From: Marc S. <mar...@gm...> - 2004-04-15 12:15:09
|
Hi all, I have a question regarding the spectrum command and b-factors. How are the color-ranges calculated by "spectrum"? I.e. i would like to know the values for the different shades like in the color_b.py-script, which gives you not only a total range, but also the bins. I would like to put a color-gradient-bar below a picture which shows numbers as well, and for that I need to know the ranges of blue, green, yellow, etc. Or is it possible to do this from within Pymol automatically (like for iso-surfaces)? Thanks in advance. -- Bye, Marc Saric |
From: Sean L. <mag...@ho...> - 2009-11-06 18:43:26
|
Mark, Please check your inbox as I've provided some added instructions. For all others, there is a python script which can be found on the PyMOL-Wiki that was specifically written to generate custom spectrum bars. It's very easy to use. http://www.pymolwiki.org/index.php/Spectrumbar To specify a spectrum bar from "gray10" to "gray90" just simply run the script and type spectrumbar gray10, gray90 For more color control: spectrumbar gray10, gray20, gray30, gray40, gray50, gray60, gray70, gray80, gray90 You can also use RGB values at any time: spectrumbar gray10, 1,0,0, gray90 The width of the bar can be specified by "radius" option and the length of bar can be specified with the "length" option. Enjoy. Sean _________________________________________________________________ Windows Live: Keep your friends up to date with what you do online. http://go.microsoft.com/?linkid=9691815 |
From: Raúl M. <but...@ya...> - 2009-11-06 20:03:06
|
Dear PyMOLers, This news has been almost as shocking as they have been sad. I met Warren in this list, and he was always ready to help. He even gave me advice on some of my own projects. His contribution to freedom and to the research of so many scientist in different parts of the world is difficult to even estimate, but he was one of the rare idealist who had the capacity, charisma and force of will to make their ideals come true. He never knew, but he was in the "thanks" section of my undergrad thesis. I want to extend my deepest condolences to his family. Please let me know if I can help the community on something. With best regards, Raúl Mera Adasme. PhD Student. Laboratory of Theoretical Inorganic Chemistry. Faculty of Sciences. University of Chile. Santiago de Chile. ____________________________________________________________________________________ ¡Obtén la mejor experiencia en la web! Descarga gratis el nuevo Internet Explorer 8. http://downloads.yahoo.com/ieak8/?l=e1 |
From: Carlos R. V. <cro...@gm...> - 2009-11-06 20:39:08
|
On Fri, 2009-11-06 at 12:02 -0800, Raúl Mera wrote: > Dear PyMOLers, > > This news has been almost as shocking as they have been sad. > > I met Warren in this list, and he was always ready to help. He even gave me advice on some of my own projects. > > His contribution to freedom and to the research of so many scientist in different parts of the world is difficult to even estimate, but he was one of the rare idealist who had the capacity, charisma and force of will to make their ideals come true. > > He never knew, but he was in the "thanks" section of my undergrad thesis. > > I want to extend my deepest condolences to his family. > > Please let me know if I can help the community on something. > > With best regards, > > > Raúl Mera Adasme. > > PhD Student. > Laboratory of Theoretical Inorganic Chemistry. > Faculty of Sciences. > University of Chile. > Santiago de Chile. I think, we as community, we must continue Warren's job, I mean, contributing with code and support to the PyMOL development. I think that Warren wanted that his creation could grow even if he is not with us. My deepest condolences to his family. Regards. ps: Sorry if my English is a mess. -- http://crosvera.blogspot.com Carlos Ríos V. Estudiante de Ing. (E) en Computación e Informática. Universidad del Bío-Bío VIII Región, Chile Linux user number 425502 |
