Thanks Marius With the second it works
A bientot Stephane -----Message d'origine----- De : Marius Retegan [mailto:marius.s.rete...@gmail.com] Envoyé : jeudi 22 septembre 2011 18:02 À : intra\sa175950 Objet : Re: [PyMOL] Write in a file the number of water at a distance from a Hello Stephane, Water molecules are composed of 3 atoms, so this print cmd.count_atoms("WATER_firstshell")/3 should give you the right answer. If you really want it your way: print cmd.count_atoms("firstshell_WATER and elem O") P.S. I haven't tried any of these commands. I hope they work. Best regards, Marius -- Dr. Marius Retegan Postdoctoral Fellow Département de Chimie Moléculaire Université Joseph Fourier 301 Rue de la Chimie BP 53, 38041 Grenoble Cedex 9, France Tel: +33 (0) 4 76 63 44 03 GnuPG http://db.tt/rr7Hd0Y On Thu, Sep 22, 2011 at 5:38 PM, intra\sa175950 <stephane.a...@cea.fr> wrote: > Hi All, > > With the help of Thomas Holder (thanks to him), now I can show and obtain > the number of water in the first shell of my six peptides (an amyloid > fibrils). However, I have a little problem with the command count_atoms in > my script > > Below my script (*.pml) for Pymol 1.3 : > > mstop > dss > hide all > > select CL, resn CL > delete CL > > ## Select WATER with residue ID SOL > select WATER, resn SOL > > ## Select Amyloid, resi 1-54 > select Amyloid, resi 1-54 and not WATER > > ## Show in cartoon Amyloid > show cartoon, Amyloid > > ## Show in different colors peptides because it is nice. > set cartoon_color, black, resi 2-8 > set cartoon_color, red, resi 11-17 > set cartoon_color, green, resi 20-26 > set cartoon_color, blue, resi 29-35 > set cartoon_color, yellow, resi 38-44 > set cartoon_color, chocolate, resi 47-53 > > ## Not use for the moment > > ##set cartoon_color, gray50, resi 56-62 > ##set cartoon_color, wheat, resi 65-71 > ##set cartoon_color, aquamarine, resi 74-80 > ##set cartoon_color, pink, resi 83-89 > ##set cartoon_color, orange, resi 92-98 > ##et cartoon_color, forest, resi 101-107 > > ## Select water in the first shell (e.g. within 3.5 A of the Amyloid atoms) > select WATER_firstshell, WATER within 3.5 A of Amyloid > > ## Give the number of water in the first shell of the fibrils > ## Works ---> Give number of water atoms (including oxygen and Hs) > print cmd.count_atoms("WATER_firstshell") > > ## Print the residu ID of each water in the first shell > iterate ("WATER_firstshell"), print resi > > set cartoon_fancy_helices=1 > set cartoon_discrete_colors, on > set antialias = 1 > > ray > > ------------------- > > As you can imagine the "firstshell_WATER" variable contains the water O and > H atoms. It is not what I want! Indeed I want that count_atoms command > counts only the number of Water oxygen. So I use > > count_atoms("firstshell_WATER" and elem O) > > This command works if I use the pymol GUI but If I use the command in my > script. Indeed > > print cmd.count_atoms("firstshell_WATER" and elem O) show a syntax error > > > Thanks in advance for your help. > > Stephane > > ------------------------------ > > Message: 7 > Date: Thu, 22 Sep 2011 11:14:36 +0200 > From: Thomas Holder <spel...@users.sourceforge.net> > Subject: Re: [PyMOL] Write in a file the number of water at a distance > from a protein surface > To: ABEL Stephane 175950 <stephane.a...@cea.fr> > Cc: "pymol-users@lists.sourceforge.net" > <pymol-users@lists.sourceforge.net> > Message-ID: <4e7afc7c.4060...@users.sourceforge.net> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > Hi Stephane, > > you can select those waters using the "within" or "gap" selection > operators. "within" measures from the atom centre, whereas "gap" takes > the VDW radius into accout but selects everything beyond instead of > near. Have a look at those examples: > > # use '... within ...' > select firstshell, solvent within 3.5 of polymer > > # or use 'not (... gap ...)' > select firstshell, solvent and not (polymer gap 0.5) > > # shows the selected water molecules as a sphere > show spheres, firstshell and elem O > > # writes the results in a file > python > stored.out = open('/tmp/water-IDs.txt', 'w') > print >> stored.out, '## At 0.5 Ang of the protein surface there are', > print >> stored.out, cmd.count_atoms('firstshell and elem O'), > print >> stored.out, 'water molecules' > print >> stored.out, '## Water ID and resi are' > cmd.iterate('firstshell', 'print >> stored.out, ID, resi') > stored.out.close() > python end > > http://www.pymolwiki.org/index.php/Selection_Algebra > http://www.pymolwiki.org/index.php/Iterate > > Hope that helps, > > Cheers, > Thomas > > On 09/21/2011 11:03 PM, ABEL Stephane 175950 wrote: >> Hi All, >> >> I have simulated a protein in water cubic box and I would like to >> know how to show and obtain the number of water in the first shell of >> the protein (or at x Ang of the protein surface) using a pymol >> script. I can to do this using the pymol GUI but I would prefer that >> the script : >> >> - shows the selected water molecules as a sphere >> - and writes the results in a file with the water ID (i.e. residue >> number), for example like this: >> >> ## At x Ang of the protein surface there are XX water molecules >> ## Water ID are >> >> Thanks in advance for your help. >> >> Stephane > > -- > Thomas Holder > MPI for Developmental Biology > > > > ------------------------------ > > Message: 8 > Date: Thu, 22 Sep 2011 10:05:46 +0000 > From: ABEL Stephane 175950 <stephane.a...