Yu Chen, I think it is because of "endianess". My phi files were
generated by Delphi on an SGI in the GRASP format. My PyMOL 088 on
Linux does not seem to mind it. I think Warren has fixed the problem of
endianess and it should be fine in the next release.
Kaushik.
On Thursday, July 10, 2003, at 10:11 AM, Yu Chen wrote:
Thanks everybody for suggestiones, and Warren for fixing the problem. I
will see if we could generate some phimap not 65x65x65.
Ksushik, I don't know why your Delphi is working fine, here is my
output
from load phimap, which it should be cause of the endianess:
PHIMapToStr: now starting phimap
PHIMapToStr: potential
PHIMapToStr: qdiffxas: qdiffxs4 with an improved surfacing routine
PHIMapToStr: j#
ObjectMap: Map Read. Range = -3388..... to 37....
Crystal: Unit Cell 1.000 1.000 1.000
Crystal: Alpha Beta Gamma 90.000 90.000 90.000
Crystal: RealToFrac Matrix
Crystal: 1.0000 0.0000 0.0000
Crystal: 0.0000 1.0000 0.0000
Crystal: 0.0000 0.0000 1.0000
Crystal: FracToReal Matrix
Crystal: 1.0000 0.0000 0.0000
Crystal: 0.0000 1.0000 0.0000
Crystal: 0.0000 0.0000 1.0000
Crystal: Unit Cell Volume 1.
Executive: object "map" created.
Best
Yu
===========================================
Yu Chen
Howard Hughes Medical Institute
Chemistry Building, Rm 122
University of Maryland at Baltimore County
1000 Hilltop Circle
Baltimore, MD 21250
phone: (410)455-6347
(410)455-2718
fax: (410)455-1174
email: c...@hhmi.umbc.edu
===========================================
On Wed, 9 Jul 2003, Warren L. DeLano wrote:
Okay, scratch that -- I fixed the problem, relying on "standard"
Fortran unformatted IO conventions to automatically determine
endianness
and map size.
PyMOL should now be able to read a PHI map of any dimensionality, so
long as record size is implicitly and correctly specified in the map
file. This may or may not be the case for ".phi" files written from
C
(for example, "fld2phi" is hard-coded for a 65x65x65 map, because the
data block's record length specifier is hardcoded to be 0x10c304 =
65*65*65*4).
Can someone send me a PHI map which is not 65x65x65 for testing
purposes? Please include the associated PDB file for visual
verification. Thanks!
Looks like we'll need to push out another release sooner rather than
later...
Cheers,
Warren
--
mailto:war...@delanoscientific.com
Warren L. DeLano, Ph.D.
Principal Scientist
DeLano Scientific LLC
Voice (650)-346-1154
Fax (650)-593-4020
-----Original Message-----
From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users-
ad...@lists.sourceforge.net] On Behalf Of Warren L. DeLano
Sent: Wednesday, July 09, 2003 2:20 PM
To: 'EPF (Esben Peter Friis)'; 'Kaushik Raha '; 'Yu Chen '
Cc: pymol-users@lists.sourceforge.net
Subject: RE: [PyMOL] Electrostatic potential maps in PyMOL
Yes, you have identified the problem: PyMOL 0.90 currently only
reads
PHI files in one of the two endian formats (not sure if it is big or
little).
The problem is, how it PyMOL to determine which format the incoming
map
is in? The file format is so darn implicit, I haven't yet come up
with
any effective way of doing it without risking a floating exception on
finicky hardware.
Any ideas? If we can just determine the "enddian-ness" of the
incoming
file, then the rest is a snap.
Warren
--
mailto:war...@delanoscientific.com
Warren L. DeLano, Ph.D.
Principal Scientist
DeLano Scientific LLC
Voice (650)-346-1154
Fax (650)-593-4020
-------------------------------------------------------
This SF.Net email sponsored by: Parasoft
Error proof Web apps, automate testing & more.
Download & eval WebKing and get a free book.
www.parasoft.com/bulletproofapps
_______________________________________________
PyMOL-users mailing list
PyMOL-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/pymol-users
