Cchem: 1 revision

2017-03-06T06:13:45Z

1 revision

Speleo3: created

2017-03-01T17:15:01Z

created

New page

The [[multisave]] command can save a multi-entry PDB file.

Every object in the given selection will have a HEADER record, and is terminated with END. Loading such a multi-entry PDB file into PyMOL will load each entry as a separate object.

This behavior is different to the [[save]] command, where a multi-object selection is written "flat" to a PDB file, without HEADER records.

''Older versions could also export a proprietary binary "pmo" file format with this command. However, "pmo" format never supported multiple entries, support was partially broken in in the 1.7 and 1.8 versions, and was finally removed in 1.8.4.''

== Changes in PyMOL 1.8.4 ==

* CRYST1 records are written if symmetry is defined
* Interpret "pattern" argument as an atom selection. Previous versions expected an object name pattern or a list of objects.
* dropped "pmo" format support

== Usage ==

multisave filename [, pattern [, state [, append ]]]

== Arguments ==

* '''filename''' = str: file path to be written
* '''pattern''' = str: atom selection (before 1.8.4: object name pattern)
* '''state''' = int: object state (-1=current, 0=all) {default: -1}
* '''append''' = 0/1: append to existing file {default: 0}

== Example ==

<syntaxhighlight lang="python">
fragment ala
fragment gly

# PyMOL >= 1.8.4 will write CRYST1 records
set_symmetry ala, 50.840, 42.770, 28.950, 90, 90, 90, P 21 21 21
set_symmetry gly, 99.930, 99.930, 276.840, 90, 90, 90, P 31 2 1

multisave multi.pdb
</syntaxhighlight>

Exported file "multi.pdb":

HEADER ala
CRYST1 50.840 42.770 28.950 90.00 90.00 90.00 P 21 21 21 0
ATOM 1 N ALA 2 -0.677 -1.230 -0.491 1.00 0.00 N
ATOM 2 CA ALA 2 -0.001 0.064 -0.491 1.00 0.00 C
ATOM 3 C ALA 2 1.499 -0.110 -0.491 1.00 0.00 C
ATOM 4 O ALA 2 2.030 -1.227 -0.502 1.00 0.00 O
ATOM 5 CB ALA 2 -0.509 0.856 0.727 1.00 0.00 C
ATOM 6 H ALA 2 -0.131 -2.162 -0.491 1.00 0.00 H
ATOM 7 HA ALA 2 -0.269 0.603 -1.418 1.00 0.00 H
ATOM 8 1HB ALA 2 -1.605 1.006 0.691 1.00 0.00 H
ATOM 9 2HB ALA 2 -0.285 0.342 1.681 1.00 0.00 H
ATOM 10 3HB ALA 2 -0.053 1.861 0.784 1.00 0.00 H
END
HEADER gly
CRYST1 99.930 99.930 276.840 90.00 90.00 90.00 P 31 2 1 0
ATOM 1 N GLY 22 -1.195 0.201 -0.206 1.00 0.00 N
ATOM 2 CA GLY 22 0.230 0.318 -0.502 1.00 0.00 C
ATOM 3 C GLY 22 1.059 -0.390 0.542 1.00 0.00 C
ATOM 4 O GLY 22 0.545 -0.975 1.499 1.00 0.00 O
ATOM 5 H GLY 22 -1.558 -0.333 0.660 1.00 0.00 H
ATOM 6 3HA GLY 22 0.482 1.337 -0.514 0.00 0.00 H
ATOM 7 HA GLY 22 0.434 -0.159 -1.479 1.00 0.00 H
END

== See Also ==

* [[save]]
* [[load]]

[[Category:Commands]]

← Older revision	Revision as of 06:13, 6 March 2017
(No difference)

Multisave - Revision history

Cchem: 1 revision

Speleo3: created