From: Sean L. <mag...@ho...> - 2009-11-07 15:06:07
|
Mark, Sorry for the earlier confusion. I think I found a hackish way of getting a gray spectrum: To specify a particular color spectrum you need to know the language of the spectral ranges. These ranges are discussed briefly in the PyMOL-Wiki (spectral range colors): http://www.pymolwiki.org/index.php/Color_Values#Spectral_range_colours The Wiki actually speaks of a "gray spectrum". In using the spectrum command, when the user specifies a "palette" this string is cross referenced in a dictionary called "palette_dict" which is located in module/pymol/constants.py. For each dictionary key, a unique set of palette values is returned (prefix, digit, minimum, maximum) and interprested. Prefix specifies which spectrum to use: "gray" = gray "s" = spectrum "o" = original "r" = reversed offset spectrum "c" = complementary spectrum "w" = complementary spectrum separated by white The minimum and maximum values correspond to the range that you want for a particular spectrum and is discussed on the Wiki page. For the gray spectrum, the values run from 00 to 99. I haven't quite deciphered what the "digit" value corresponds to but for the non-gray spectrum it is set to 3 but I noticed that it produces drastically different results if you set it to 1 or 2 for the gray spectrum. It may be related to a jump value of some sort but don't quote me on that! Unfortunately, none of the gray spectral values exist in that palette dictionary. Having said that, you can hack it by adding it to the dictionary itself: 1) Go to the directory where PyMOL is installed 2) Navigate to module/pymol/constants 3) Look for 'red_cyan' : ('c',3,916,999), 'cyan_red' : ('c',3,999,916), 4) Underneath it, add your own gray spectrum 'red_cyan' : ('c',3,916,999), 'cyan_red' : ('c',3,999,916), 'grey10_grey90' :('gray',1,10,90), 5) Then, open PyMOL, load your molecule, and type "spectrum b, grey10_grey90" and this should give you a gray spectrum. Once again, you may need to play with the "digit" value as a value of "3" vs. a value of "1" can produce very different results. I'll leave it up to the user as a lesson to figure out what it means (cause I haven't). Sean _________________________________________________________________ Windows Live: Friends get your Flickr, Yelp, and Digg updates when they e-mail you. http://go.microsoft.com/?linkid=9691817 |
From: Thomas E. <te...@mb...> - 2009-11-09 00:09:26
|
Dear pymol users, I noticed something strange when superimposing 2 opposite pairs of chains. E.g. DEBUG: template 1BQG_A query 2MUC_A Query Transformation: X2 = +0.86747*(X1+2.29751) + -0.49574*(Y1+60.99794) + -0.04181*(Z1+64.71239) Y2 = -0.49701*(X1+2.29751) + -0.85983*(Y1+60.99794) + -0.11697*(Z1+64.71239) Z2 = +0.02204*(X1+2.29751) + +0.12225*(Y1+60.99794) + -0.99226*(Z1+64.71239) DEBUG: template 2MUC_A query 1BQG_A Query Transformation: X2 = +0.86747*(X1+30.95128) + -0.49701*(Y1+61.15895) + +0.02204*(Z1+56.70381) Y2 = -0.49574*(X1+30.95128) + -0.85983*(Y1+61.15895) + +0.12225*(Z1+56.70381) Z2 = -0.04181*(X1+30.95128) + -0.11697*(Y1+61.15895) + -0.99226*(Z1+56.70381) Although looking at the rotation matrices one is the transpose of the other, the translation vectors are not opposite. Can someone explain that? |
