[PyMOL] dimerization

2011-02-25 Thread kanika sharma
Does anyone know how to apply these biometric constraints to generate a dimer of my molecule REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B REMARK 350 BIOMT1 1 1.00 0.00 0.000.0 REMARK 350

[PyMOL] labeling by a pseudoatom

2011-02-25 Thread rv...@libero.it
Hello everyone, trying to use a pseudoatom as label I met several problems: 1) How to move the label (pseudoatom) to a target residue? Is there a simple command to do? 2) How to change the label without messaging the user? The 'label' command appears not have a 'quiet' option. 3

Re: [PyMOL] select clipped atoms

2011-02-25 Thread Johannes Wollbold
Tsjerk Wassenaar wrote: Hi Johannes, It's not that hard. The clipping planes are defined by the z coordinate (in the viewing matrix). So you can get the atoms for a selection, transform to get the new z coordinate only, and check whether it's in between the planes: m = cmd.get_model(select

Re: [PyMOL] select clipped atoms

2011-02-25 Thread Tsjerk Wassenaar
Hi Johannes, It's not that hard. The clipping planes are defined by the z coordinate (in the viewing matrix). So you can get the atoms for a selection, transform to get the new z coordinate only, and check whether it's in between the planes: m = cmd.get_model(selection).atom v = cmd.get_view() m

Re: [PyMOL] select clipped atoms

2011-02-25 Thread Johannes Wollbold
Jason Vertrees wrote: > Having said this, you can however, can get the clipping information > from PyMOL and write scripts against that yourself to determine atom > inclusion. See get_view (http://www.pymolwiki.org/index.php/Get_View) > for more help. > Hi Jason, thank you again for the hint.

Re: [PyMOL] Color scale changed in APBS?

2011-02-25 Thread Wataru Kagawa
Thank you for the suggestion. I've looked at the gamma setting, but it was 1.0, so the washed out effect is not because of the gamma setting. I've noticed that raytracing removes the washed out effect of the scale bar, but not so much of the protein surface color. Is there by any chance that the

Re: [PyMOL] rotation of protein

2011-02-25 Thread Hongbo Zhu
Hi, Kanika, are you looking for biological units of proteins when you say stable dimer? If this is the case, I recommend the page: http://pdbwiki.org/index.php/Biological_unit at the bottom of the page you can find four very useful servers for the determination of biological units of proteins (

[PyMOL] rotation of protein

2011-02-25 Thread kanika sharma
Hi, i am working to generate a dimer of my protein..I have made a duplicate of my proteinCan any one tell me how to rotate my molecule to get maximum stability..??? Regards.. Kanika -- Free Software Download: Index, S

Re: [PyMOL] installing_running vasco

2011-02-25 Thread Hongbo Zhu
I forgot to mention that the msms shipped with your VASCo (v1.0.2) is installed at: VASCo_1.0.2/unix/VASCo-Modules-1.0.2/ppix_modules/cprogr/unix/msms cheers, hongbo On 02/24/2011 05:18 PM, Yarrow Madrona wrote: > > Hello pymol users, > > I apologize if this posting is not appropriate for the p

Re: [PyMOL] installing_running vasco

2011-02-25 Thread Hongbo Zhu
Hi, Yarrow, It says MSMS calculation error. *Possible reason* MSMS is a brilliant program for computing protein solvent excluded surfaces. It is a 3rd-party program (see http://mgltools.scripps.edu/downloads ) and its binary is included in VASCo. The version shipped with VASCo by default is f

[PyMOL] Saving the Connolly surface of a PDB

2011-02-25 Thread Francois Berenger
Hello, Is it possible to save the Connolly surface computed by Pymol without any rotation and translation added compared to the PDB from which the atom coordinates were read? I looked at the .obj file output and find there was some centering done and also some rotation added. Thanks a lot, F. -