Re: [PyMOL] Sequence numbers in MacPyMOL 1.6.0.0 with background set to white

2013-09-04 Thread Engin Özkan
I forgot to explicitly say, this is only for the Sequence View panel, which has a black background regardless of the background parameter. And it applies to both sequence numbers and chain labels. Sequences themselves are displayed correctly. Engin On 9/4/13 12:59 PM, Engin Özkan wrote: > Hi e

Re: [PyMOL] Sequence numbers in MacPyMOL 1.6.0.0 with background set to white

2013-09-04 Thread Oganesyan, Vaheh
Engin, If you go to Edit_all and change the seq_view_label_color to grey the numbers will become visible with white bkgr. Vaheh -Original Message- From: Engin Özkan [mailto:eoz...@stanford.edu] Sent: Wednesday, September 04, 2013 4:40 PM To: pymol-users@lists.sourceforge.net Sub

Re: [PyMOL] Sequence numbers in MacPyMOL 1.6.0.0 with background set to white

2013-09-04 Thread Engin Özkan
Thanks, Vaheh. As I did say that in my first post, actually purple, brown, forest etc. work too. But none of the primary colors (RGB or CMYK) does. And a number of them (like pink) give wrong colors. And thanks for confirming the issue. Engin On 9/4/13 4:03 PM, Oganesyan, Vaheh wrote: > Engin,

Re: [PyMOL] set line_width command doesn't work

2013-09-04 Thread H. Adam Steinberg
You just have to Ray the figure to see the changes. On Sep 4, 2013, at 10:21 AM, "sunyeping" wrote: > Dear all > > I want to make line presentation in pymol looks more thicker so I enter "set > line_width, 3", but the lines in the viewer window don't show any change. > Have you meet such ci

Re: [PyMOL] Embedding PyMol in a custom designed GUI

2013-09-04 Thread Massimiliano Pippi
On Wed, Sep 4, 2013 at 2:29 PM, Alessia Visconti wrote: > This is a good news (and starting point), thanks for the tip! > On the other hand I need to translate all my code in C++. Any thought of > making a version for a Python Qt application? ;) > Good for you, embedding PyMol in a PyQt applicatio

[PyMOL] Fwd: issue with the allign command

2013-09-04 Thread Tsjerk Wassenaar
For the record... -- Forwarded message -- From: Pascal Auffinger Date: Wed, Sep 4, 2013 at 3:54 PM Subject: Re: [PyMOL] issue with the allign command To: tsje...@gmail.com Hi Tsjerk, Apparently, the problem comes from the fact that I used set retain_order ! This used not to

Re: [PyMOL] color change upon ray-tracing

2013-09-04 Thread Thomas Holder
Hi Vaheh, there should be no color difference, apart from lighting effects. Ray tracing always draws cylinders for mesh, real-time rendering supports lines and cylinders. Real-time rendering and ray tracing should be almost identical with these settings: PyMOL> set use_shaders PyMOL> set mesh_as

[PyMOL] Sequence numbers in MacPyMOL 1.6.0.0 with background set to white

2013-09-04 Thread Engin Özkan
Hi everybody, Using MacPyMOL 1.6.0.0 Incentive Build, I no longer can see residue numbers in the sequence if the background is set to white. I have been playing with all the seq_view_* settings (thanks for documenting them clearly within the Edit All Settings window!), especially seq_view_labe

[PyMOL] set line_width command doesn't work

2013-09-04 Thread sunyeping
Dear all   I want to make line presentation in pymol looks more thicker so I enter "set line_width, 3", but the lines in the viewer window don't show any change. Have you meet such circumstance? The pymol (version 1.5.0.1) is installed in centos5.9 system and other functions seem well. Thanks.  

Re: [PyMOL] using pymol commands in a script

2013-09-04 Thread David Hall
I couldn't reproduce the exact error message you received, but I will note: (1) your splitting of lines leaves out the chain, so chain is never defined (2) line 9 of your python is missing an opening quotation mark before (resi matching the closing quotation mark right before the % sign (3) line 9

Re: [PyMOL] Embedding PyMol in a custom designed GUI

2013-09-04 Thread Alessia Visconti
This is a good news (and starting point), thanks for the tip! On the other hand I need to translate all my code in C++. Any thought of making a version for a Python Qt application? ;) Cheers, Alessia On 4 September 2013 13:18, Massimiliano Pippi wrote: > On Wed, Sep 4, 2013 at 12:48 PM, Alessi

Re: [PyMOL] Embedding PyMol in a custom designed GUI

2013-09-04 Thread Massimiliano Pippi
On Wed, Sep 4, 2013 at 12:48 PM, Alessia Visconti wrote: > Hi all, > as Raj, I'm also wondering if there is any way to embed PyMOL in my PyQt4 > GUI. > Does anyone has any suggestion about where/how to start? > if you need to embed PyMol in a C++ Qt application you can take a look at this: https:

Re: [PyMOL] Embedding PyMol in a custom designed GUI

2013-09-04 Thread Андрей Гончар
Hi Try to run self.pymolInstance.finish_launching() after self.pymolInstance.start() 2013/9/4 Alessia Visconti > Hi all, > as Raj, I'm also wondering if there is any way to embed PyMOL in my PyQt4 > GUI. > Does anyone has any suggestion about where/how to start? > > Thanks in advance, > Aless

Re: [PyMOL] Embedding PyMol in a custom designed GUI

2013-09-04 Thread Alessia Visconti
Hi all, as Raj, I'm also wondering if there is any way to embed PyMOL in my PyQt4 GUI. Does anyone has any suggestion about where/how to start? Thanks in advance, Alessia > Hello all, > > I have recently been looking for tips or help on embedding PyMol into a GUI > built upon Qt4. I looked at th

[PyMOL] using pymol commands in a script

2013-09-04 Thread Anasuya Dighe
Hi everyone, How to write PyMol commands in Python script, save a session and then save a .png file of the same ? I have an input file which has the protein information i.e name, chain, and a list of residues. I want to plot the C-alpha atoms of these residues for each protein & calculate distance