From: Tsjerk W. <ts...@gm...> - 2009-11-09 08:22:15
|
Hi Thomas, Say, the first system is x and the second y, where y=R(x+s) is the first transformation. Then the reverse transformation follows as y = R(x + s) y = Rx + Rs Rx = y - Rs x = t(R)(y-Rs) Note that that is also equal to: x = t(R)y - s Hope it helps, Tsjerk On Mon, Nov 9, 2009 at 1:09 AM, Thomas Evangelidis <te...@mb...> wrote: > Dear pymol users, > > I noticed something strange when superimposing 2 opposite pairs of > chains. E.g. > > DEBUG: template 1BQG_A query 2MUC_A > Query Transformation: > X2 = +0.86747*(X1+2.29751) + -0.49574*(Y1+60.99794) + > -0.04181*(Z1+64.71239) > Y2 = -0.49701*(X1+2.29751) + -0.85983*(Y1+60.99794) + > -0.11697*(Z1+64.71239) > Z2 = +0.02204*(X1+2.29751) + +0.12225*(Y1+60.99794) + > -0.99226*(Z1+64.71239) > > > DEBUG: template 2MUC_A query 1BQG_A > Query Transformation: > X2 = +0.86747*(X1+30.95128) + -0.49701*(Y1+61.15895) + > +0.02204*(Z1+56.70381) > Y2 = -0.49574*(X1+30.95128) + -0.85983*(Y1+61.15895) + > +0.12225*(Z1+56.70381) > Z2 = -0.04181*(X1+30.95128) + -0.11697*(Y1+61.15895) + > -0.99226*(Z1+56.70381) > > Although looking at the rotation matrices one is the transpose of the > other, the translation vectors are not opposite. Can someone explain > that? > > > > ------------------------------------------------------------------------------ > Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day > trial. Simplify your report design, integration and deployment - and focus on > what you do best, core application coding. Discover what's new with > Crystal Reports now. http://p.sf.net/sfu/bobj-july > _______________________________________________ > PyMOL-users mailing list (PyM...@li...) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > Archives: http://www.mail-archive.com/pym...@li... > -- Tsjerk A. Wassenaar, Ph.D. Junior UD (post-doc) Biomolecular NMR, Bijvoet Center Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands P: +31-30-2539931 F: +31-30-2537623 |
From: Thomas E. <te...@mb...> - 2009-11-09 15:05:52
|
Well practically speaking the opposite superimpositions are not performed in the same fashion. Lets take 1ONE and 2ONE as an example, 2 different conformations of the same molecule. Since the aa composition is identical (at least from what I've seen the chains have the same length), I measured the distances between Ca atoms of 1ONE and 2ONE after "align 1ONE and chain A, 2ONE and chain A", and the respective distances after "align 2ONE and chain A, 1ONE and chain A". The RMSD is 0.230642045187 which implies that the 2 chains are not in relative positions after 1ONEx2ONE and 2ONEx1ONE. Here's the function I 've written to do that: # a function to measure Ca distances of oposite pairs of superimpossed chains (the proteins must have the same aa composition) def check_for_symmetry(tstruct, qstruct): # align the pair cmd.fetch(tstruct) cmd.extract(pdb2entry[tstruct]+"1", tstruct + " and chain "+ pdb2entry[tstruct][-1:] + " and not hetatm") cmd.fetch(qstruct) cmd.extract(pdb2entry[qstruct]+"1", qstruct +" and chain "+ pdb2entry[qstruct][-1:] + " and not hetatm") print "Aligning "+pdb2entry[tstruct]+"1"+" with "+pdb2entry[qstruct]+"1" cmd.align(pdb2entry[tstruct]+"1", pdb2entry[qstruct]+"1") #cmd.do("cealign "+pdb2entry[qstruct]+"1, "+pdb2entry[tstruct]+"1") # align the symmetric pair cmd.fetch(tstruct) cmd.extract(pdb2entry[tstruct]+"2", tstruct + " and chain "+ pdb2entry[tstruct][-1:] + " and not hetatm") cmd.fetch(qstruct) cmd.extract(pdb2entry[qstruct]+"2", qstruct +" and chain "+ pdb2entry[qstruct][-1:] + " and not hetatm") print "Aligning "+pdb2entry[qstruct]+"1"+" with "+pdb2entry[tstruct]+"1" cmd.align(pdb2entry[qstruct]+"2", pdb2entry[tstruct]+"2") #cmd.do("cealign "+pdb2entry[qstruct]+"2, "+pdb2entry[tstruct]+"2") # measure distances pymol.stored.protein_dict = {} cmd.iterate(pdb2entry[tstruct]+"1", "stored.protein_dict[(chain,resi)]=1") Residues = pymol.stored.protein_dict.keys() Residues.sort() RMSD = 0 for res in Residues: chain = res[0] resi = res[1] dist1 = cmd.distance('tmp',pdb2entry[tstruct]+"1 and chain "+chain+" and resi "+resi+" and name ca",pdb2entry[qstruct]+"1 and chain "+chain+" and resi "+resi+" and name ca") dist2 = cmd.distance('tmp',pdb2entry[tstruct]+"2 and chain "+chain+" and resi "+resi+" and name ca",pdb2entry[qstruct]+"2 and chain "+chain+" and resi "+resi+" and name ca") print "The difference in distance betweem residue IDs ", resi," is : ",dist1, "-",dist2," = ",dist1-dist2 RMSD += (dist1-dist2)**2 RMSD = sqrt(RMSD/len(Residues)) print "RMSD of distances between identical residues in 1ONE x 2ONE and this in 2ONE x 1ONE: ", RMSD check_for_symmetry("1ONE", "2ONE") PS: Jason, I suspect the same happens with CEalign although I couldn't manage to run it for technical reasons, but by looking at the transformation matrices produced by the stand-alone version, the translation vectors are not opposite. > Hi Thomas, > > Say, the first system is x and the second y, where y=R(x+s) is the > first transformation. Then the reverse transformation follows as > > y = R(x + s) > y = Rx + Rs > Rx = y - Rs > x = t(R)(y-Rs) > > Note that that is also equal to: x = t(R)y - s > > Hope it helps, > > Tsjerk > > On Mon, Nov 9, 2009 at 1:09 AM, Thomas Evangelidis > <te...@mb...> wrote: >> Dear pymol users, >> >> I noticed something strange when superimposing 2 opposite pairs of >> chains. E.g. >> >> DEBUG: template 1BQG_A query 2MUC_A >> Query Transformation: >> X2 = +0.86747*(X1+2.29751) + -0.49574*(Y1+60.99794) + >> -0.04181*(Z1+64.71239) >> Y2 = -0.49701*(X1+2.29751) + -0.85983*(Y1+60.99794) + >> -0.11697*(Z1+64.71239) >> Z2 = +0.02204*(X1+2.29751) + +0.12225*(Y1+60.99794) + >> -0.99226*(Z1+64.71239) >> >> >> DEBUG: template 2MUC_A query 1BQG_A >> Query Transformation: >> X2 = +0.86747*(X1+30.95128) + -0.49701*(Y1+61.15895) + >> +0.02204*(Z1+56.70381) >> Y2 = -0.49574*(X1+30.95128) + -0.85983*(Y1+61.15895) + >> +0.12225*(Z1+56.70381) >> Z2 = -0.04181*(X1+30.95128) + -0.11697*(Y1+61.15895) + >> -0.99226*(Z1+56.70381) >> >> Although looking at the rotation matrices one is the transpose of the >> other, the translation vectors are not opposite. Can someone explain >> that? >> >> >> >> ------------------------------------------------------------------------------ >> Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day >> trial. Simplify your report design, integration and deployment - >> and focus on >> what you do best, core application coding. Discover what's new with >> Crystal Reports now. http://p.sf.net/sfu/bobj-july >> _______________________________________________ >> PyMOL-users mailing list (PyM...@li...) >> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users >> Archives: http://www.mail-archive.com/pym...@li... >> > > > > -- > Tsjerk A. Wassenaar, Ph.D. > Junior UD (post-doc) > Biomolecular NMR, Bijvoet Center > Utrecht University > Padualaan 8 > 3584 CH Utrecht > The Netherlands > P: +31-30-2539931 > F: +31-30-2537623 > ----- End message from ts...@gm... ----- |
