Re: [PyMOL] is there a way to update ribbon, sticks, etc. with new coordinates?

d were thuus not shown in the original session). So you have to tell PyMOL to also visualize them, if needed. HTH, Luca -- Luca Jovine, Ph.D. Professor of Structural Biology, Member of EMBO and the Nobel Assembly Karolinska Inst

Re: [PyMOL] surface display in new pymol

Hi Venki, You need to first issue the following command: set surface_mode, 1 Best, Luca On Jun 8, 2011, at 17:05 , V. Ramakrishnan wrote: On versions 1.3, 1.4, I cannot display a surface of anything that is not in the standard dictionary. For example trying to draw a surface of

[PyMOL] On-the-fly electron density re-contouring?

in the documentation, but it would be so useful... Thanks, Luca - Luca Jovine, Ph.D. Karolinska Institutet Department of Biosciences and Nutrition Center for Structural Biochemistry (CSB) Hälsovägen 7, S-141 57 Huddinge, Sweden Voice: +46.(0)8.6083-301

[PyMOL] PyMOL/O stereo 3D on G5 Quad with Quadro FX 4500

- Luca Jovine, Ph.D. Karolinska Institutet Department of Biosciences and Nutrition Center for Structural Biochemistry (CSB) Hälsovägen 7-9, S-141 57 Huddinge, Sweden Voice: +46.(0)8.6083-301 FAX: +46.(0)8.6089-290 E-mail: luca.jov...@biosci.ki.se W3: http://www.biosci.ki.se

[PyMOL] nuccyl's URL has changed!

Dear PyMOL users, Recently I moved, and so has nuccyl's home page. Please update your bookmarks to: http://www.biosci.ki.se/groups/ljo/software/nuccyl.html With best regards, Luca - Luca Jovine, Ph.D. Karolinska Institutet Department

Fwd: [PyMOL] PyMOL author??

...and, Ribbons was certainly not created by... Ribbons! (unless Mike Carson has started using a pseudonym, that is) Oh boy... Luca Begin forwarded message: From: Anastassis Perrakis a.perra...@nki.nl Date: April 27, 2005 15:41:46 EDT To: Jim Nettles jnet...@emory.edu Cc: Mark A Saper

[PyMOL] nuccyl 1.5.2 released

residue U8 within chain A is now called A_U8 instead of just U8). With best regards, Luca --- Luca Jovine, Ph.D. Brookdale Department of Molecular, Cell Developmental Biology Mount Sinai School of Medicine Annenberg Building, Room 25-18 1

[PyMOL] Re: PyMolWiki

pretty sure people who work with them would benefit from such a section in the Wiki. Thanks, Luca --- Luca Jovine, Ph.D. Brookdale Department of Molecular, Cell Developmental Biology Mount Sinai School of Medicine Annenberg Building, Room

[PyMOL] Re: cartoon_nucleic_acid_mode

be interesting to hear the opinion of other PyMOL users! Thanks and best regards, Luca --- Luca Jovine, Ph.D. Brookdale Department of Molecular, Cell Developmental Biology Mount Sinai School of Medicine Annenberg Building, Room 25-18 1

Re: [PyMOL] cartoon representation of nucleic acids

://www.mssm.edu/students/jovinl02/research/nuccyl.html To see the available cartoon styles type help cartoon within PyMOL, and to display all possible settings type set cartoon_ and press the tab key. Good luck! Luca --- Luca Jovine, Ph.D

Re: [PyMOL] pymol and OS X v. 10.3.5 update -- a word of caution

or so, upon waking from sleep. The other was a problem with mail. Both were solved upon manually re-installing 10.3.5 using the 88 MB updater. Just a suggestion... Ciao Luca Luca Jovine, Ph.D. Brookdale Department of Molecular, Cell

Re: [PyMOL] large molecules

and not highly affect the quality of an overall view of something as large as a virus... I doubt people will check individual strands within such a picture! Hope this helps, good luck - Luca Luca Jovine, Ph.D. Brookdale Department

[PyMOL] nuccyl 1.5 released

Luca Jovine, Ph.D. Brookdale Department of Molecular, Cell Developmental Biology Mount Sinai School of Medicine Annenberg Building, Room 25-18 One Gustave L. Levy Place, New York, NY 10029-6574, USA Voice: +1.212.241-8620 FAX: +1.509.356-2832 E-Mail: lucajov...@mac.com

[PyMOL] nuccyl 1.4 released

, suggestions and criticisms are highly welcome. With best regards, Luca Luca Jovine, Ph.D. Brookdale Department of Molecular, Cell Developmental Biology Mount Sinai School of Medicine Annenberg Building, Room 25-18 One Gustave L. Levy Place

[PyMOL] nuccyl 1.1 released

/research/nuccyl.html I hope you find nuccyl useful; please let me know should you have any question or comment. With best regards - Luca Luca Jovine, Ph.D. Brookdale Department of Molecular, Cell Developmental Biology Mount Sinai School

[PyMOL] PyMOL and programming languages other than Python

a useful alternative (well, until they learn Python anyway!) Just a thought... Ciao, Luca Luca Jovine, Ph.D. Brookdale Department of Molecular, Cell Developmental Biology Mount Sinai School of Medicine Annenberg Building, Room 25-18 One

Re: [PyMOL] loop radius?

