[PyMOL] symexp

[kanika sharma]

I used symexp command for 3QK9 using distance of 2.75 to generate
ASU(asymmetric unit). Does symexp generate these symmetry mates from the
remark290 of PDB file? I couldnot find the code for symexp in pymolwiki. Can
anyone help out?




Regards,
Kanika

[Hongbo Zhu]

Hi, Kanika,

The source code can be found at function
ExecutiveSymExp()
in the file
./trunk/pymol/layer3/Executive.c

Normally, a PDB is equivalent to an ASU (except for some cases like
capsid). "Symexp is used to reconstruct neighboring ASUs."
( http://pymolwiki.org/index.php/Symexp )
It seems REMARK 290 that contains crystallographic symmetry
transformations is used for computing the positions of neighboring ASUs.

But be careful with some of the capsid cases (e.g. 3p0s). The symexp
will not generate any neighboring molecules as they are not related by
crystallographic symmetry, but non-crystallographic symmetry.

BTW, it seems symexp has a bug when running on 3p0s. It does not return
after displaying the message:
"ExecutiveSymExp: Generating symmetry mates..."

regards,
hongbo

Post by kanika sharma
I used symexp command for 3QK9 using distance of 2.75 to generate
ASU(asymmetric unit). Does symexp generate these symmetry mates from the
remark290 of PDB file? I couldnot find the code for symexp in pymolwiki.
Can anyone help out?
Regards,
Kanika
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Hongbo ZHU
Postdoctoral Researcher
Structural Bioinformatics

Technische Universität Dresden
Biotechnology Center
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E-Mail: hongbo.zhu at biotec
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[Thomas Holder]

Post by Hongbo Zhu
It seems REMARK 290 that contains crystallographic symmetry
transformations is used for computing the positions of neighboring ASUs.

the CRYST1 record is sufficient for generating symmetry mates, so
pymol most likely does not read REMARK 290.

Cheers,
Thomas

[kanika sharma]

Should not the positions of ASU's generated by REMARK290 be same as the
symmetry mates generated?

[Tsjerk Wassenaar]

Hi Kanika,

They should. The CRYST1 record holds all the information required to
build the crystal. Do note that the symexp command generates
neighbouring symmetry mates, given a cut off distance. It does not
build the filled unit cell. Thomas put a script on the wiki last year
to build you that: http://www.pymolwiki.org/index.php/Supercell

Cheers,

Tsjerk

Post by kanika sharma
Should not the positions of ASU's generated by REMARK290 be same as the
symmetry mates generated?
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[Hongbo Zhu]

You are right, Thomas! The information is redundant in REMARK 290.

I just performed a small test which confirms your conclusion:
remove CRYST1 will make symexp to complain "ExecutiveSymExp-Error: No
symmetry loaded!" even if REMARK 290 is present, while removing REMARK
290 does not have any effect on symexp.

don't know whether it make sense to monitor both cryst1 and remark 290...

Post by Thomas Holder

Post by Hongbo Zhu
It seems REMARK 290 that contains crystallographic symmetry
transformations is used for computing the positions of neighboring ASUs.

the CRYST1 record is sufficient for generating symmetry mates, so
pymol most likely does not read REMARK 290.
Cheers,
Thomas