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Displaying electron density in PyMol

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Michael Thompson

7 Jan 2011 7 Jan '11

7:51 p.m.

Hi All, Does phenix have a utility that will allow me to produce an electron density map that can be opened in PyMol, similar to the "FFT" utility in ccp4? Thanks for the help, Mike Thompson -- Michael C. Thompson Graduate Student Biochemistry & Molecular Biology Division Department of Chemistry & Biochemistry University of California, Los Angeles [email protected]

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Tom Terwilliger

7 Jan 7 Jan

8:15 p.m.

Hi Mike, You should be able to use phenix.mtz2map to do this, with output=xplor. Note that you can get a complete list of jiffies like this with: phenix.list All the best, Tom T On Jan 7, 2011, at 2:51 PM, Michael Thompson wrote:

Hi All,

Does phenix have a utility that will allow me to produce an electron density map that can be opened in PyMol, similar to the "FFT" utility in ccp4?

Thanks for the help,

Mike Thompson

-- Michael C. Thompson

Graduate Student

Biochemistry & Molecular Biology Division

Department of Chemistry & Biochemistry

University of California, Los Angeles

[email protected] _______________________________________________ phenixbb mailing list [email protected] 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: [email protected] 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

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Nathaniel Echols

8:37 p.m.

On Fri, Jan 7, 2011 at 2:15 PM, Tom Terwilliger wrote:

Hi Mike, You should be able to use phenix.mtz2map to do this, with output=xplor.

Minor nitpick: the default output format is CCP4 maps, which will also work in PyMOL. There's really no reason to ever use XPLOR maps unless you need to use a program that only accepts those. -Nat

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Bryan Lepore

8:45 p.m.

On Fri, Jan 7, 2011 at 5:15 PM, Tom Terwilliger wrote:

Note that you can get a complete list of jiffies like this with: phenix.list

tried a few installations, i get this : TypeError: coercing to Unicode: need string or buffer, NoneType found ... thats on Fedora or Ubuntu... -Bryan

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Engin Özkan

9:32 p.m.

Same here on Mac i386 using the latest release 1.7. [engin-ozkans-macbook-pro:~] eozkan% phenix.list_1.7-629 Traceback (most recent call last): File "/usr/local/phenix-1.7-629/phenix/phenix/command_line/list.py", line 12, in <module> listing=os.listdir(path_to_phenix) TypeError: coercing to Unicode: need string or buffer, NoneType found On 1/7/11 2:45 PM, Bryan Lepore wrote:

...
Note that you can get a complete list of jiffies like this with: phenix.list

On Fri, Jan 7, 2011 at 5:15 PM, Tom Terwilliger wrote: tried a few installations, i get this :

TypeError: coercing to Unicode: need string or buffer, NoneType found

... thats on Fedora or Ubuntu...

-Bryan _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb

-- Engin Özkan Post-doctoral Scholar Laboratory of K. Christopher Garcia Howard Hughes Medical Institute Dept of Molecular and Cellular Physiology 279 Campus Drive, Beckman Center B173 Stanford School of Medicine Stanford, CA 94305 ph: (650)-498-7111

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Thomas C. Terwilliger

8 Jan 8 Jan

2:06 p.m.

New subject: phenix.list

Hi all, Sorry about the bug in phenix.list (I should have tested it on more than my own systems before putting it in there). Ralf has fixed it; versions starting today should work correctly. Thanks for pointing out the problem! All the best, Tom

...
Same here on Mac i386 using the latest release 1.7.

[engin-ozkans-macbook-pro:~] eozkan% phenix.list_1.7-629 Traceback (most recent call last): File "/usr/local/phenix-1.7-629/phenix/phenix/command_line/list.py", line 12, in <module> listing=os.listdir(path_to_phenix) TypeError: coercing to Unicode: need string or buffer, NoneType found

On 1/7/11 2:45 PM, Bryan Lepore wrote:

...
...
Note that you can get a complete list of jiffies like this with: phenix.list

On Fri, Jan 7, 2011 at 5:15 PM, Tom Terwilliger wrote: tried a few installations, i get this :

TypeError: coercing to Unicode: need string or buffer, NoneType found

... thats on Fedora or Ubuntu...

-Bryan _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb

-- Engin Özkan Post-doctoral Scholar Laboratory of K. Christopher Garcia Howard Hughes Medical Institute Dept of Molecular and Cellular Physiology 279 Campus Drive, Beckman Center B173 Stanford School of Medicine Stanford, CA 94305 ph: (650)-498-7111

_______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb

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Nathaniel Echols

7 Jan 7 Jan

9:33 p.m.

On Fri, Jan 7, 2011 at 2:45 PM, Bryan Lepore wrote:

On Fri, Jan 7, 2011 at 5:15 PM, Tom Terwilliger wrote:

...
Note that you can get a complete list of jiffies like this with: phenix.list

tried a few installations, i get this :

TypeError: coercing to Unicode: need string or buffer, NoneType found

Wow, I wonder how long that's been broken. Sorry, should be working again tomorrow. -Nat

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Pavel Afonine

10 Jan 10 Jan

3:55 a.m.

Hi, I searched and didn't find any test for phenix.list, so no surprises it was broken or will be broken sooner or later. Yes, it's very useful tool - I didn't realist we have it. I have two minor suggestions: - since most of tool names are pretty cryptic, it would be very helpful to have a short line explaining the tool. For example: phenix.refine - crystallographic structure refinement phenix.maps - compute maps phenix.fmodel - compute structure factors etc... - may be we need filer out some of them and leave only those that the end-users may be interested in. For example, I have no idea what those are: boost.gcd boost.lcm and so on. Pavel. On 1/7/11 3:33 PM, Nathaniel Echols wrote:

On Fri, Jan 7, 2011 at 2:45 PM, Bryan Lepore wrote:

...
...
Note that you can get a complete list of jiffies like this with: phenix.list

On Fri, Jan 7, 2011 at 5:15 PM, Tom Terwilliger wrote: tried a few installations, i get this :

TypeError: coercing to Unicode: need string or buffer, NoneType found Wow, I wonder how long that's been broken. Sorry, should be working again tomorrow.

-Nat

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Nathaniel Echols

7 Jan 7 Jan

8:19 p.m.

On Fri, Jan 7, 2011 at 1:51 PM, Michael Thompson wrote:

Does phenix have a utility that will allow me to produce an electron density map that can be opened in PyMol, similar to the "FFT" utility in ccp4?

phenix.mtz2map refine_map_coeffs.mtz will generate a map filling the unit cell - add a PDB file to create the map around the molecule instead. I probably need to write documentation for this, just so everyone know's it's available, but it's very simple to use. -Nat

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Pavel Afonine

10 Jan 10 Jan

3:46 a.m.

Hi Mike, phenix.maps is the tool to compute any number of most of useful maps, and output them in most commonly used formats (X-plor, as map coefficients, ccp4 map format, etc). You can use this tool from the command line - just type phenix.maps and follow the instructions. Alternatively, this is available from the GUI. Note, phenix.maps compute maps - not converts between formats. Pavel. On 1/7/11 1:51 PM, Michael Thompson wrote:

Hi All,

Does phenix have a utility that will allow me to produce an electron density map that can be opened in PyMol, similar to the "FFT" utility in ccp4?

Thanks for the help,

Mike Thompson

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participants (7)

Bryan Lepore
Engin Özkan
Michael Thompson
Nathaniel Echols
Pavel Afonine
Thomas C. Terwilliger
Tom Terwilliger