[PyMOL] show dashes lines in cartoon to connect loops not resolved in structure

Hi , One of the features I like in Chimera is that breaks in the protein chain due to unresolved residues are indicated by dashes. Is there a plugin or built in feature that enables this in pymol. Thanks Hari -- Check out

[PyMOL] select polymer within ribosome cif file ?

Hi all, I am trying to select a particular chain ( the 5S RNA) within the E.coli ribosome cif file ( pdb ID 4V69) The sequence info page at rcsb indicates that this chain has the information given below. I dont know the chain id or segid for this chain and in general have not worked with cif

Re: [PyMOL] Xquartz/pymol issues OSX Sierra: rotation stops after a few milliseconds

the open-source pymol Thanks Hari On Wed, Jan 11, 2017 at 5:55 PM hari jayaram <hari...@gmail.com> wrote: > Sorry to post back in. > > As I posted yesterday , I have been trying to get pymol working on a > Macbook Air ( and MacBook Pro since yesterday ) and am now convinced the &

Re: [PyMOL] Xquartz/pymol issues OSX Sierra: rotation stops after a few milliseconds

else seeing this with 1.8.2.1 and OSX? Thanks hari I have used homebrew to install pymol version 1.8.2.1 On Tue, Jan 10, 2017 at 7:02 AM hari jayaram <hari...@gmail.com> wrote: Hello All Sorry for that post. The problem got fixed by a restart. I failed to follow the unwritten rule o

Re: [PyMOL] Xquartz/pymol issues OSX Sierra: rotation stops after a few milliseconds

al account ...and the buttery smooth rotation returnedPhew :-) Sorry for the confusion Thanks Hari On Tue, Jan 10, 2017 at 6:49 AM hari jayaram <hari...@gmail.com> wrote: > Hi , > I was happily using brew installed pymol 1.7.6 on my Macbook Pro (running > OSX Sierra) and then had

[PyMOL] Xquartz/pymol issues OSX Sierra: rotation stops after a few milliseconds

Hi , I was happily using brew installed pymol 1.7.6 on my Macbook Pro (running OSX Sierra) and then had a hardware failure. I switched computers to MacBook Air running the same version of OSX (Sierra 10.12.2 ) and Xquartz (2.7.11) and now pymol ( and coot and other X11 using applications)

Re: [PyMOL] homebrew pymol builds fine but get Symbol not found: _png_check_sig on launch

2, 2013 at 10:48 AM, hari jayaram hari...@gmail.com wrote: Hi , I was able to use the latest homebrew pymol formula and install pymol after making sure that tcl-tk was installed with --enable-threads and --with-x11 and python was configured --with-brewed-tk The pymol build proceeded

[PyMOL] Maximum number of objects/menu items in internal GUI ? machine has lots of RAM and big GPU- Solved

any issues into the session file. All resulting objects were bound by all and could be toggled on and off. I am reproducing the exchange with Jason below. Thanks again Hari Jason Vertrees jason.vertr...@schrodinger.com to: hari jayaram hari...@gmail.com date: Thu, Mar 22, 2012 at 10:31 AM Hari

Re: [PyMOL] Maximum number of objects/menu items in internal GUI ? machine has lots of RAM and big GPU

if your video card is out of memory. Cheers, -- Jason On Fri, Mar 9, 2012 at 5:59 PM, hari jayaram hari...@gmail.com wrote: Hi I am scripting a visualization that involves roughly thirty to fifty PDB files with four objects each i.e 120 to 150 objects. I have a 64 bit machine with 16

[PyMOL] Maximum number of objects/menu items in internal GUI ? machine has lots of RAM and big GPU

Hi I am scripting a visualization that involves roughly thirty to fifty PDB files with four objects each i.e 120 to 150 objects. I have a 64 bit machine with 16 GB RAM and a Quadro FX 3700 card running Ubuntu Lucid. At the end of the script I get a menu with what seems like all of the objects

Re: [PyMOL] Help: Linux active Stereo on screen seems OK with flickering in pymol window, but glasses dont seem to be shuttering

is 120 Hz. Cheers, -- Jason On Wed, Jul 20, 2011 at 12:41 PM, hari jayaram hari...@gmail.com wrote: Hi, I am using the nvidia driver : 195.36.24 OS: Ubuntu Lucid lynx 10.04 , 64 bit I have a working xinerama config with two LCD screens one a regular dell LCD at 2560x1600

Re: [PyMOL] Help: Linux active Stereo on screen seems OK with flickering in pymol window, but glasses dont seem to be shuttering

the stereo_angle and/or the the stereo_shift might help you. Hope this helps ! Marc Le 21 juil. 2011 à 14:05, hari jayaram a écrit : Thanks Rafael and Jason, I upgraded to the latest driver version for Linux i.e 275.19 and now have stereo working with some caveats. I am running the PLANAR SA2311

