor
On 21 June 2018 at 17:29, Paul Emsley wrote:
>
> On 20/06/18 20:49, Anurag Misra wrote:
>
> What is the meaning of the last field — the one in curly brackets -- that
> describes the symmetry transformation of a given molecule in coot?
>
>
> See Section 4.11 of Coot User Manual: "Symmetry"
>
> For example, for
> a given X Y Z, coot displays the symmetry transformation of an equivalent
> position as " -X, Y+1/2, Z + (0 -1 1) & { 1 0 1 }”.
>
> Can the symmetry molecule be written like bellow by summing respective values?
>
>
>
>
> In the general case, no. Move your molecule closer to the origin - so that
> the pre-translation is (0,0,0) - then coot will report "conventional"
> symmetry.
>
> Regards,
>
> Paul.
>
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
>
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Re: [ccp4bb] Regarding symmetry notion in coot
On 20/06/18 20:49, Anurag Misra wrote:
> What is the meaning of the last field — the one in curly brackets -- that
> describes the symmetry transformation of a given molecule in coot?
See Section 4.11 of Coot User Manual: "Symmetry"
> For example, for
> a given X Y Z, coot displays the symmetry transformation of an equivalent
> position as " -X, Y+1/2, Z + (0 -1 1) & { 1 0 1 }”.
>
> Can the symmetry molecule be written like bellow by summing respective values?
>
>
In the general case, no. Move your molecule closer to the origin - so
that the pre-translation is (0,0,0) - then coot will report
"conventional" symmetry.
Regards,
Paul.
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https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
[ccp4bb] Regarding symmetry notion in coot
Dear all,
What is the meaning of the last field — the one in curly brackets -- that
describes the symmetry transformation of a given molecule in coot? For
example, for
a given X Y Z, coot displays the symmetry transformation of an equivalent
position as " -X, Y+1/2, Z + (0 -1 1) & { 1 0 1 }”.
Can the symmetry molecule be written like bellow by summing respective values?
-X+0+1, Y+1/2+(-1)+0, Z+1+1
Thanks.
Best regards,
Anurag
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