Dear All,
This is my first post to the group - so Hello! I have searched with not much
success to find an answer to my question, so I thought I would try posting here
for some expert advice.
I should start by saying that I am not a crystallographer, but please don't
hold that against me!
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Dear James,
if I understand correctly you want to transform structure B onto
structure A and then compare the crystallographic packing of A and B.
I might be wrong, but I think the most convenient way for the users
would be a display program which
Of
James Davidson
Sent: Wednesday, March 13, 2013 1:58 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Best practice for transformed PDB coordinates?
Dear All,
This is my first post to the group - so Hello! I have searched
Hi James
First off, welcome to CCP4BB!
I think a bit of matrix algebra solves your problem.
Define for the original PDB file:
Xf = SoXo (SCALE transformation orth - fract).
Xs = OoXo (ORIGX orth - submitted)
where upper case means matrix or vector, lower case (subscript) identifies
different
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Best practice for transformed PDB coordinates?
Hi James
First off, welcome to CCP4BB!
I think a bit of matrix algebra solves your problem.
Define
*Subject:* Re: [ccp4bb] Best practice for transformed PDB coordinates?
Hi James
First off, welcome to CCP4BB!
I think a bit of matrix algebra solves your problem.
Define for the original PDB file:
Xf = SoXo (SCALE transformation orth - fract).
Xs = OoXo (ORIGX orth - submitted
On 13 March 2013 14:51, herman.schreu...@sanofi.com wrote:
**
As I see it, there is no need to change the orthogonal coordinates. They
are used in connection with the SYMTRY records to generate the symmetry
mates. Changing the orthogonal coordinates would mean changing the SYMTRY
records,
In the early days of the PDB coordinates were submitted
in many different coordinate systems:
orthogonal
fractional
grid (normalize each cell edge to 100 so that all coordinates
are between 0 and 100)
build physical model using 2 cm per Angstrom parts and then
measure coordinates
Cc: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Best practice for transformed PDB coordinates?
Hi Herman
Yes your solution would also work, and is also safer in the event that
other programs don't know how to handle SCALE ORIGX records
Hi James -
If you need the transformed coordinates in the original form for another
program, this may not help, but if you just want to compare the packing between
structures, have a look at PyMOL's matrix_copy command
(http://pymolwiki.org/index.php/Matrix_copy).
# load your files
load
...@gmail.com]
Sent: Wednesday, March 13, 2013 4:22 PM
To: Schreuder, Herman RD/DE
Cc: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Best practice for transformed PDB
coordinates?
On 13 March 2013 14:51, herman.schreu...@sanofi.com wrote
--
*From:* Ian Tickle [mailto:ianj...@gmail.com]
*Sent:* Wednesday, March 13, 2013 4:22 PM
*To:* Schreuder, Herman RD/DE
*Cc:* CCP4BB@JISCMAIL.AC.UK
*Subject:* Re: [ccp4bb] Best practice for transformed PDB coordinates?
On 13 March 2013 14:51, herman.schreu
for the help!
Kind regards
James
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of
Ian Tickle
Sent: 13 March 2013 15:59
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Best practice for transformed PDB coordinates?
Herman,
Yes you are right. I was assuming that since
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