[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

. Cheers, Thomas -- Andreas Förster X-ray Crystallograhpy Facility Manager Centre for Structural Biology Imperial College London -- Comprehensive Server

[PyMOL] symexp eats chain ID

). 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 Imperial College London

Re: [PyMOL] Ligand - binding

://www.mail-archive.com/pymol-users@lists.sourceforge.net -- Andreas Förster Crystallization and Xray Facility Manager Centre for Structural Biology Imperial College London

[PyMOL] cylindrical helices

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

[PyMOL] pymol fails to compile

’: 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 Crystallization and Xray Facility

[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 Xray Facility

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 objects I

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

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 Zhang Labs Department of Biochemistry, Imperial College London http

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 are

[PyMOL] apbs2 plugin failure

fails. 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] Installation PyMOL failure in Linux (CentOS)

- 'compile_pymol_sh_error.txt' layer0/Isosurf.c: In function 'IsosurfGetRange': layer0/Isosurf.c:2197:0: error: unterminated argument list invoking macro fprintf Regards, Masataka -- Andreas Förster, Research Associate Paul Freemont Xiaodong Zhang Labs Department

Re: [PyMOL] Visualise molecules to scale?

will ray trace the images. /Daniel -- Andreas Förster, Research Associate Paul Freemont Xiaodong Zhang Labs Department of Biochemistry, Imperial College London http://www.msf.bio.ic.ac.uk

Re: [PyMOL] distance bug

. Cheers, -- Jason -- Andreas Förster, Research Associate Paul Freemont Xiaodong Zhang Labs Department of Biochemistry, Imperial College London http://www.msf.bio.ic.ac.uk -- All the data

Re: [PyMOL] Mutagenesis script

/pymol-users@lists.sourceforge.net -- Andreas Förster, Research Associate Paul Freemont Xiaodong Zhang Labs Department of Biochemistry, Imperial College London http://www.msf.bio.ic.ac.uk

Re: [PyMOL] Delete frames in movie

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, Imperial College London http

Re: [PyMOL] PYMOL MOVIE

-archive.com/pymol-users@lists.sourceforge.net -- Andreas Förster, Research Associate Paul Freemont Xiaodong Zhang Labs Department of Biochemistry, Imperial College London http://www.msf.bio.ic.ac.uk

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) \

[PyMOL] installation from cvs fails

-- Andreas Förster, Research Associate Paul Freemont Xiaodong Zhang Labs Department of Biochemistry, Imperial College London http://www.msf.bio.ic.ac.uk -- Achieve unprecedented app

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

-- Andreas Förster, Research Associate Paul Freemont Xiaodong Zhang Labs Department of Biochemistry, Imperial College London http://www.msf.bio.ic.ac.uk -- The ultimate all-in-one performance toolkit

Re: [PyMOL] viewing axis

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 College London http://www.msf.bio.ic.ac.uk

Re: [PyMOL] Pymol 64-bits MacOSX

@lists.sourceforge.net -- Andreas Förster, Research Associate Paul Freemont Xiaodong Zhang Labs Department of Biochemistry, Imperial College London http://www.msf.bio.ic.ac.uk -- Download

Re: [PyMOL] Showing electric field lines

/sfu/solaris-dev2dev ___ 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

Re: [PyMOL] Problem Compiling Pymol 1.2.x

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 Freemont Xiaodong Zhang Labs Department of Biochemistry, Imperial

Re: [PyMOL] dcd files

. 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 Xiaodong Zhang Labs Department of Biochemistry, Imperial College London http

Re: [PyMOL] Grid View of a Group

://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 Department of Biochemistry, Imperial College London http

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

-- ___ 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 Department of Biochemistry, Imperial

Re: [PyMOL] Commands which change coordinates

___ 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 Department

[PyMOL] xquartz flicker with pymol

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

[PyMOL] PyMOL install on Redhat EL5 and glut error

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] PyMOL install on Redhat EL5 and glut error

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

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

http://moblin-contest.org/redirect.php?banner_id=100url=/ ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users -- Andreas Förster, Research Associate Paul Freemont

[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

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

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

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

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

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

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

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 yahoo

Re: [PyMOL] Help with labels?

-- 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

@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users -- 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

[PyMOL] alignment

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

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 http://www.biochem.utah.edu

Re: [PyMOL] Series of general questions

) 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

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 Bldg. Salt

Re: [PyMOL] Electrostatic potential maps in PyMOL

for fld2phi * * save as: fld2phi.c* * compile with: gcc -o fld2phi fld2phi.c* ** -- Andreas Förster Dept of Biochem

RE: [PyMOL] pymol crashes with large pdb files

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 84108, 001.801.463.3607 http