Re: [PyMOL] Goodsell colouring

k > ___ > 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 > -- A

[PyMOL] svn compile error

-- Andreas Förster X-ray Crystallography Facility Manager Centre for Structural Biology Imperial College London -- Download BIRT iHub F-Type - The Free Enterprise-Grade BIRT Server from

Re: [PyMOL] Fast mmCIF loading in latest Open-Source updates

downloads mmcif instead of pdb > > We welcome any kind of testing and feedback. > > Cheers, >Thomas > -- Andreas Förster X-ray Crystallograhpy Facility Manager

[PyMOL] symexp eats chain ID

to chain (null). What's up with this? PyMOL 1.7.3.0 on RHEL 6.3 64-bit installed from cvs 9/9/14. Thanks. Andreas -- Andreas Förster Crystallization and X-ray Facility Manager Centre for Structural Biology Impe

[PyMOL] pymol svn

Dear all, trying to update PyMOL with the usual svn co svn://svn.code.sf.net/p/pymol/code/trunk/pymol I get an "svn: Network connection closed unexpectedly" error. This is on two different computers/OSs. Has anything changed? Thanks. Andreas -- Andre

Re: [PyMOL] Ligand - binding

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 > -- Andreas Förster Crystal

[PyMOL] cylindrical helices

helices, and in perpendicular orientations. Best regards. Andreas -- Andreas Förster Crystallization and Xray Facility Manager Centre for Structural Biology Imperial

[PyMOL] pymol fails to compile

Dear all, following up on my previous post, pymol-v1.6.0.0.tar.bz2 from http://sourceforge.net/projects/pymol/ compiles just fine on my machine. It's the most recent source from svn that doesn't. Andreas -- Andreas Förster Crystallization and Xra

[PyMOL] pymol fails to compile

function layer1/CGO.c: In function ‘CGORenderRay’: layer1/CGO.c:6185: warning: ‘vertexVals’ may be used uninitialized in this function layer1/CGO.c: In function ‘CGOSimplify’: layer1/CGO.c:5136: warning: ‘normalVals’ may be used uninitialized in this function -- Andreas Förster

Re: [PyMOL] Show and hide different sets of measurements

Use the group command: group nameOfGroup, object1 distance1 (disclaimer: I haven't tried this) Andreas On 03/05/2013 1:20, Martin Hediger wrote: > Dear PyMOL users > > Assume I have two objects loaded in a PyMOL session and in each I'm > interested in a specific distance. So in both object

Re: [PyMOL] Splitting a PDB file into its constituent chains, and making multiple (smaller) PDB files

.pdb > > Also, in case I have a large number of multiple chain PDB files, how could I > go > about splitting each of them? > > Please help. > > - Anasuya Dighe > > -- Andreas Förster, Research Associate Paul Freemont & Xiaodong Zhan

Re: [PyMOL] apbs2 plugin failure

Did I say thanks? It seems I was using an older version of the plugin. The one downloaded just now works fine. Thanks! Andreas On 10/01/2013 9:18, Troels Emtekær Linnet wrote: > Hi Andreas. > > The line: > /usr/lib64/python2.6/site-packages/pmg_tk/startup/apbs_tools.py > > shows that you

[PyMOL] apbs2 plugin failure

renced before assignment When I chose "User PyMOL generated PQR and PyMOL generated Hydrogens and termini" or "User PyMOL generated PQR and existing hydrogens and termini", I can set the grid, run APBS and visualize the result just fine. I'm happy with that, but maybe som

Re: [PyMOL] Isstall on CentOS 6

on CentOS 6? > Thanks -- Andreas Förster, Research Associate Paul Freemont & Xiaodong Zhang Labs Department of Biochemistry, Imperial College London http://www.msf.bio.ic.ac.uk -- Virt

Re: [PyMOL] Installation PyMOL failure in Linux (CentOS)

x27;: >> layer0/Isosurf.c:2197:0: error: unterminated argument list invoking macro >> "fprintf" > > - 'compile_pymol.sh' : again by initial trying > http://www.pymolwiki.org/index.php/Linux_Install#Install_from_source > - 'compile_pymol_sh_error.txt

Re: [PyMOL] Visualise molecules to scale?

a certain number of angstroms per pixel or so. I will ray > trace the images. > > /Daniel > -- Andreas Förster, Research Associate Paul Freemont & Xiaodong Zhang Labs Department of Biochemistry, Imperial

