[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

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] 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)

om_count is about 85,000 for them. > > The movie script is as in the previous message. > > As of now, I'll try smaller hash_max's and also if that's not good, > reduce the size of my circular lipid bilayer. > > Many thanks for the quick response! > >

RE: [PyMOL] secondary structure and movie

rren L. DeLano, Ph.D. > Principal Scientist > DeLano Scientific LLC > Voice (650)-346-1154 > Fax (650)-593-4020 > > > -Original Message- > > From: pymol-users-ad...@lists.sourceforge.net > > [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of

[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

t; by 2-3 fold if you set hash_max to 150-200. > > To answer to your second question: > > import os > os.system"(mencoder \*.png -mf on:fps=30 -o mvc1ec2.avi > -ovc lavc -lavcopts > vcodec=mpeg4:vbitrate=6000:vhq:keyint=30") > > Cheers, > Warren ---

[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

------ 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] 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] Surface and SASA

Hi Dr. Warren! I know about MSMS license. Indeed, I'm suggesting an approach similar to what VMD did, i.e., it can link, run and catch results to plot, all that as a option conditioned to one gets or not MSMS installed, separately, in one's machine. Sanner had done and released a

Re: [PyMOL] Surface and SASA

Hi List! Dear Dr. Warren, have you consider using MSMS to generate surface in Pymol, as VMD already does? Since MSMS can generate a list too, by using another programs, I could calculate properties to each point in the mesh. So, I wonder, applying a colour method linked to such p

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 Instituto de

[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 Biológica

Re: [PyMOL] install

I think ir you install Python 2.1 or you wait Pymol compiled to Python 2.2. On Thu, 7 Mar 2002, Fei Xu wrote: > Hi! Everyone: > I am installing pymol.My versioin is 0.78 for window. I use python2.2. > When I run pymol , it saiys that it can't find python21.dll. > what should I do? does it requir

[PyMOL] About Surface

Hi List, PyMol is really amazing. Besides what we can do with it now, there is a great potential of evolution. I'm particularly interested in how pymol generate surface (a internal algorithm?) and how to compare it to vdW, solvent, Connolly and MSMS surfaces. Moreover, I know Del