[Dock-fans] Re: dms issues

Eric Pettersen pett at cgl.ucsf.edu
Wed Nov 16 22:55:28 PST 2005


I don't know about the C++ code, but you can edit a Python file in your 
Chimera distribution to get Chimera to read this file (at least the 
part you enclosed).  If you edit line 43 of <your Chimera install 
dir>/share/ReadMS/genVRML.py and change:

	fields = line.split()

to:

	fields = line.replace('-', ' -').split()

then the file is read in okay.  You need to maintain the same 
indentation as in the file -- indentation is significant to Python.  
The change places a space in front of any '-' on all lines.

--Eric

	Eric Pettersen
	UCSF Computer Graphics Lab
	pett at cgl.ucsf.edu


> Dear Dock experts,
>
> I have run through the Dock tutorial with the provided files and then
> I began with my own little receptor and I have hit a wall. I am trying
> to produce the rec.ms file from the rec_fixed.pdb file and the command
> seems to work but when I try to open it in chimera I get an error/bug
> report. After examining the files and comparing the rec.ms with the
> demo equivalent I noticed that the x coordinates are much larger in my
> file so causing a lack of spacing between the atom type and the x
> coordinate columns when there are 3 or more digits infront of the
> decimal point. Please see attached questiondms file for proof. I think
> this may be the problem but as I am not an expert in C++ I am
> struggling to find the solution so that I can alter the script to
> allow for larger numbers in that column? Can anyone help me and
> suggest where I need to alter the C++ program and with what command?
>
> Thank you in advance
> --
> Beth Ashbirdge
> Department of Chemistry
> University College,
> Durham University,
> UK




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