From: Thomas E. <te...@mb...> - 2009-11-09 16:36:41
|
As Tsjerk pointed out, there was a mistake in the code. Just for the record this is the right function: pdb2entry = { "1ONE": "1ONE_A", "2ONE": "2ONE_A" } # a function to measure Ca distances of oposite pairs of superimpossed chains (the proteins must have the same aa composition) def check_for_symmetry(tstruct, qstruct): # align the pair cmd.fetch(tstruct) cmd.extract(pdb2entry[tstruct]+"1", tstruct + " and chain "+ pdb2entry[tstruct][-1:] + " and not hetatm") cmd.fetch(qstruct) cmd.extract(pdb2entry[qstruct]+"1", qstruct +" and chain "+ pdb2entry[qstruct][-1:] + " and not hetatm") cmd.delete(tstruct) cmd.delete(qstruct) print "Aligning "+pdb2entry[tstruct]+"1"+" with "+pdb2entry[qstruct]+"1" cmd.align(pdb2entry[tstruct]+"1", pdb2entry[qstruct]+"1") #cmd.do("cealign "+pdb2entry[qstruct]+"1, "+pdb2entry[tstruct]+"1") # align the symmetric pair cmd.fetch(tstruct) cmd.extract(pdb2entry[tstruct]+"2", tstruct + " and chain "+ pdb2entry[tstruct][-1:] + " and not hetatm") cmd.fetch(qstruct) cmd.extract(pdb2entry[qstruct]+"2", qstruct +" and chain "+ pdb2entry[qstruct][-1:] + " and not hetatm") print "Aligning "+pdb2entry[qstruct]+"1"+" with "+pdb2entry[tstruct]+"1" cmd.align(pdb2entry[qstruct]+"2", pdb2entry[tstruct]+"2") #cmd.do("cealign "+pdb2entry[qstruct]+"2, "+pdb2entry[tstruct]+"2") # measure distances pymol.stored.protein_dict = {} cmd.iterate(pdb2entry[tstruct]+"1", "stored.protein_dict[(chain,resi)]=1") Residues = pymol.stored.protein_dict.keys() Residues.sort() RMSD = 0 for res in Residues: chain = res[0] resi = res[1] dist1 = cmd.distance('tmp',pdb2entry[tstruct]+"1 and chain "+chain+" and resi "+resi+" and name ca",pdb2entry[qstruct]+"1 and chain "+chain+" and resi "+resi+" and name ca") dist2 = cmd.distance('tmp',pdb2entry[tstruct]+"2 and chain "+chain+" and resi "+resi+" and name ca",pdb2entry[qstruct]+"2 and chain "+chain+" and resi "+resi+" and name ca") print "The difference in distance betweem residue IDs ", resi," is : ",dist1, "-",dist2," = ",dist1-dist2 RMSD += (dist1-dist2)**2 RMSD = sqrt(RMSD/len(Residues)) print "RMSD of distances between identical residues in 1ONE x 2ONE and this in 2ONE x 1ONE: ", RMSD check_for_symmetry("1ONE", "2ONE") After this correction the RMSD falls to 2.06853295972e-06, which a reasonably good number. |
From: Robert C. <rob...@qu...> - 2009-11-09 14:14:39
|
Hi Mark and Sean, On Sat, 07 Nov 2009 10:05:59 -0500 Sean Law <mag...@ho...> wrote: > Sorry for the earlier confusion. I think I found a hackish way of getting > a gray spectrum: <snip Sean's extensive explanation> I know I'm biased, since I wrote the color_b.py script, but I fail to see what is difficult about typing: color_b "selectionname", gradient=user, user_rgb=[.2,.2,.2,.5,.5,.5,.8,.8,.8] In order to colour "selectionname" in a gray spectrum that goes from 20% gray, has a midpoint of 50% gray and ends at 80% gray (where 20% gray is the same as the colour called gray20, i.e. close to black and 80% gray is almost white). Cheers, Rob -- Robert L. Campbell, Ph.D. Senior Research Associate/Adjunct Assistant Professor Botterell Hall Rm 644 Department of Biochemistry, Queen's University, Kingston, ON K7L 3N6 Canada Tel: 613-533-6821 Fax: 613-533-2497 <rob...@qu...> http://pldserver1.biochem.queensu.ca/~rlc |
From: Tsjerk W. <ts...@gm...> - 2009-11-09 16:41:36
|
