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 tR

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

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

m, Luca ----- 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.bio

[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 Depar

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 Date: April 27, 2005 15:41:46 EDT To: Jim Nettles Cc: Mark A Saper , Pymol Subject: Re: [PyMOL] PyMOL a

[PyMOL] nuccyl 1.5.2 released

presenting 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 Buildi

[PyMOL] Re: cartoon_nucleic_acid_mode

representing nucleic acid molecules, without any clear advantage? It would also be interesting to hear the opinion of other PyMOL users! Thanks and best regards, Luca --- Luca Jovine, Ph.D. Brookdale Department of Molecular, Cell &a

[PyMOL] Re: PyMolWiki

leotides!), and I'm 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 Medi

Re: [PyMOL] cartoon representation of nucleic acids

http://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 --------

Re: [PyMOL] installing APBS on PBG4

/usr/bin/ld: Undefined symbols: restFP saveFP collect2: ld returned 1 exit status Hi Michael, these symbols are in: /usr/lib/libgcc.a try linking with -lgcc ! -Luca Luca Jovine, Ph.D. Brookdale Department of Molecular

Re: [PyMOL] External GUI window problem

first need to launch X11 in order to see the external GUI. -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 P

Re: [PyMOL] Pymol in the service of architecture

yTrans can convert PDB into 3DS: http://www.okino.com/conv/imp_pdb.htm However, I think this will only export the coordinates themselves, not their rendering etc. Hope this helps - Luca ---- Luca Jovine, Ph.D. Brookdale Department of

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

es for a second 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

Re: [PyMOL] large molecules

save a lot of memory 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. Bro

[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

[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 P

Re: [PyMOL] loop radius?

print "%s => %s" % (name, 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 ---------

[PyMOL] PyMOL and programming languages other than Python

rategy might represent 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 Annen

[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 Schoo

[PyMOL] Ribbon+cylinder representation of nucleic acids: now it can be done in PyMOL!

u can download the program from the same link. I hope you will find nuccyl useful; please let me know of any problem you encounter, and of course suggestions and criticisms will always be welcome. Ciao, Luca Luca Jovine, Ph.D. Broo

Re: [PyMOL] incorporating rTools --how?

edit the single line of file 1cse.pml as follows: OSX> sudo vi 1cse.pml 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 ----

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

e screen :( Did anyone else 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

Re: [PyMOL] RGB2CMYK

hings 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 & Developmental

Re: [PyMOL] colouring by hydrophobicity

cys","(resn cys and "+s+")") cmd.color("color_tyr","(resn tyr and "+s+")") cmd.color("color_pro","(resn pro and "+s+")") cmd.color("color_thr","(resn thr and "+s+")")

Re: [PyMOL] Moving through movie frames

me-number PYMOL API 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 Ann

[PyMOL] 0.86 session files and Ribbons-like RNA representation

ylinders as implemented in Ribbons is a very clear way of showing the overall folding of RNA/DNA, and it would be great to have a comparable feature in PyMOL. Thanks and best regards, Luca ---- Luca Jovine, Ph.D. Department of Molecul

Re: [PyMOL] help compiling pymol on OSX

, exit code 2 Failed: compiling glut-3.7-3 failed So what does this mean and how do I get around it. Craig ---- Luca Jovine, Ph.D. Department of Molecular, Cell & Developmental Biology Mount Sinai School of Medicine Annenberg Building, Ro

Re: [PyMOL] Apple new version X11

I've installed X11 server through XDarwin. Will the installation of PyMOL for OS X described on your web page work with XDarwin's implementation of X11 or do I have to install Apple's version. Is there any advantage in installing Apple's X11? Will Apple X11 installation overwrite XDarwin?

[PyMOL] PyMOL movie example (SRP S-domain assembly)

we used to combine the various assembly steps as yet another example, I attach the URL: http://www.mssm.edu/students/jovinl02/research/srp_assembly_movie.html Ciao, Luca Luca Jovine, Ph.D. Department of Molecular, Cell & Developme

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

[PyMOL] Phosphate trace for nucleic acids

;)") cmd.hide('ribbon',"("+s+")") cmd.show('cartoon',"("+s+")") cmd.set('cartoon_sampling',1,"("+s+")") cmd.set('cartoon_tube_radius',0.5,"("+s+")&

Re: [PyMOL] get_view

times one still needs them...) -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: +

[PyMOL] Latest Apple G4 graphic cards and PyMOL

which card should we go for. Any suggestion? Thanks in advance and best regards, Luca ---- Luca Jovine, Ph.D. Department of Molecular, Cell & Developmental Biology Mount Sinai School of Medicine Annenberg Building, Room 25-18 One Gustave L. L

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

say model 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 Jo

RE: [PyMOL] Re: mice for OSX PyMOL

list. 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 1

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

Re: [PyMOL] get_view on native mac os X

ping into the graphics window. Hope 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 10029-657

Re: [PyMOL] Native OS X versions of Pymol

: http://prdownloads.sourceforge.net/pymol/pymol-0_79a.dmg.gz Best regards, 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

[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

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

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: +1.509.356-2832 E-Mail: lucajov...@m

[PyMOL] Up & down arrow problem under OSX

rds, 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: +1.509.356-2832 E-Mail: lucajov...@mac.com W3: http: