[phenixbb] map output from ncs_average
Tom Terwilliger
terwilliger at lanl.gov
Fri Dec 9 10:51:11 PST 2011
Hi Ursula,
Can you try:
phenix.pymol
then as you and Nat mentioned:
load ncs_average.map, format=ccp4
I tried this just now and it worked ok.
If that fails, can you first run:
phenix_regression.wizards.test_command_line_resolve_memory test_ncs_average
cd test_ncs_average
and then try the pymol load with that file (that's what I just did).
All the best,
Tom T
On Dec 9, 2011, at 11:40 AM, Ursula Schulze-Gahmen wrote:
> Yes, I used the same command. By the way, I can open the map file in Coot. I am thinking of updating my version of Pymol since I am using a relatively old version.
> Any other suggestion?
>
> Ursula
>
> On Fri, Dec 9, 2011 at 10:32 AM, Nathaniel Echols <nechols at lbl.gov> wrote:
> On Fri, Dec 9, 2011 at 10:28 AM, Ursula Schulze-Gahmen
> <uschulze-gahmen at lbl.gov> wrote:
> > I used ncs_average to create an averaged fo-fc map. From the manual I
> > thought that the output map is a CCP4 map. I have however difficulties to
> > read it into Pymol as ccp4 map. It is not recognized. Any suggestions?
>
> What command did you use to load it in PyMOL? You might need to do
> this to get it to recognize the file type:
>
> load ncs_average.map, format=ccp4
>
> (PyMOL expects .ccp4 as the extension here - .map is assumed to be an
> XPLOR map. Most of the programs in PHENIX will use .ccp4 as the
> extension, but there are probably inconsistencies.)
>
> -Nat
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>
>
> --
> Ursula Schulze-Gahmen, Ph.D.
> Assistant Researcher
> UC Berkeley, QB3
> 356 Stanley Hall #3220
> Berkeley, CA 94720-3220
>
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Thomas C. Terwilliger
Mail Stop M888
Los Alamos National Laboratory
Los Alamos, NM 87545
Tel: 505-667-0072 email: terwilliger at LANL.gov
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