Re: [PyMOL] Having problems using clean function

Hi, I have the same problem. But instead of "Unable to validate freemol.mengine" it's "Unable to import freemol.mengine module" followed by "This pymol build appears to not include full modeling capabilities." The message would take a long time to appear and pymol seems frozen if it is loaded wi

[PyMOL] Using super correctly

Dear all, I'm having a tough time using the super command correctly. I want to superimpose two 5S structures. In pymol, I'll do the following load 2awb.pdb load 3cc2.pdb create ec-5s, 2awb and chain a create hm-5s, 3cc2 and chain 9 If I issue *super ec-5s, hm-5s* then the cryptic error "Execu

Re: [PyMOL] Using super correctly

eic acid sequences well. > >> > >> super ec-5s, hm-5s, seq=-1 > >> > >> works. > >> > >> I'll leave it to someone else to say what that does. I just noted > >> that align works, super doesn't, guessed it had to do with sequen

[PyMOL] Using Shaders

Dear all, Is there a way to use the shaders without the unsightly gaps in the models? Shaders on Shaders off

Re: [PyMOL] Using Shaders

dering I'm > guessing Quadro or Intel Mobile. > > If Quadro try, > > set cylinder_shader_ff_workaround, on > > There is a known bug in some Quadro cards which this setting fixes. > > Cheers, > > -- Jason > > On Wed, Feb 22, 2012 at 1:03 PM, QT wrote: &g

[PyMOL] VMD module in Rev 4019-4020 break build

Dear pymol users, Revision 4019 added a bunch of changes to the VMD module and three files require gmplugin.h that is missing from the module src directory moldenplugin.c:38:#include "qmplugin.h" basissetplugin.c:43:#include "qmplugin.h" gamessplugin.c:160:#include "qmplugin.h" Please fix =) Be

[PyMOL] CEalign parameter d0 and d1

Dear all, I have a question regarding CEalign d0 and d1 parameter. What exactly are their functions? I don't know enough C++ to decipher the algorithm but they are used findPath() in ccealignmodule.cpp. It seems that that d0 controls a similarity matrix and d1 the path length. A d1 below a cer

Re: [PyMOL] CEalign parameter d0 and d1

; After this, all N top scoring paths are stored in the path cache and the > best path is returned. > > Cheers, > > -- Jason > > > On Wed, Apr 17, 2013 at 3:34 AM, QT wrote: > >> Dear all, >> >> I have a question regarding CEalign d0 and d1 paramet

[PyMOL] Can not compile r4044

Dear all, I'm getting this error when typing "python setup.py" Traceback (most recent call last): File "setup.py", line 327, in pyogl_extension("pymol.opengl.gl.openglutil_num", ["contrib/pyopengl/openglutil_num.c"]), File "/usr/lib64/python2.7/distutils/core.py", line 105, in setup

[PyMOL] Camera Orientation

Hello everyone, I have a question regarding camera orientation. I'm using pymol to explore the surface of the peptide tunnel in the ribosome and would like to change the camera orientation so that I can look around "in there" without getting occluded. Clipping plane is not useful because I don't

Re: [PyMOL] Camera Orientation

de" spaces without having nearby elements appear to intersect > the camera surface (or front clipping plane). > > set field_of_view, 45 > > Cheers, > Warren > -- > DeLano Scientific LLC > Subscriber Support Services > mailto:supp...@delsci.com > > > ---

Re: [PyMOL] Camera Orientation

rt cmd >for x in range(360): > cmd.move("z",cmd.get_view()[11]) > cmd.turn("y",1) > cmd.move("z",-cmd.get_view()[11]) > cmd.refresh() > > threading.Thread(target=spin).start() > > python end > > Cheers, > Wa

[PyMOL] Surface Residues

Dear all, Once again, I need some help from pymol experts. I would like to select surface residues via the surface calculation algorithm of Pymol. Is this possible? What is the surface calculation algorithm that Pymol use and is it scattered among many source-code files or is it contained in ju

[PyMOL] ray with cuda

Dear all, Is it possible to ray using cuda? I know VMD has some plugin that allows cuda integration and was wondering if Pymol has a similar thing. Best, Quyen -- Download Intel® Parallel Studio Eval Try the new software

Re: [PyMOL] ray with cuda

wrote: > Quyen, > > No, not yet. It's something I very excited to get done though. > > -- Jason > > On Fri, Apr 2, 2010 at 4:44 PM, QT wrote: > > Dear all, > > > > Is it possible to ray using cuda? I know VMD has some plugin that allows > > cuda in

[PyMOL] Compile error svn 4162

Dear all, I'm having a compile error that I've never had before on the current svn revision 4162. Compile broke on file CifDataValueFormatter.cpp g++ -pthread -std=c++0x -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_FREETYPE -DNO_MMLIBS -D_PYMOL_NUMPY -Iov/sr

Re: [PyMOL] Compile error svn 4162

Dear Thomas, Yes, confirmed fixed in rev 4163. Thank you. Best, Quyen On Tue, Oct 18, 2016 at 5:41 AM, Thomas Holder < thomas.hol...@schrodinger.com> wrote: > Hi Quyen, > > This should be fixed in svn rev 4163. > > Cheers, > Thomas > > On 18 Oct 2016, at 01