[PyMOL] slab mode fine-tuning

2011-03-29 Thread Nadine Utz
Dear pymol users, I am looking for a way to zoom in a molecule, like the slab mode when you are rolling the scroll wheel. The reason why rolling the scroll wheel does not work in my case is that the resulting change is too coarse grained, i.e. either I cannot see all the atoms I want to or

[PyMOL] Pymol 1.4 OpenGL issue with openSuSE 11.3 / 11.4

2011-03-29 Thread Greipel.Joachim
Dear pymol users, pymol 1.4 on openSuSE with NVIDIA Quadro FX 3700/3800 and new NVIDIA drivers (260.xxx and 270.xxx) does not recognize the OpenGL Version correctly. As a result there is a kind of software OpenGL used. The NVIDIA drivers provide OpenGL 3.3.0 but pymol 1.4 complains:

Re: [PyMOL] Pymol 1.4 OpenGL issue with openSuSE 11.3 / 11.4

2011-03-29 Thread Schubert, Carsten [PRDUS]
Joachim, I'm running into the same issue on a SuSe SLED10 box. The 32bit binary (on the 64bit OS) displays the same behavior, i.e. only the MESA libs were used. The 64bit version actually core dumps during startup. I opened up a bug report with Schrodinger and they were already working on it (I

Re: [PyMOL] slab mode fine-tuning

2011-03-29 Thread Schubert, Carsten [PRDUS]
Nadine, Probably the command line is your best friend here. Look into the 'clip near,x' and 'clip far,x' command, which allows to move the front and back clipping planes in x increments. Positive values move towards you, negative values of x away from you. If that does not provide enough fine

Re: [PyMOL] Pymol 1.4 OpenGL issue with openSuSE 11.3 / 11.4

2011-03-29 Thread Roger Rowlett
This appears to be a common problem with 1.4 and Jason is aware of it. The same issue exists in Ubuntu 9.04 with Nvidia 180.xx drivers, 32 bit. The Win version works OK. Roger Rowlett On Mar 29, 2011 7:53 AM, Schubert, Carsten [PRDUS] cschu...@its.jnj.com wrote: Joachim, I'm running into the

Re: [PyMOL] slab mode fine-tuning

2011-03-29 Thread Robert Campbell
Hi, On Tue, 29 Mar 2011 6:12 AM Nadine Utz [mailto:nad...@mmb.pcb.ub.es] wrote: Dear pymol users, I am looking for a way to zoom in a molecule, like the slab mode when you are rolling the scroll wheel. The reason why rolling the scroll wheel does not work in my case is that the

[PyMOL] Calling pymol from python - access to global variables

2011-03-29 Thread Tsjerk Wassenaar
Hi, I'm having some trouble accessing a function defined at top level with alter_state in a python script launching pymol. Maybe I shouldn't be wanting to do this, but what I'm trying, and failing to do is exemplified by this script: ### #!/usr/bin/env python import pymol if __name__ ==

Re: [PyMOL] Calling pymol from python - access to global variables

2011-03-29 Thread Thomas Holder
Hi Tsjerk, use either the global pymol.stored variable or the alter_state 'space' argument. -- #!/usr/bin/env python if __name__ == __main__: import __main__ __main__.pymol_argv = [ 'pymol', '-cq' ] import pymol pymol.finish_launching() else: import pymol def identity(x,y,z):

[PyMOL] Newline character in labels

2011-03-29 Thread Andreas Spitzmüller
Hi, I'd like to label a couple of CA atoms in with their AA code, residue number and b-factor. Since this gets a long label, I want to split it to get two lines. For example, if I have the CA atom of Asn124 with a b-factor of 36.2, I want it to be labelled as follows: Asn124 36.2

Re: [PyMOL] Pymol 1.4 OpenGL issue with openSuSE 11.3 / 11.4

2011-03-29 Thread Jason Vertrees
Hi Joachim, Sorry for the delay. I'm spending the entire day on the floor of the ACS meeting, showing off PyMOL. pymol 1.4 on openSuSE with NVIDIA Quadro FX 3700/3800 and new NVIDIA drivers (260.xxx and 270.xxx) does not recognize the OpenGL Version correctly. As a result there is a kind of

Re: [PyMOL] Newline character in labels

2011-03-29 Thread Jason Vertrees
Hi Andreas, This is currently not possible. If this is a feature you'd like to see implemented, please go here http://pymol.org/contact and leave us a message. It'll be tracked internally so we don't drop the ball if we decide to implement it. Cheers, -- Jason On Tue, Mar 29, 2011 at 12:03

Re: [PyMOL] Newline character in labels

2011-03-29 Thread Tsjerk Wassenaar
Hi Andreas, In the meantime, you can set double labels by using a pseudoatom, labeling it with the second part, and placing the label at the spot desired. Cheers, Tsjerk On Wed, Mar 30, 2011 at 3:59 AM, Jason Vertrees jason.vertr...@schrodinger.com wrote: Hi Andreas, This is currently not