Re: [PyMOL] distance bug

s to our attention. > > Cheers, > > -- Jason > -- Andreas Förster, Research Associate Paul Freemont & Xiaodong Zhang Labs Department of Biochemistry, Imperial College London http://www.msf.bio.ic.ac.uk -

Re: [PyMOL] Mutagenesis script

__ > 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 --

Re: [PyMOL] PYMOL MOVIE

Dear MfG, formerly known as Holfelder, here's an expanded script: load x_1.pdb zoom #orient molecule at this point as you desire ray png x_1 disable x_1 for i in range (2,10001): \ cmd.load("x_%d.pdb" %i) \ cmd.super("x_%d" %i, "x_1") \ cmd.ray() \ cmd.png("x_%05d" %i) \ cmd.di

Re: [PyMOL] PYMOL MOVIE

___ > 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 -- Andreas Förster,

Re: [PyMOL] Delete frames in movie

ames. How is that possible? Mset resets > the whole movie and mview does not seem to do what I would like it to > do... > > Best, > > Matthias > -- Andreas Förster, Research Associate Paul Freemont & Xiaodong Zhang Labs Department of Biochemistry,

[PyMOL] installation from cvs fails

.4??) Thanks. Andreas -- Andreas Förster, Research Associate Paul Freemont & Xiaodong Zhang Labs Department of Biochemistry, Imperial College London http://www.msf.bio.ic.ac.uk

Re: [PyMOL] No PowerPC / Universal builds of 1.3?

time?) > > Thanks > F > -- Andreas Förster, Research Associate Paul Freemont & Xiaodong Zhang Labs Department of Biochemistry, Imperial College London http://www.msf.bio.ic.ac.uk

Re: [PyMOL] viewing axis

o view the axes (x, y and z), of a pdb file using pymol? > > Chandan > > -- > Chandan kumar Choudhury > NCL, Pune > INDIA > > -- Andreas Förster, Research Associate Paul Freemont & Xiaodong Zhang Labs Department of Biochemistry, Imperial Col

[PyMOL] spheres representation

em will go away, but I'm curious if anyone else sees that too. Thanks. Andreas -- Andreas Förster, Research Associate Paul Freemont & Xiaodong Zhang Labs Department of Biochemistry, Imperial College London http://w

Re: [PyMOL] Pymol 64-bits MacOSX

//lists.sourceforge.net/lists/listinfo/pymol-users > Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net > -- Andreas Förster, Research Associate Paul Freemont & Xiaodong Zhang Labs Depa

Re: [PyMOL] Showing electric field lines

(0)1223 492 583 (office) > > > > -- > SOLARIS 10 is the OS for Data Centers - provides features such as DTrace, > Predictive Self Healing and Award Winning ZFS. Get Solaris 10 NOW > http://p.sf.net

Re: [PyMOL] Problem Compiling Pymol 1.2.x

nstallation, but I don't have the faintest idea as to what it > could be. > > I was wonderig if anyone else has encountered this problem and/or might > have a possible solution? > > Thanks in advance. > -- Andreas Förster, Research Associate Paul Freemon

Re: [PyMOL] dcd files

a > > -- > Paola Beassoni - PhD > Dpto. Biologia Molecular - FCEFQyN > Universidad Nacional de Rio Cuarto > Río Cuarto - Argentina > 00-54-358-4676422 > 00-54-358-4676232 (Fax) > -- Andreas Förster, Research Associate Paul Freemont & Xiaodon

Re: [PyMOL] Grid View of a Group

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 > -- Andreas Förster, Research Associate Paul Freemont & Xiaodong Z

Re: [PyMOL] cmd.translate

t; raise pymol.CmdException > > > I am sure this is a simple syntax issue but I am unsure of how to write > the vector into the cmd.tranlate format. > > any help would be appreciated. > > thanks > zach cp > > -- > ___________ > PyMOL-users mailing list (P

Re: [PyMOL] Finding parameter settings in old PyMol session

)? Thanks in advance, Wulf -- ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users -- Andreas Förster, Research Associate Paul Freemont & Xiaodong Zhang Labs De

Re: [PyMOL] Commands which change coordinates

ions today-http://p.sf.net/sfu/adobe-com ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users -- Andreas Förster, Research Associate Paul F

