Re: [phenixbb] phenix.pdbtools question

Thanks for the tip. A CRYST1 card solved the problem. Simon On 21 Oct 2008, at 16:08, James Fraser wrote:

I've noticed this error too. It occured when I was missing a CRYST 1 line in my PDB. I'm not sure if just any old CRYST 1 line will work, but if you generate one that has a very large P1 cell, your error should go away.

jf

On Tue, Oct 21, 2008 at 7:47 AM, Pavel Afonine wrote:

...

Hi Simon,

there must be something weird in your file... Could you please send me it?

Pavel.

On 10/21/2008 3:01 AM, Simon Kolstoe wrote:

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Dear phenix list,

I am wanting to model a poly-proline structure. I created the file in PyMOL, saved it as a pdb, and then tried to regularize it with:

phenix.pdbtools polypro.pdb --geometry_regularization

However the program reported (snipped to the last few lines):

ATOM 63 CD PRO 6 -3.290 3.487 -2.968 1.00 0.00 C ATOM 69 2HD PRO 6 -2.824 2.626 -3.453 1.00 0.00 H Distance model: 1.09209 (ideal: 0.97) ATOM 63 CD PRO 6 -3.290 3.487 -2.968 1.00 0.00 C ATOM 70 3HD PRO 6 -4.165 3.171 -2.396 1.00 0.00 H Distance model: 1.44721 (ideal: 1.473) ATOM 57 N PRO 6 -2.321 4.145 -2.118 1.00 0.00 N ATOM 63 CD PRO 6 -3.290 3.487 -2.968 1.00 0.00 C Distance model: 1.53855 (ideal: 1.525) ATOM 58 CA PRO 6 -1.810 5.407 -2.632 1.00 0.00 C ATOM 59 C PRO 6 -2.332 6.603 -1.817 1.00 0.00 C Distance model: 1.23088 (ideal: 1.231) ATOM 59 C PRO 6 -2.332 6.603 -1.817 1.00 0.00 C ATOM 60 O PRO 6 -3.080 6.424 -0.856 1.00 0.00 O Sorry: Number of bonds with excessive lengths: 74

I thought the whole purpose of geometry regularization was to get rid of excessive lengths, not just tell me they are there!! How do I get the program to really regularize my geometry?

Thanks,

Simon _______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb

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-- James Fraser [email protected] Alber Lab 356 Stanley Hall, QB3 UC Berkeley Berkeley, CA 94720 http://ucxray.berkeley.edu/~jfraser/ _______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb