[PyMOL] frustrating rms command

fit, rms_cur, intra_fit, intra_rms, intra_rms_cur, pair_fit Thanks Alan -- Alan Wilter Sousa da Silva, D.Sc. PDBe group, PiMS project http://www.pims-lims.org/ EMBL - EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK +44 (0)1223 492 583 (office) -

Re: [PyMOL] Showing electric field lines

tin-dimer ) I wonder if there would be a clever way of setting 'pdime' according to the number of cpus available. For a dual-core, 'pdime 2 1 1' should work. Many thanks for your plugin. Alan On Mon, Feb 15, 2010 at 10:42, Alan wrote: > Dear Michael, > > I am using Py

Re: [PyMOL] Showing electric field lines

x27;pdb2pqr location' is. APBS Tools2 also creates > pymol-generated-PE0.dx but is happy to work with it. (In fact, it says > 'Could not find pymol-generated.dx so searching for > pymol-generated-PE0.dx.') The field lines ca

Re: [PyMOL] Showing electric field lines

thing wrong or I don't have the right version of Pymol and/or Apbs. May you clarify me here? This addition to the plugin would be very welcome. Thanks in advance, Alan On Sat, Feb 13, 2010 at 04:55, wrote: > Message: 3 > Date: Wed, 10 Feb 2010 20:26:47 -0500 > From: Michael Lerner

Re: [PyMOL] launching pymol from a script

Hi there, Please, did someone check that? It would be very appreciated. Thanks Alan On Mon, Jan 4, 2010 at 16:49, Alan wrote: > Hi there, > > I use both pymol via Fink (on MBP 10.6.2) all in 64 bits and MacPymol 1.2r3 > (licensed to PDBe). > > Both work fine but I tried >

[PyMOL] launching pymol from a script

a list of commands. Enter "help " for information on a specific command. Hit ESC anytime to toggle between text and graphics. [1]25649 segmentation fault ./pymol.sh Would someone know what else I can try to do? Many thanks in advance, Alan -- Alan Wilter Sousa da Silva, D.S

Re: [PyMOL] launch pymol from inside an IDLE ( python-ide)

Hi, Instead of using Mac IDLE, use Fink IDLE: which idle2.5 /sw/bin/idle2.5 It works! Cheers, Alan On Tue, Jun 10, 2008 at 1:25 AM, wrote: > Date: Wed, 4 Jun 2008 11:24:16 -0400 > From: "hari jayaram" > Subject: [PyMOL] launch pymol from inside an IDLE ( python-ide) &

[PyMOL] Gratuitous Eye-Candy Tweaks

based tkinter but I would like to listen from others if they would be able to have it. Besides, any tip abou the issue above would be ver appreciate. Many thanks in advance. Alan -- Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate Department of Biochemistry, University of Cambridge. 80 Te

Re: [PyMOL] compiling pymol on Mac intel

Hurrah! It's working, even X11, all fine. Thanks a lot Warren. Cheers, Alan On 02/07/07, DeLano Scientific wrote: Alan, svn update and try rebuilding. The problem was that the existing setup.py was still linking against Apple-provided Python as opposed to Fink Python. Also note that

[PyMOL] compiling pymol on Mac intel

. Cheers, Alan On 27/06/07, DeLano Scientific wrote: Alan, Okay, I found the glitch with the OSX defines -- my bad. However, I also rediscovered what the hidden difficultly is with compiling PyMOL under X11, and that is: Mac OS X's built-in python has an Aqua-based Tcl/Tk/Tkinter implementatio

[PyMOL] compiling pymol on Mac intel

scripts written for it). Otherwise, how to tell setup to install pymol for X11? If I can use MacPymol (and compile it), that's would be great. So, any hint here would be very appreciated. Many thanks in advance. Cheers, Alan -- Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate Dep

[PyMOL] importing pymol modules in a python script

l/pymol/modules/pymol/__init__.py", line 353, in ? import _cmd ImportError: No module named _cmd Is there a way to run the python script with pymol stuff imported or only via 'pymol -c'? Many thanks in advance. Alan -- Alan Wilter S. da Silva, D.Sc. - Research Associate Department

[PyMOL] nt_gly.pkl wrong

58.066 32.699 -0.358 1.00 0.00 H ATOM 8 2HT TYR22 58.065 32.977 -1.992 0.00 0.00 H ATOM 9 3HT TYR22 58.265 31.307 -1.322 0.00 0.00 H END There TYR H in a GLY ;-) Cheers, Alan -- Alan Wilter S. da Silva, D.Sc. - Research

Re: [PyMOL] Saving PDB with CONECT information

know how to to do it by mouse, but how to 'add hydrogens' and 'make pk1 positive', e. g., by command? Thanks a lot for PyMol. Cheers, Alan On 20/03/06, Warren DeLano wrote: > Alan, > > > Is PyMol able to save the built protein/molecule in a PDB > > file with C

[PyMOL] Saving PDB with CONECT information

Hello List! Is PyMol able to save the built protein/molecule in a PDB file with CONECT information. If so, how to do it? Thanks in advance for any help. Cheers, Alan -- Alan Wilter S. da Silva, D.Sc. - Research Associate Department of Biochemistry, University of Cambridge. 80 Tennis Court Road

[PyMOL] Re: building peptides (gilleain torrance)

Thx Gilleain! Cheers, Alan > Message: 1 > Date: Wed, 15 Mar 2006 09:37:55 + > From: "gilleain torrance" > To: Pymol > Subject: [PyMOL] Re: building peptides > > Hi, > > The wiki has a page on this: > > http://www.pymolwiki.org/index.php/Peptide

[PyMOL] building peptides

;create peptide res-res-res' 'set NH3 in res 1 and COO- in res 3' save aa.pdb, all --- Thanks a lot for any help. Cheers, Alan -- Alan Wilter S. da Silva, D.Sc. - Research Associate Department of Biochemistry, University of Cambridge. 80 Tennis Court Road, Cambridge CB2 1GA, UK.

Re: [PyMOL] ugly font in GUI, FAQ wrong

Thanks Renato. My distribution is Ubuntu. But, what I want is independent of distribution. There's a default font being used by Pymol and I want to change it, like you do in nedit, for instance. Cheers, Alan On 14/10/05, Joao Renato Carvalho Muniz wrote: > Hey Alan > > Wha

[PyMOL] ugly font in GUI, FAQ wrong

computer it is really bad. I'd thank any help here. Cheers, Alan -- Alan Wilter S. da Silva, D.Sc.

[PyMOL] setting for publications

advance, Cheers, Alan -- -- Alan Wilter Sousa da Silva -- D.Sc. - IBCCF/UFRJ Projeto BioPAUA - HP/LNCC Petrópolis (RJ), Brasil www.lncc.br/~alan

[PyMOL] local protein contact potential

Hi dr. DeLano! You've mentioned in a older e-mail: "1) PyMOL has an automated menu action that generates a "local protein contact potential" with a constant dielectric screening function." How to achieve that? Will it generate a surface map? Thanks

[PyMOL] RE: rendering pictures to publish

Thank you all for your help. Cheers, Alan -- -- Alan Wilter Sousa da Silva -- D.Sc. - IBCCF/UFRJ Projeto BioPAUA - HP/LNCC Petrópolis (RJ), Brasil www.lncc.br/~alan

[PyMOL] rendering pictures to publish

would be very welcome. Thanks in advance, Cheers, Alan -- -- Alan Wilter Sousa da Silva -- D.Sc. - IBCCF/UFRJ Projeto BioPAUA - HP/LNCC Petrópolis (RJ), Brasil www.lncc.br/~alan

[PyMOL] still abou surfaces

surface of some drugs that we have been studied here. How about it? Or is there another alternative? Thanks in advance for any commentary. Cheers, -- -- Alan Wilter Sousa da Silva -- D.Sc. - IBCCF/UFRJ Projeto BioPAUA - HP/LNCC Petrópolis (RJ

[PyMOL] Does (PDB) size really matter? (Jason Vertrees)

I've done with VMD. See an example: http://www.lac.inpe.br/~alan/IntroducingMD.avi I'm wondering if (and that's my suggestion to you Jason) it'd be a nice idea parting you movie in several takes (as I did for the example above), like "playing-as-a-director-in-a-real-movi

RE: [PyMOL] secondary structure and movie

Thank you very much Dr. DeLano. However mdo 1, dss state=1 gave errors, but mdo 1: dss state=1 Worked fine. It is a bug? If so, manual need to be also updated. I'm using 0.92. Gonna update to 0.93. Cheers, On Fri, 31 Oct 2003, Warren L. DeLano wrote: > Alan, > >

[PyMOL] secondary structure and movie

, all that said, what I want to do is loading a multi-pdb file and see dss calculating different ss for each frame. How could I do it? Cheers, - -- Alan Wilter Sousa da Silva -- B.Sc. - Dep. Física - UFPA M.Sc. - Dep. Física - PUC/RJ D.Sc. - IBCCF

