Bad number format Xplor file format

Hello All, I try to convert electron density obtained from iterative phasing in *.xplor file format to view in the chimera. Something went wrong which I could not figure out. The generated density reads as follows for the first few lines. ########################################################## 241 -120 120 241 -120 120 241 -120 120 3.26000E+02 3.26000E+02 3.26000E+02 9.00000E+01 9.00000E+01 9.00000E+01 ZYX 0 2.21928E-166 0.00000E+00 1.59337E-167 0.00000E+00 1.14399E-168 0.00000E+00 8.21346E-170 0.00000E+00 5.89700E-171 0.00000E+00 4.23386E-172 0.00000E+00 ############################################################# While I try to view the electron density in chimera it says"SyntaxError:Bad number format in line 2.21928E-166 0.00000E+00 1.59337E-167 0.00000E+00 1.14399E-168 0.00000E+00" WOuld you please help me out Many thanks

Hello Ishwor, I don’t know what you mean by “convert” or “generated” or what you used to do that. Chimera can directly read an xplor "unformatted ASCII density map”, see list of known formats here: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/filetypes.html#volume> … but maybe your map is not really in that format, so you are just getting errors that the format is wrong. Without example data, this is only a guess. Bests, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Aug 12, 2018, at 7:51 PM, ISHWOR POUDYAL <ishwor_p_19@yahoo.com> wrote:
Hello All, I try to convert electron density obtained from iterative phasing in *.xplor file format to view in the chimera. Something went wrong which I could not figure out. The generated density reads as follows for the first few lines.
########################################################## 241 -120 120 241 -120 120 241 -120 120
3.26000E+02 3.26000E+02 3.26000E+02 9.00000E+01 9.00000E+01 9.00000E+01
ZYX
0
2.21928E-166 0.00000E+00 1.59337E-167 0.00000E+00 1.14399E-168 0.00000E+00
8.21346E-170 0.00000E+00 5.89700E-171 0.00000E+00 4.23386E-172 0.00000E+00
#############################################################
While I try to view the electron density in chimera it says "SyntaxError:Bad number format in line 2.21928E-166 0.00000E+00 1.59337E-167 0.00000E+00 1.14399E-168 0.00000E+00"
WOuld you please help me out Many thanks

HI Ishwor, The XPLOR format requires lines where the first 12 columns holds the first number, the second 12 columns holds the second number, … 12 columns per number. The example lines you provide do not use 12 columns per number. The software that wrote that file is not writing it in the correct format. My guess is that software fails because of the 3 digit exponents (e.g "E-166”) — probably the writing software only fails to follow the 12 columns per number rule when you have 3-digit exponents. In single-precision (32-bit floats) you would never get 3 digit exponents and perhaps the error is that the writing program was converted from single precision to double precision. Tom
On Aug 12, 2018, at 7:51 PM, ISHWOR POUDYAL <ishwor_p_19@yahoo.com> wrote:
Hello All,
I try to convert electron density obtained from iterative phasing in *.xplor file format to view in the chimera. Something went wrong which I could not figure out. The generated density reads as follows for the first few lines.
########################################################## 241 -120 120 241 -120 120 241 -120 120
3.26000E+02 3.26000E+02 3.26000E+02 9.00000E+01 9.00000E+01 9.00000E+01
ZYX
0
2.21928E-166 0.00000E+00 1.59337E-167 0.00000E+00 1.14399E-168 0.00000E+00
8.21346E-170 0.00000E+00 5.89700E-171 0.00000E+00 4.23386E-172 0.00000E+00
#############################################################
While I try to view the electron density in chimera it says "SyntaxError:Bad number format in line 2.21928E-166 0.00000E+00 1.59337E-167 0.00000E+00 1.14399E-168 0.00000E+00"
WOuld you please help me out
Many thanks _______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
participants (3)
-
Elaine Meng
-
ISHWOR POUDYAL
-
Tom Goddard