, setting.get_setting_text(name)) cmd.extend('setting_list',setting_list) then simply type the following from within PyMOL: PyMOL run setting_list.py PyMOL setting_list Hope this helps - Luca Luca Jovine, Ph.D. Brookdale Department

Re: [PyMOL] incorporating rTools --how?

load /sw/lib/pymol/modules/pmg_tk/startup/rubor/scripts/1cse.ent now you can automatically load entry 1CSE from ScriptBox within rTools. Hope this helps! Good luck, Luca Luca Jovine, Ph.D. Brookdale Department of Molecular, Cell

[PyMOL] Problem with session saving using PyMOL 0.88 under OSX

experience the same problem? I had exactly the same result on two different machines. A part from this, I think the new version is great - particularly the roving feature. Ciao, Luca Luca Jovine, Ph.D. Brookdale Department of Molecular, Cell

Re: [PyMOL] RGB2CMYK

useful for this kind of things is ColorWrite (http://www.adaptiveview.com/cw); it's a Java application, so you can run it under OS X, Linux, Solaris and Windows. Good luck, Luca Luca Jovine, Ph.D. Brookdale Department of Molecular, Cell

Re: [PyMOL] Moving through movie frames

cmd.frame( int frame_number ) NOTES Frame numbers are 1-based SEE ALSO count_states Ciao, Luca Luca Jovine, Ph.D. Department of Molecular, Cell Developmental Biology Mount Sinai School of Medicine Annenberg Building, Room 25-18

Re: [PyMOL] Low-cost movie construction (OSX)

Luca Jovine, Ph.D. Department of Molecular, Cell Developmental Biology Mount Sinai School of Medicine Annenberg Building, Room 25-18 One Gustave L. Levy Place, New York, NY 10029-6574, USA Voice: +1.212.241-8620 FAX: +1.509.356-2832 E-Mail: lucajov...@mac.com W3: http://www.mssm.edu

[PyMOL] Possible glass-free 3D monitor for OSX PyMol?

price ranges from 3000 to 6000 USD), but I wonder how PyMol (and O) would work with this system... Have a look at: http://www.actualdepth.com/ Ciao, Luca PS: I am in no way affiliated with this company!!! Luca Jovine, Ph.D

RE: [PyMOL] Re: mice for OSX PyMOL

. Anybody know of an improvement mouse-wise for OS X? Luca Jovine, Ph.D. Department of Molecular, Cell Developmental Biology Mount Sinai School of Medicine Annenberg Building, Room 25-18 One Gustave L. Levy Place, New York, NY 10029-6574, USA

Re: [PyMOL] Mac OS X install, general PyMOL function - badly need overview

Hello Jim, I have downloaded the version (0.79.dmg.gz) of the PyMol package suggested by Luca Jovine, but don't know how to get a working version of Python installed. The only links I can find are to Python .exe files for versions 2.1 and 1.5.2, and I have no idea which of the other

Re: [PyMOL] get_view on native mac os X

this helps! Luca Luca Jovine, Ph.D. Department of Molecular, Cell Developmental Biology Mount Sinai School of Medicine Annenberg Building, Room 25-18 One Gustave L. Levy Place, New York, NY 10029-6574, USA Voice: +1.212.241-8620 FAX

[PyMOL] How to ouput a PDB file with transformed coordinates?

if this is obvious, Thanks Luca Luca Jovine, Ph.D. Department of Molecular, Cell Developmental Biology Mount Sinai School of Medicine Annenberg Building, Room 25-18 One Gustave L. Levy Place, New York, NY 10029-6574, USA Voice: +1.212.241-8620 FAX

[PyMOL] Help! Color by atom/H-bond display/mouse on OSX

Luca Jovine, Ph.D. Department of Molecular, Cell Developmental Biology Mount Sinai School of Medicine Annenberg Building, Room 25-18 One Gustave L. Levy Place, New York, NY 10029-6574, USA Voice: +1.212.241-8620 FAX: +1.509.356-2832 E-Mail: lucajov...@mac.com W3