Eric,
For now,
set retain_order, on
Before writing out your PDB file -- that will insure that nothing changes.
I'll look into whether the default behavior can be changed before the next
release...
Cheers,
Warren
> -----Original Message-----
> From: pymol-users-ad...@lists.sourceforge.net
> [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of
> Eric Zollars
> Sent: Friday, February 13, 2004 3:59 PM
> To: 'pymol-users@lists.sourceforge.net'
> Subject: [PyMOL] save molecule format
>
> All-
> When using the Pymol ability to save a structure as a PDB
> file it appears that the "standard" PDB format is changed in
> at least one instance. When a sidechain has more than one
> conformation in the crystal structure (A, B), the saved PDB
> file will have the two conformations before the amide of the
> group instead of after.
> Doing nothing more than loading and then saving a
> structure to a new file yields the following results.
> Original file:
> ATOM 87 N SER A 13 2.735 9.167 21.169 1.00
> 9.31 N
> ATOM 88 CA SER A 13 2.455 9.048 19.752 1.00
> 10.35 C
> ATOM 89 C SER A 13 1.623 10.233 19.278 1.00
> 9.48 C
> ATOM 90 O SER A 13 1.775 10.681 18.144 1.00
> 10.31 O
> ATOM 91 CB ASER A 13 1.719 7.737 19.462 0.34
> 10.21 C
> ATOM 92 CB BSER A 13 1.705 7.743 19.467 0.66
> 14.26 C
> ATOM 93 OG ASER A 13 2.552 6.621 19.728 0.34
> 11.15 O
> ATOM 94 OG BSER A 13 0.474 7.699 20.166 0.66
> 22.03 O
>
> After saving to pdb:
> ATOM 87 CB ASER A 13 1.719 7.737 19.462 0.34
> 10.21 C
> ATOM 88 OG ASER A 13 2.552 6.621 19.728 0.34
> 11.15 O
> ATOM 89 CB BSER A 13 1.705 7.743 19.467 0.66
> 14.26 C
> ATOM 90 OG BSER A 13 0.474 7.699 20.166 0.66
> 22.03 O
> ATOM 91 N SER A 13 2.735 9.167 21.169 1.00
> 9.31 N
> ATOM 92 CA SER A 13 2.455 9.048 19.752 1.00
> 10.35 C
> ATOM 93 C SER A 13 1.623 10.233 19.278 1.00
> 9.48 C
> ATOM 94 O SER A 13 1.775 10.681 18.144 1.00
> 10.31 O
>
> As far as I can tell it only happens with those sidechains
> with multiple conformations. Anyone else have this problem?
> Is there a quick fix?
>
> Pymol 0.93 on Fedora Core 1.
>
> Thanks.
> Eric Zollars
>
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