@cea.fr> > Subject: [PyMOL] RE : Write in a file the number of water at a > distance from a protein surface > To: Thomas Holder <spel...@users.sourceforge.net> > Cc: "pymol-users@lists.sourceforge.net" > <pymol-users@lists.sourceforge.net> > Message-ID: > <3e39b768bb199548ab18f7289e7534af0ad...@exdag0-b0.intra.cea.fr> > Content-Type: text/plain; charset="iso-8859-1" > > Thank you for your response, i will try your suggestion > > A bientot > > Stephane > ________________________________________ > De : Thomas Holder [ad...@thomas-holder.de] de la part de Thomas Holder > [spel...@users.sourceforge.net] > Date d'envoi : jeudi 22 septembre 2011 11:14 > ? : ABEL Stephane 175950 > Cc : pymol-users@lists.sourceforge.net > Objet : Re: [PyMOL] Write in a file the number of water at a distance from a > protein surface > > Hi Stephane, > > you can select those waters using the "within" or "gap" selection > operators. "within" measures from the atom centre, whereas "gap" takes > the VDW radius into accout but selects everything beyond instead of > near. Have a look at those examples: > > # use '... within ...' > select firstshell, solvent within 3.5 of polymer > > # or use 'not (... gap ...)' > select firstshell, solvent and not (polymer gap 0.5) > > # shows the selected water molecules as a sphere > show spheres, firstshell and elem O > > # writes the results in a file > python > stored.out = open('/tmp/water-IDs.txt', 'w') > print >> stored.out, '## At 0.5 Ang of the protein surface there are', > print >> stored.out, cmd.count_atoms('firstshell and elem O'), > print >> stored.out, 'water molecules' > print >> stored.out, '## Water ID and resi are' > cmd.iterate('firstshell', 'print >> stored.out, ID, resi') > stored.out.close() > python end > > http://www.pymolwiki.org/index.php/Selection_Algebra > http://www.pymolwiki.org/index.php/Iterate > > Hope that helps, > > Cheers, > Thomas > > On 09/21/2011 11:03 PM, ABEL Stephane 175950 wrote: >> Hi All, >> >> I have simulated a protein in water cubic box and I would like to >> know how to show and obtain the number of water in the first shell of >> the protein (or at x Ang of the protein surface) using a pymol >> script. I can to do this using the pymol GUI but I would prefer that >> the script : >> >> - shows the selected water molecules as a sphere >> - and writes the results in a file with the water ID (i.e. residue >> number), for example like this: >> >> ## At x Ang of the protein surface there are XX water molecules >> ## Water ID are >> >> Thanks in advance for your help. >> >> Stephane > > -- > Thomas Holder > MPI for Developmental Biology > > > > ------------------------------ > > ---------------------------------------------------------------------------- > -- > All the data continuously generated in your IT infrastructure contains a > definitive record of customers, application performance, security > threats, fraudulent activity and more. Splunk takes this data and makes > sense of it. Business sense. IT sense. Common sense. > http://p.sf.net/sfu/splunk-d2dcopy1 > > ------------------------------ > > _______________________________________________ > PyMOL-users mailing list > PyMOL-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/pymol-users > > > End of PyMOL-users Digest, Vol 64, Issue 17 > ******************************************* > > > > ---------------------------------------------------------------------------- -- > All the data continuously generated in your IT infrastructure contains a > definitive record of customers, application performance, security > threats, fraudulent activity and more. Splunk takes this data and makes > sense of it. Business sense. IT sense. Common sense. > http://p.sf.net/sfu/splunk-d2dcopy1 > _______________________________________________ > PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net > ------------------------------------------------------------------------------ All the data continuously generated in your IT infrastructure contains a definitive record of customers, application performance, security threats, fraudulent activity and more. Splunk takes this data and makes sense of it. Business sense. IT sense. Common sense. http://p.sf.net/sfu/splunk-d2dcopy1 _______________________________________________ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