[PyMOL] xquartz flicker with pymol

ice packs, bug fixes and security patches. Thanks a lot. Andreas -- Andreas Förster, Research Associate Paul Freemont & Xiaodong Zhang Labs Department of Biochemistry, Imperial College London

Re: [PyMOL] PyMOL install on Redhat EL5 and glut error

in my case on Fedora. Marius -- Andreas Förster, Research Associate Paul Freemont & Xiaodong Zhang Labs Department of Biochemistry, Imperial College London

[PyMOL] PyMOL install on Redhat EL5 and glut error

In setup.py, I see that lib_dirs is defined as /usr/X11/libs, which does not exist. Should I be messing with this? Andreas -- Andreas Förster, Research Associate Paul Freemont & Xiaodong Zhang Labs Department of Biochemistry, Imperial College London

Re: [PyMOL] Script for iterated `align`ment

e Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK & win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100&url=/ ____

[PyMOL] orientation-less scenes

Hey all, is there an equivalent to scenes that doesn't store orientation? The idea is to have two (or more) visualizations, eg. surface vs. sticks, or different side chains highlighted, and to be able to switch between them quickly by hitting F1, F2, etc. With conventional scenes any rotatio

Re: [PyMOL] help with batch mode

Hey Michael, with some commands, you can use the (somewhat poorly documented) option 'quiet=0' to get results sent to standard output, like so: load ./final/final.001.pdb load ./final/final.002.pdb fit (final.002///13-30/c,ca,n), (final.001///13-30/c,ca,n), quiet=0 Andreas Michael Summers

Re: [PyMOL] apbs plugin for macpymol

Thanks to Michael and Warren for a quick and correct but somewhat baffling solution. In OSX, one renames an application and it starts up looking quite dissimilar from before. I'm still new to the Gospel according to Steve, and I wouldn't mind enlightenment. In any case, using MacPyMOL as PyM

[PyMOL] apbs plugin for macpymol

Hey all, I would like to use apbs from within PyMOL. I have downloaded and installed the latest version of apbs, and apbs_tools.py exists in $PYMOL_PATH/modules/pmg_tk/startup/. However, I find no "plugins" entry in any of the PyMOL menus. Am I blind or daft? But the question I'd really l

Re: [PyMOL] Precompiled pymol won't work on Fedora 6

Dear Nian, on my Fedora 6 system there was absolutely no problem compiling and later running PyMOL. Here's the rundown: Get Pmw from sf.net, unpack and put into python site-packages directory, eg. /usr/lib/python2.5/site-packages/Pmw. In Pmw1.3, there is a setup.py that professes to do thi

Re: [PyMOL] Movie frame rate

Hey Claudia, my favorite way of making movies is importing the folder containing the png files as frames into ImageReady. There you can assign a delay for each image separately or all simultaneously to give you a movie of the desired length. Verifying this on my computer I just found out th

Re: [PyMOL] seperate clipping planes for each object

Hey Martin, from earlier discussions on the mailing list, I remember the suggested solution being the creation two or more different images with the individual objects and properly adjusted clipping planes and merging of them in PS or gimp. Others please correct me if I'm wrong. Andreas

Re: [PyMOL] (small) Pymol feature request--filter for edit settings window

my mind. I think it would be relatively easy to implement, although my python programming skills are somewhat limited. Thanks, Michelle Gill -- --> Andreas Förster <-- 8 rue Doudart de Lagrée, 38000 Grenoble ++33.(0)438.866201 and ++33.(0)456.452000 www.biochem.utah.edu/~andreas docandreas.blogspot.com

[PyMOL] EMizing an xray structure

Merci bien. Andreas -- --> Andreas Förster <-- Institut de Biologie Structural, Grenoble www.biochem.utah.edu/~andreas

[PyMOL] pymol install succeeds - freeglut issues resolved - other issues

tely lost again, then flash of very bright light (or was it the dawn of the new day?): libpng-devel! And this indeed solved the last problem, and pymol is now installed! Thanks Rob, thanks Warren!! Andreas -- --> Andreas Förster <-- 8 rue Doudart de Lagrée, 38000 Grenob

[PyMOL] pymol install fails - freeglut issues

GL/glu.h, but aren't Mesa and freeglut supposed to do the same thing? Both provide libGLU.so. Should I install Mesa? And wasn't there some FireGL/xorg/Mesa incopatibility issue? Any suggestions? Andreas -- --> Andreas Förster <-- 8 rue Doudart de Lagrée,

