Re: [PyMOL] Open Source PyMOL v1.5.0.1

2012-02-15 Thread zjxu
Dear, I compiled PyMOL 1.5.0.1 from SVN revision 3979 on Centos 5 with python 2.7.1. and found "splash screen 1.3.x" too. Best, Zhijian Xu Troels Emtekær Linnet wrote: > Hi. > > I can confirm that you can compile pymol 1.5.0.1 on RHEL 6, with > python 2.6.6 from the RHEL repositories. > http:/

Re: [PyMOL] PyMol API equivalent for 'create complex'

2012-02-15 Thread Rituparna Sengupta
Hi, I tried using 'or'. I didn't get any errors, but now that I'm checking the outputs, I found that I got the area for just the ligand and not the complex, when I use 'get_area' on the complex. I noticed I get the area for whichever (ligand/target) is before the "or" operator, not the one after

Re: [PyMOL] Open Source PyMOL v1.5.0.1

2012-02-15 Thread Tim Travers
Hi all, I was wondering if the issue below on compiling molfile support has a fix? It looks like the include file was updated but not the C source. Thanks, Tim I cannot compile the molfile support: > > x86_64-pc-linux-gnu-gcc -pthread -Ofast -pipe -ftracer -march=corei7-avx > -mtune=corei7-avx

Re: [PyMOL] v1.5.0.1: maps and sessions bug

2012-02-15 Thread Pete Meyer
Hi Jason, This is with the 1.5.0.1 release (source build from pymol-v1.5.0.1.tar.bz2, md5 8d44de94cff8bce79ce521a1116b0760). Sorry if this was a duplicate bug report; I guess I hadn't checked the list archives well enough. Pete Jason Vertrees wrote: > Hi Pete, > > You're right -- in v1.5.0 t

Re: [PyMOL] v1.5.0.1: maps and sessions bug

2012-02-15 Thread Jason Vertrees
Hi Peter, Can you please send me a sample session that reproduces this problem? Opening/Saving session files tested here works fine. Cheers, -- Jason On Wed, Feb 15, 2012 at 3:59 PM, Pete Meyer wrote: > Hi Jason, > > This is with the 1.5.0.1 release (source build from pymol-v1.5.0.1.tar.bz2, >

Re: [PyMOL] v1.5.0.1: maps and sessions bug

2012-02-15 Thread Jason Vertrees
Hi Pete, You're right -- in v1.5.0 there was this problem which forced us to release a "hotfix". PyMOL v1.5.0.1, the current release, fixes this problem. Cheers, -- Jason On Wed, Feb 15, 2012 at 2:13 PM, Pete Meyer wrote: > Anyone thinking about upgrading to 1.5 should be aware that there's a

[PyMOL] v1.5.0.1: maps and sessions bug

2012-02-15 Thread Pete Meyer
Anyone thinking about upgrading to 1.5 should be aware that there's a bug in loading session (pse) files containing map objects. Loading pse files (I checked ones created with 1.2 or 1.4) deletes these objects and reports an error: "ExectiveSetSession-Error: after names.\nExectiveSetSession-Wa

Re: [PyMOL] Open Source PyMOL v1.5.0.1

2012-02-15 Thread Jason Vertrees
Hi, This also sounds like a graphics driver issue or issue with MESA (http://www.mesa3d.org/). Please ensure both are updated to their latest versions. Cheers, -- Jason On Wed, Feb 15, 2012 at 5:30 AM, Андрей Гончар wrote: > Hi all! > I've just installed a new version of PyMol, but when I sele

Re: [PyMOL] 1.5 version runs slow with "large" objects

2012-02-15 Thread Jason Vertrees
Hi Vitaly, Have you installed the latest graphics drivers for your card? Cheers, -- Jason On Tue, Feb 14, 2012 at 5:27 PM, Vitali Stanevich wrote: > Hi, > > I recently installed a new version of licensed pymol 1.5. It works ok with > small molecules (<25 kDa). But, unfortunately, I found that

Re: [PyMOL] Open Source PyMOL v1.5.0.1

2012-02-15 Thread Troels Emtekær Linnet
Hi. I can confirm that you can compile pymol 1.5.0.1 on RHEL 6, with python 2.6.6 from the RHEL repositories. http://www.pymolwiki.org/index.php/Linux_Install#Red_Hat_Enterprise_Linux_RHEL_6_compile_and_install_with_MPEG_support_for_x86_64_bit Still splash screen 1.3.x ... Funny bug. Best Troel

Re: [PyMOL] PyMOL-users Digest, Vol 69, Issue 12

2012-02-15 Thread Troels Emtekær Linnet
If you need publication citation, I would go for the Cealign ww.pymolwiki.org/index.php/Cealign There is references you can read and understand. :-) See a list of alignment methods and tools http://www.pymolwiki.org/index.php/Align#SEE_ALSO Best T Troels Emtekær Linnet Lyongade 24. 4.mf, 23

Re: [PyMOL] compiling Open Source PyMOL v1.5.0.1

2012-02-15 Thread Troels Emtekær Linnet
Hi Thomas. I succeded with the last version of Pymol 1.4.x compilation, and have written it here. http://www.pymolwiki.org/index.php/Linux_Install#Red_Hat_Enterprise_Linux_RHEL_6_compile_and_install_with_MPEG_support_for_x86_64_bit sudo yum install subversion gitsudo yum install python-imaging py

[PyMOL] Question

2012-02-15 Thread Bachar Cheaib
Dear All, I am a Pymol's user I would like to know how could I find the algorithm publication of three functions for superimposition of multi-structures? 1- fit 2- align 3- super I would thanks in advance for your reply Sincerely B. Ch On Wed, Feb 15, 2012 at 12:20 PM, Bachar Cheaib wrote:

Re: [PyMOL] PyMOL-users Digest, Vol 69, Issue 12

2012-02-15 Thread Bachar Cheaib
Dear All, I am a Pymol's user I would like to know how could I find the algorithm publication of three functions for superimposition of multi-structures? 1- fit 2- align 3- super I would thanks in advance for your reply Sincerely BaCh On Wed, Feb 15, 2012 at 11:31 AM, wrote: > Send PyMOL

Re: [PyMOL] Open Source PyMOL v1.5.0.1

2012-02-15 Thread Андрей Гончар
Hi all! I've just installed a new version of PyMol, but when I select a repersentation different to the default, it displays a blank screen and returns unsupported IR in fragment shader 13 unsupported IR in fragment shader 13 unsupported IR in fragment shader 13 unsupported IR in fragment shader 1