[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:


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
> _______________________________________________
> phenixbb mailing list
> phenixbb at phenix-online.org
> http://phenix-online.org/mailman/listinfo/phenixbb
> -- 
> Ursula Schulze-Gahmen, Ph.D.
> Assistant Researcher
> UC Berkeley, QB3
> 356 Stanley Hall #3220
> Berkeley, CA 94720-3220
> _______________________________________________
> phenixbb mailing list
> phenixbb at phenix-online.org
> http://phenix-online.org/mailman/listinfo/phenixbb

Thomas C. Terwilliger
Mail Stop M888
Los Alamos National Laboratory
Los Alamos, NM 87545

Tel:  505-667-0072                 email: terwilliger at LANL.gov
Fax: 505-665-3024                 SOLVE web site: http://solve.lanl.gov
PHENIX web site: http:www.phenix-online.org
ISFI Integrated Center for Structure and Function Innovation web site: http://techcenter.mbi.ucla.edu
TB Structural Genomics Consortium web site: http://www.doe-mbi.ucla.edu/TB
CBSS Center for Bio-Security Science web site: http://www.lanl.gov/cbss

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://phenix-online.org/pipermail/phenixbb/attachments/20111209/52872c46/attachment.htm>

More information about the phenixbb mailing list