Hmm, this should've been replied to the list. The info may be useful to others. Tsjerk ---------- Forwarded message ---------- From: Tsjerk Wassenaar <ts...@gm...> Date: Mon, Nov 9, 2009 at 5:02 PM Subject: Re: [PyMOL] asymmetric transformation matrices To: Thomas Evangelidis <te...@mb...> Hi Thomas, You're not doing what you think you're doing. > # a function to measure Ca distances of oposite pairs of superimpossed > chains (the proteins must have the same aa composition) > def check_for_symmetry(tstruct, qstruct): > # align the pair > cmd.fetch(tstruct) You fetch the first structure, which is placed in state 1 > cmd.extract(pdb2entry[tstruct]+"1", tstruct + " and chain "+ > pdb2entry[tstruct][-1:] + " and not hetatm") You extract part of that structure, which is removed from the state > cmd.fetch(qstruct) You fetch the other structure, which is also loaded into state 1 > cmd.extract(pdb2entry[qstruct]+"1", qstruct +" and chain "+ > pdb2entry[qstruct][-1:] + " and not hetatm") You extract part of that structure > print "Aligning "+pdb2entry[tstruct]+"1"+" with "+pdb2entry[qstruct]+"1" > cmd.align(pdb2entry[tstruct]+"1", pdb2entry[qstruct]+"1") > #cmd.do("cealign "+pdb2entry[qstruct]+"1, "+pdb2entry[tstruct]+"1") > # align the symmetric pair > cmd.fetch(tstruct) You fetch the first structure again, but this time it's appended to state 2 > cmd.extract(pdb2entry[tstruct]+"2", tstruct + " and chain "+ > pdb2entry[tstruct][-1:] + " and not hetatm") You try to extract chain A again. But that is tried on state 1, while that state has no chain A anymore. The object is empty! > cmd.fetch(qstruct) Same story for the other object > cmd.extract(pdb2entry[qstruct]+"2", qstruct +" and chain "+ > pdb2entry[qstruct][-1:] + " and not hetatm") Empty object... Then in the next part you calculate the RMSD of distances in an empty object (all 0) and the aligned one. That RMSD ends up close to the actual RMSD from the alignment (restricted on CA atoms: 0.280), for obvious reasons. I hope this helps, Tsjerk -- Tsjerk A. Wassenaar, Ph.D. Computational Chemist Medicinal Chemist Neuropharmacologist -- Tsjerk A. Wassenaar, Ph.D. Computational Chemist Medicinal Chemist Neuropharmacologist |
From: Shu-Hsien S. <sh...@bu...> - 2004-04-15 14:28:36
|
Hi, Our system administrator of a linux cluster have trouble upgrading from 0.93 to 0.95: [mfitzpat@man local]$ sudo rpm -U --test pymol-0.95-1.rh73.py22.i386.rpm [mfitzpat@man local]$ sudo rpm -U pymol-0.95-1.rh73.py22.i386.rpm warning: user warren does not exist - using root warning: user warren does not exist - using root warning: user warren does not exist - using root warning: user warren does not exist - using root warning: user warren does not exist - using root warning: user warren does not exist - using root warning: user warren does not exist - using root [mfitzpat@man local]$ sudo rpm -V pymol-0.95-1 package pymol-0.95-1 is not installed Any ideas? Thanks! shuhsien -----Original Message----- From: pym...@li... [mailto:pym...@li...] On Behalf Of Marc Saric Sent: Thursday, April 15, 2004 8:15 AM To: pym...@li... Subject: [PyMOL] spectrum Hi all, I have a question regarding the spectrum command and b-factors. How are the color-ranges calculated by "spectrum"? I.e. i would like to know the values for the different shades like in the color_b.py-script, which gives you not only a total range, but also the bins. I would like to put a color-gradient-bar below a picture which shows numbers as well, and for that I need to know the ranges of blue, green, yellow, etc. Or is it possible to do this from within Pymol automatically (like for iso-surfaces)? Thanks in advance. -- Bye, Marc Saric ------------------------------------------------------- This SF.Net email is sponsored by: IBM Linux Tutorials Free Linux tutorial presented by Daniel Robbins, President and CEO of GenToo technologies. Learn everything from fundamentals to system administration.http://ads.osdn.com/?ad_id=1470&alloc_id=3638&op=click _______________________________________________ PyMOL-users mailing list PyM...@li... https://lists.sourceforge.net/lists/listinfo/pymol-users |