Re: [PyMOL] stereo view rendering

Jan Kosinski wrote: Is it possible to render a stereo view in pymol? Jan Kosinski Easily. Load the attached script and use it. Andreas -- --> Andreas Förster <-- 8 rue Doudart de Lagrée, 38000 Grenoble ++33.(0)438.866201 and ++33.(0)456.452000 b5foan at skype and

Re: [PyMOL] Help with labels?

to get the shadows right Andreas -- Andreas Förster Dept of Biochem, Univ of Utah, 20N 1900E, #2460 Eccles Bldg. Salt Lake City, UT 84132, phone: 001.801.585.3919 home: 465 3rd Av, SLC, UT 84103, 001.801.364.0529 http://www.biochem.utah.edu/~andreas

[PyMOL] align output

-- Andreas Förster Dept of Biochem, Univ of Utah, 20N 1900E, #2460 Eccles Bldg. Salt Lake City, UT 84132, phone: 001.801.585.3919 home: 465 3rd Av, SLC, UT 84103, 001.801.364.0529 http://www.biochem.utah.edu/~andreas

Re: [PyMOL] Coloring residues without the N-C-C backbone

c_contest.php > ___ > PyMOL-users mailing list > PyMOL-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/pymol-users -- Andreas Förster Dept of Biochem, Univ of Utah, 20N 1900E, #2460 Eccles Bldg. Sa

[PyMOL] alignment

m wondering if there is a more elegant solution. Thanks for your help. Andreas -- Andreas Förster Dept of Biochem, Univ of Utah, 20N 1900E, #2460 Eccles Bldg. Salt Lake City, UT 84132, phone: 001.801.585.3919 home: 465 3rd Av, SLC, UT 84103, 001.801.364.0529 http://www.biochem.utah.edu/~andreas

[PyMOL] rms commands

wrong?? I'm using pymol 0.95 under WinXPpro and pymol 0.95rh9 under linux/FC2. Andreas -- Andreas Förster Dept of Biochem, Univ of Utah, 20N 1900E, #2460 Eccles Bldg. Salt Lake City, UT 84132, phone: 001.801.585.3919 home: 465 3rd Av, SLC, UT 84103, 001.801.364.0529

Re: [PyMOL] Series of general questions

select sidechain atoms of an existing selection my_sel: > select sidechain_of_my_sel, (my_sel & !n;n,c,o) > > > Gareth -- Andreas Förster Dept of Biochem, Univ of Utah, 20N 1900E, #2460 Eccles Bldg. Salt Lake City, UT 84132, phone: 001.801.585.3919 home: 465 3rd Av, SLC, UT 84103, 001.801.364.0529 http://www.biochem.utah.edu/~andreas

Re: [PyMOL] map size/memory/crashing

). Andreas -- Andreas Förster Dept of Biochem, Univ of Utah, 20N 1900E, #2460 Eccles Bldg. Salt Lake City, UT 84132, phone: 001.801.585.3919 home: 465 3rd Av, SLC, UT 84103, 001.801.364.0529 http://www.biochem.utah.edu/~andreas

[PyMOL] dss & ribbon representation

he CA with straight lines in ribbon representation. It looks conspicuously like O. Is there a way of smoothing the ribbon? set ribbon_smooth, 1 doesn't do the trick. Thanks a bunch Andreas -- Andreas Förster Dept of Biochem, Univ of Utah, 20N 1900E, #2460 Eccles

Re: [PyMOL] Electrostatic potential maps in PyMOL

nds isomesh and isodot have the same syntax > and do exactly what you think. > > > > Best regards (and please forgive me for quoting source code here :) > > Esben > > > ** > * Source code for fld2

RE: [PyMOL] pymol crashes with large pdb files

ytracing (at the cost of > performance), try reducing hash_max to 80 or 60. > > set hash_max,60 -- Andreas Förster Dept of Biochem, Univ of Utah, 20N 1900E, #2460 Eccles Bldg. Salt Lake City, UT 84132, phone: 001.801.585.3919 home: 1736 Kensington, SLC, UT 841

Re: [PyMOL] pymol crashes with large pdb files

Gerstein Lab > 203-589-6765 Yale University > -------- -- Andreas Förster Dept of Biochem, Univ of Utah, 20N 1900E, #2460 Eccles Bldg. Salt Lake Cit