--
Bingding Huang
PhD student
Bioinformatics group
Biotec & Department of Computing
Tazberg 47, 01307
TU Dresden, Germany
Tel: 0049 351 46340064 (Office)
Tel: 0049 351 4403368 (Home)
Fax: 0049 351 46340061
Mobile: 01772981375
E-mail: bhu...@biotec.tu-dresden.de
--- Begin Message ---
Hi Warren,
After I do more 50 times orient command on different selections, the
coordinates change
unreasonable. They look like:
ATOM 1 N CYS E 1 -74.641 -1.8582868161980399616.000 1.00
43.48 1ACB N
ATOM 2 CA CYS E 1 -74.641 -1.8582868161980399616.000 1.00
35.11 1ACB C
ATOM 3 C CYS E 1 -74.641 -1.8582868161980399616.000 1.00
32.90 1ACB C
ATOM 4 O CYS E 1 -74.641 -1.8582868161980399616.000 1.00
41.38 1ACB O
ATOM 5 CB CYS E 1 -74.641 -1.8582868161980399616.000 1.00
31.14 1ACB C
ATOM 6 SG CYS E 1 -30.674 0.1262868161980399616.000 1.00
34.72 1ACB S
ATOM 7 N GLY E 2 -30.674 0.1262868161980399616.000 1.00
21.94 1ACB N
ATOM 8 CA GLY E 2 -74.641 -1.8582868161980399616.000 1.00
20.45 1ACB C
ATOM 9 C GLY E 2 -74.641 -1.8582868161980399616.000 1.00
35.31 1ACB C
I am wondering what happens. Maybe the transform matric is not right!
Do you have any idea about it?
Here is the programm code:
cmd.load("1acb.pdb")
for i in range(100):
string ="resi "+str(i)+ " and chain E"
string2 =str(i)+ " expand 2.5"
print string
print string2
istr =str(i)
cmd.select(istr, string)
cmd.select(istr, string2)
cmd.orient(i);
cv=list(cmd.get_view())
cmd.transform_selection("all", \
cv[0:3]+[0.0]+ \
cv[3:6]+[0.0]+ \
cv[6:9]+[0.0]+ \
cv[12:15]+[1.0])
ex2=cmd.get_extent(i)
x=ex2[1][0]-ex2[0][0]
y=ex2[1][1]-ex2[0][1]
z=ex2[1][2]-ex2[0][2]
print "delta for " ,i
print x
print y
print z
cmd.save("1acb_new.ent".1acb)
Warren DeLano wrote:
This is tricky because the view matrix isn't quite the same format as the
coordinates translation matrix. Here's some code that will do what you
want:
# transform selection coordinates by the camera view
cv=list(cmd.get_view())
cmd.transform_selection("all", \
cv[0:3]+[0.0]+ \
cv[3:6]+[0.0]+ \
cv[6:9]+[0.0]+ \
cv[12:15]+[1.0])
cmd.reset()
Cheers,
Warren
--
Warren L. DeLano, Ph.D.
Principal Scientist
. DeLano Scientific LLC
. 400 Oyster Point Blvd., Suite 213
. South San Francisco, CA 94080
. Biz:(650)-872-0942 Tech:(650)-872-0834
. Fax:(650)-872-0273 Cell:(650)-346-1154
. mailto:war...@delsci.com
-----Original Message-----
From: pymol-users-ad...@lists.sourceforge.net
[mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of
Bingding Huang
Sent: Thursday, April 21, 2005 1:36 AM
To: pymol-users@lists.sourceforge.net
Subject: [PyMOL] orient the molecule
Hi,
When I try "orient" command to orient the molecule, the
camera changes but the coodinates don't change.
I wonder whether it is possible that when I orient the
molecule the coodinates also change.
Thanks
Bingding
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--
Bingding Huang
PhD student
Bioinformatics group
Biotec & Department of Computing
Tazberg 47, 01307
TU Dresden, Germany
Tel: 0049 351 46340064 (Office)
Tel: 0049 351 4403368 (Home)
Fax: 0049 351 46340061
Mobile: 01772981375
E-mail: bhu...@biotec.tu-dresden.de
--- End Message ---