RE: [PyMOL] Pymol script screenplay

On Thu, 2 Oct 2003, Warren L. DeLano wrote: > Alan, > > VMD is more memory efficient that PyMOL. Probably the main > reason for this is that PyMOL pre-calculates and stores all of the > geometries it is going to show down to the last vertex. > > You can red

[PyMOL] Pymol script screenplay

-mf on:fps=30 -o mvc1ec2.avi -ovc lavc -lavcopts vcodec=mpeg4:vbitrate=6000:vhq:keyint=30 Thanks in advance for any help. Cheers, -- -- Alan Wilter Sousa da Silva -- B.Sc. - Dep. Física - UFPA M.Sc. - Dep. Física - PUC/RJ D.Sc. - IBCCF/UFR

[PyMOL] cgo_text and number of states

f frames/states of a trj file (MD)? Many thanks in advance. Cheers, -- Alan Wilter Sousa da Silva -- B.Sc. - Dep. Física - UFPA M.Sc. - Dep. Física - PUC/RJ D.Sc. - IBCCF/UFRJ Bolsista Pesquisador LAC-INPE São José dos Campos (SP), Brasil www.lac.inpe.br/~alan

[PyMOL] Movie script

ive some tip or even suggest me an improvement in my actual script? I would like to have a movie following that takes: frame 1 x10, a 180 rotation in 36 frames, MD in many frames, a 180 rotation in 36 frames again, last frame x10. Any help would be very welcome. Cheers, --

Re: [PyMOL] energy minimisation in python

//sourceforge.net/mailarchive/forum.php?thread_id=1419207&forum_id=60 > Cheers, -- -- Alan Wilter Sousa da Silva -- B.Sc. - Dep. Física - UFPA M.Sc. - Dep. Física - PUC/RJ D.Sc. - IBCCF/UFRJ Bolsista Pesquisador LAC-INPE São José dos Campos (SP), Brasil www.lac.inpe.br/~alan

Re: [PyMOL] Re: PyMOL-users digest, Vol 1 #408 - 11 msgs

Hi Dan! Thank you too... for decriphering what I tried to say. > > But pymol rpm for RH is *NOT* a friend of MDK, I suggest you use > > pymol-0_90-bin-linux-libc6-i386.tgz Pymol is quite awesome by itself, but running with proper hardware... Cheers, Alan Quoting Daniel Rigden

[PyMOL] Re: PyMOL-users digest, Vol 1 #408 - 11 msgs

lieve there's many MDK users of pymol like me and Dan. Cheers, Alan Silvae On Tue, 9 Sep 2003, Warren L. DeLano wrote: > Dan, > > Opinions may vary, but I see RPMs are pretty heavily tied to the > distribution. The kind of errors you're seeing are to be expected when

Re: [PyMOL] Surface and SASA

27; data output. I know a little bit about Connoly code but it suffers the same license problem. I steadily support GNU directions and I believe that it will not uncharacterise your beautiful program. Sincerely, On Mon, 10 Feb 2003, Warren L. DeLano wrote: > > Alan, > &g

Re: [PyMOL] Surface and SASA

properties... well you can imagine. Cheers, --- Alan Wilter S. da Silva --- Laboratório de Física Biológica Instituto de Biofísica Carlos Chagas Filho Universidade do Brasil/UFRJ Rio de Janeiro, Brasil

Re: [PyMOL] Pymol and Autodock

On Thu, 6 Feb 2003, Warren L. DeLano wrote: > Read-in performace would be better if you could convert your > multiligand PDB file to an SD file. Sorry, what's SD? TIA, Cheers, --- Alan Wilter S. da Silva --- Laboratório de Física Biológica

[PyMOL] Viewing Water molecules, problems with bond

Hi List, I'm trying to create a image of protein/subtrate + HOH. The problem is the HOH made connections where isn't supposed to be! How can I solve this? Many thanks in advance, --- Alan Wilter S. da Silva --- Laboratório de Física

Re: [PyMOL] install

uld I do? does it require python21.dll absolutely? > > HAve a nice day! > > Fei Xu --- Alan Wilter S. da Silva --- Laboratório de Física Biológica Instituto de Biofísica Carlos Chagas Filho Universidade do Brasil/UFRJ Rio de Janeiro, Brasil

[PyMOL] About Surface

know Delano has plans to integrate Electrostatic Potential calculation in PyMol but I would like to know if we will be able to map the elec. pot. over such surface. Also, can I improve the surface resolution and make it transparent? --- Alan Wilter S. da