Re: [PyMOL] changing ray_trace_line

Yarrow, You can also try setting ray_trace_slope_factor to something large like 5. Cheers, -- Jason On Thursday, May 17, 2012, Yarrow Madrona wrote: Same thing happens. I get cross hatches with ray_trace_mode set at two and the gain anything above 0. Without the gain I don't get cross

[PyMOL] Transparency error on Mac with 1.5 svn source

Hello everyone, I just compiled PyMOL on my Mac and I have an error when I try to adjust the transparency settings : ERROR: CGOOptimizeToVBONotIndexed() BEFORE glGenBuffers returns err=1282 The programs runs nicely (so far), but that problem is quite disturbing ... I have the same issue with

Re: [PyMOL] Transparency error on Mac with 1.5 svn source

Hi Marc, That's our error. Please file this case on the open-source bug tracker (http://sourceforge.net/tracker/?group_id=4546atid=104546) and we'll get to it as soon as we can. Cheers, -- Jason On Fri, May 18, 2012 at 1:45 PM, Marc Piuzzi piu...@ibpc.fr wrote: Hello everyone, I just

Re: [PyMOL] some parts of protein structure is not seen

Hi Hendry, We're happy to help, but we need more information. Do you have a PDB which replicates this problem? Also, what version of PyMOL are you using? Is this on a laptop or desktop? Finally, what video card do you have? Cheers, -- Jason On Fri, May 18, 2012 at 4:25 AM, Hendry

Re: [PyMOL] problem compiling latest svn on RHEL system

So, i took the solution to install CentOS 6.2 on one machine. Together with the EPEL repository, I could install all the necessary libraries. And then compile on CentOS. It now works fine for all our RHEL 6.2 computers in the group. Thanks! 2012/5/18 Jason Vertrees

[PyMOL] cartoon from c-alphas JMol vs PyMol

Hi all, If you open a c-alpha pdb (3ixz for example) in PyMol, you can show the c-alphas as spheres, or you can show a cartoon as a tube (ribbon like) but you can make a traditional flat faced PyMol cartoon. Yet when you open the same pdb in JMol it shows the traditional PyMol cartoon as the

Re: [PyMOL] cartoon from c-alphas JMol vs PyMol

Hi Adam, set cartoon_trace_atoms set cartoon_throw, 1 If you want secondary structures, then you'll need to assign them using the 'alter' command. Cheers, -- Jason On Fri, May 18, 2012 at 5:13 PM, H. Adam Steinberg a...@steinbergs.us wrote: Hi all, If you open a c-alpha pdb (3ixz for

Re: [PyMOL] some parts of protein structure is not seen

Malai, The PDB is corrupt. Please put an ENDMDL after your TER line. Cheers, -- Jason On Fri, May 18, 2012 at 3:31 PM, Jason Vertrees jason.vertr...@schrodinger.com wrote: Hi Hendry, We're happy to help, but we need more information. Do you have a PDB which replicates this problem? Also,