xMDFF Error

From: Joey Farrell (jpfarrell_at_uchicago.edu)
Date: Thu Sep 03 2020 - 23:19:47 CDT

Hi all,

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.

vmd >

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!


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