From: Yu C. <ch...@hh...> - 2004-04-15 14:32:20
|
The warning is ok, just ignore. And to check the rpm package, use "pymol" as package name, not with version numbers. like 'rpm -q pymol' Chen On Thu, 15 Apr 2004, Shu-Hsien Sheu wrote: > Hi, > > Our system administrator of a linux cluster have trouble upgrading from 0.93 > to 0.95: > > [mfitzpat@man local]$ sudo rpm -U --test pymol-0.95-1.rh73.py22.i386.rpm > [mfitzpat@man local]$ sudo rpm -U pymol-0.95-1.rh73.py22.i386.rpm > warning: user warren does not exist - using root > warning: user warren does not exist - using root > warning: user warren does not exist - using root > warning: user warren does not exist - using root > warning: user warren does not exist - using root > warning: user warren does not exist - using root > warning: user warren does not exist - using root > [mfitzpat@man local]$ sudo rpm -V pymol-0.95-1 package pymol-0.95-1 is not > installed > > Any ideas? > > Thanks! > shuhsien > > -----Original Message----- > From: pym...@li... > [mailto:pym...@li...] On Behalf Of Marc Saric > Sent: Thursday, April 15, 2004 8:15 AM > To: pym...@li... > Subject: [PyMOL] spectrum > > Hi all, > > I have a question regarding the spectrum command and b-factors. How are > the color-ranges calculated by "spectrum"? > > I.e. i would like to know the values for the different shades like in > the color_b.py-script, which gives you not only a total range, but also > the bins. > > I would like to put a color-gradient-bar below a picture which shows > numbers as well, and for that I need to know the ranges of blue, green, > yellow, etc. > > Or is it possible to do this from within Pymol automatically (like for > iso-surfaces)? > > Thanks in advance. > > -- > Bye, > Marc Saric > > > ------------------------------------------------------- > This SF.Net email is sponsored by: IBM Linux Tutorials > Free Linux tutorial presented by Daniel Robbins, President and CEO of > GenToo technologies. Learn everything from fundamentals to system > administration.http://ads.osdn.com/?ad_id=1470&alloc_id=3638&op=click > _______________________________________________ > PyMOL-users mailing list > PyM...@li... > https://lists.sourceforge.net/lists/listinfo/pymol-users > > > > ------------------------------------------------------- > This SF.Net email is sponsored by: IBM Linux Tutorials > Free Linux tutorial presented by Daniel Robbins, President and CEO of > GenToo technologies. Learn everything from fundamentals to system > administration.http://ads.osdn.com/?ad_id=1470&alloc_id=3638&op=click > _______________________________________________ > PyMOL-users mailing list > PyM...@li... > https://lists.sourceforge.net/lists/listinfo/pymol-users > |
From: Michael B. <mb...@gm...> - 2004-04-15 14:47:16
|
On Thu, Apr 15, 2004 at 10:27:32AM -0400, Shu-Hsien Sheu wrote: > [mfitzpat@man local]$ sudo rpm -V pymol-0.95-1 package pymol-0.95-1 is > not installed Just a shot in the dark, but are you sure the package is called pymol-0.95-1 and not just pymol? Michael |