From: Joey Farrell (jpfarrell_at_uchicago.edu)
Date: Thu Sep 03 2020 - 23:19:47 CDT
When using the provided template NAMD and TCL files for xMDFF, I seem to run into an error during the PHENIX density map generation portion of the script.
The entire map.log file is incredibly long (as the entire structure file is printed to the log several times), but the following is an excerpt of the last 50 lines using the tail function. It is worth noting that while the xmdff_template.namd and TCL script are stock / downloaded from the tutorial, I am using the protocol on my own structure.
- phenix.maps is available in PHENIX GUI.
- The scope of parameters 'map_coefficients' defines the map that will be
output as Fourier map coefficients. The scope of parameters 'map' defines
the maps that will be output as CCP4 or X-plor format.
- To create several maps: duplicate either 'map_coefficients' or 'map' or both
scopes of parameters as many times as many maps is desired. Then edit each
of them to define the maps.
- A map is defined by specifying a map type using 'map_type' keyword available
within each scope of parameters: 'map_coefficients' or 'map'. The general
supported format for 'map_type' is: [p][m]Fo+[q][D]Fc[_filled]. For
example: 2Fo-Fc, 2mFobs-DFcalc, 3Fobs-2Fmodel, Fo-Fc, mfobs-Dfcalc, anom,
llg. The 'map_type' parser will automatically recognize which map is
- The program creates as many files with CCP4 or X-plor formatted maps as
is requested, and it creates only one MTZ formatted file with
all Fourier map coefficients in it.
- The CCP4 or X-plor formatted maps can be computed in the entire unit cell
or around selected atoms only.
- Twinning (if detected) will be accounted for automatically. This can be
disabled by using "skip_twin_detection=True" keyword.
- All arrays used in map calculation, for example: Fobs, Fmodel, Fcalc, Fmask,
m, D, etc., can be output into a CNS or MTZ formatted reflection file.
- For those who likes to experiment: bulk solvent correction and anisotropic
scaling can be turned off, the data can be filtered by sigma and resolution.
- For some map types certain 'map_coefficients' or 'map' scope parameters may
not be applicable. For example, for "map_type=anomalous" the keywords
"fill_missing_f_obs" and some other are not applicable.
- For LLG map calculation, if you specify the wavelength any existing heavy
atoms (P or heavier) will be modeled as anomalous scatterers using the
theoretical values of f' and f''.
No map input specified - using default map types
Sorry: model file is not given: maps.input.pdb_file_name=None is not a file
ccp4plugin) Error opening file map.ccp4
ERROR: Unable to read input file. Exiting...
Info) VMD for LINUXAMD64, version 1.9.2 (December 29, 2014)
Info) Exiting normally.
Let me know if there is anything that would seem worth looking into. I would be happy to send any input file that I am using via email if this would be diagnostically helpful.
I additionally see from a search of the mailing list that one potential cause of this error could be using VMD version 1.9.2 (or earlier). As a result of imperfect installations of VMD versions 1.9.3 and 1.9.4 on our cluster, I have been only able to attempt this xMDFF procedure on VMD 1.9.2. Is this definitely the cause of the error? And would there be any solution other than fixing the installations of the later versions? Here is a link to the referenced previous mailing-list response: http://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l.2017-2018/1911.html
Thank you in advance!
This archive was generated by hypermail 2.1.6 : Fri Dec 31 2021 - 23:17:09 CST