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*** CCP4 home page http://www.ccp4.ac.uk ***
Hi Everyone,
I was able to get that CNS composite omit map read in Coot via more than one
of the suggested solutions to my problem of map size limit in "xdlmapman".
Below is a brief summary for those interested:
1. Downloading RAVE from the USF and running command line MAPMAN from within
worked perfectly as described below.
2. Using the modified version of Joel Bard's cns-omit2coot.com script from
the Coot website also worked perfectly. Interestingly, this method gave a
map that although looks identical to that calculated in (1) above, reports
different sigma values when contoured to look the same in coot. (why?) So
when the two maps are adjusted to appear at the same sigma level, Coot says
that they are at different levels (ie. the MAPMAN map says 1.8 sigma when
the cns-omit2coot.com map says 1.0 sigma).
3. I could not get GUI xdlmapman, when run directly from a csh terminal, to
accept my oversized map by simply typing "setenv MAPSIZE xx000000" before
starting xdlmapman. Maybe this is an issue with my settings in Linux
(Feodra Core 4) or something.
4. Lastly, as for reducing the size of the map or recalculating with a lower
grid resolution I was trying to avoid that although it could resolve the
issue, mainly because I don't like living with that limitation and because
the map took 50 hours to calculate. Also calculating the map directly in
CCP4 has not worked for me in the past and I've heard that people generally
prefer CNS composite omit maps.
Thanks very much to all those who replied, the help is greatly appreciated.
MSM
From: "Green, Todd" <[EMAIL PROTECTED]>
To: <[EMAIL PROTECTED]>
Subject: Re: [ccp4bb]: xdlmapman and maximum size
Date: Fri, 3 Nov 2006 10:52:23 -0600
i should have mentioned this before. why don't you just run mapman from the
rave website:
download:
ftp://xray.bmc.uu.se/pub/gerard/linux/rave_linux.tar.gz
then run these commands:
gunzip rave_linux.tar.gz
tar xvf rave_linux.tar
cd rave_linux
csh
setenv MAPSIZE a_very_large_number
./lx_mapman
re m1 omit.map cns
wr m1 omit_ccp4.map ccp4
quit
now run coot and read in the map.
let me know if this doesn't work and we'll go from there.
cheers -
todd
mapman manual:
http://alpha2.bmc.uu.se/usf/mapman_man.html
-----Original Message-----
From: Green, Todd
Sent: Thu 11/2/2006 2:56 PM
To: Michael McCormick
Subject: RE: [ccp4bb]: xdlmapman and maximum size
type it in the terminal and then start ccp4i. "setenv MAPSIZE
a_very_large_number" i believe is csh specific syntax.
so in the terminal i believe your sequence should go(if you are not already
running csh):
csh
setenv MAPSIZE a_very_large_number
ccp4i
cheers - todd
-----Original Message-----
From: [EMAIL PROTECTED] on behalf of Michael McCormick
Sent: Thu 11/2/2006 2:43 PM
To: [EMAIL PROTECTED]
Cc: [email protected]
Subject: Re: [ccp4bb]: xdlmapman and maximum size
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*** CCP4 home page http://www.ccp4.ac.uk ***
Excellent, thank you.
But where do I enter this parameter? I can't find a text entry dialogue
and
the program only runs in the graphical interface form according to CCP4
documentation.
MSM
>From: Dyda <[EMAIL PROTECTED]>
>To: "Michael McCormick" <[EMAIL PROTECTED]>
>Subject: Re: [ccp4bb]: xdlmapman and maximum size
>Date: Thu, 2 Nov 2006 15:15:35 -0500 (EST)
>
>setenv MAPSIZE a_very_large_number
>
>Best
>[32m*******************************************************************************
>Fred Dyda, Ph.D. Phone:301-402-4496
>Laboratory of Molecular Biology Fax: 301-496-0201
>DHHS/NIH/NIDDK e-mail:[EMAIL PROTECTED]
>Bldg. 5. Room 303
>Bethesda, MD 20892-0560 URGENT message: [EMAIL PROTECTED]
>http://intramural.niddk.nih.gov/research/faculty.asp?People_ID=1577
>*******************************************************************************[m
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