[PyMOL] Help: Linux active Stereo on screen seems OK with flickering in pymol window, but glasses dont seem to be shuttering

Hi, I am using the nvidia driver : 195.36.24 OS: Ubuntu Lucid lynx 10.04 , 64 bit I have a working xinerama config with two LCD screens one a regular dell LCD at 2560x1600 and the other a stereo capable PLANAr LCD at 1920x1080. Both screens were configured to near working stereo based on the

[PyMOL] color surface by bfactor discrepancy between range reported on shell and range used

Hi, I am using svn pymol rev 3953 on a 64 bit Ubuntu box. I have a custom script that maps extent of conservation into the b-factor record of a pdb for visualization. I noticed a small feature in pymol My protein atoms in chain A have b-factors from 0 to 11 to indicate conservation extent , .

Re: [PyMOL] color surface by bfactor discrepancy between range reported on shell and range used

Hi Jason Thanks for your detailed reply and for pointers on the iterate command for mapping the bfactors. I think I understand whats going on and there was a fault in my understanding i.e I was wrong. Even though my script puts the conservation record as b-factor to all atoms of any given

Re: [PyMOL] Problem with distutils build 3951 on Ubuntu Lucid 10.04 : X Error of failed request: BadRequest

Hi Jason, Thanks for your reply. This was indeed a driver problem . Ubuntu had pushed a natty kernel headershttps://lists.ubuntu.com/archives/ubuntu-devel-announce/2011-June/000854.html to lucid users by mistake and that update broke my nvidia 195.36.24 x86_64 driver. To fix it , In desperation,

[PyMOL] Problem with distutils build 3951 on Ubuntu Lucid 10.04 : X Error of failed request: BadRequest

Hi I just build the svn build of pymol 3951 on 64 bit Ubuntu Lucid . I first had to installing libglew and libglew-dev after which the build progressed fine , but when I run the built pymol I get the following errors ( below) and pymol does not launch. I tried with a clean repo checked out

Re: [PyMOL] Possible bug in set cartoon_cylindrical_helices

17, 2010 at 8:14 PM, hari jayaram hari...@gmail.com wrote: Hi Jason , and Nat , I just tried it on my mac laptop and the set cartoon_cylindrical_helices  works just as it should. Followng that I tried it on two separate ubuntu 64 bit boxes , running pymol version 1.2 and 1.3 and  python

Re: [PyMOL] Possible bug in set cartoon_cylindrical_helices

anything else? Cheers, -- Jason On Thu, Jun 17, 2010 at 6:41 PM, hari jayaram hari...@gmail.com wrote: I am trying to show a molecule in ribbon representation , where all the helices except one helix are in ribbon form and a solitary helix is shown as a  cylinder. Can someone confirm

[PyMOL] Lucid Lynx Ubuntu 10.04 segmentation fault on Help-About Pymol : plugins dont work either

Hi I am using a subversion build of pymol built using setuptools i,e python setup.py install on 64 bit ubuntu Lucid Lynx 10.04. I can use the main program without any problems , but when I try to install and run the apbs plugin , pymol segmentation faults immediately. Incidentally , doing a

[PyMOL] psw full screen , on screen menu and see typed commands in full screen mode

Hi I can get the animations launched from inside powerpoint to show up and go between my stored scenes. Is there some way to toggle on the internal_gui display from this full screen mode. I know the command set internal_gui,1 But when I type it on the full screen molecule, nothing happens.

[PyMOL] compiled Pymol on MacOSX , The Pmw menu window does not open properly and Python Icon bouncing on dock

Hi , Because I wanted to use some of the Python API commands in scripts I wanted to install a distutils build of Pymol on my Snow Leopard System running 10.6.2 . I am using the svn version 3897. After I installed Pmw and added the fontconfig.h containing directory to my INCLUDE path and added

Re: [PyMOL] compiled Pymol on MacOSX , The Pmw menu window does not open properly and Python Icon bouncing on dock

...@cowsandmilk.net wrote: Do you know about the fink builds of pymol? http://pdb.finkproject.org/pdb/package.php/pymol-py26 . You might have more success modifying that package to pull the source from subversion. -David On Wed, Mar 24, 2010 at 11:48 AM, hari jayaram hari...@gmail.com wrote

[PyMOL] getting Residue environment distances and residue-residue distances programatically

Hi I want to write a python/pymol script that will give me residue -residue distances within a pdb file programmatically I know that within pymol I can get a distance object using select r55 , chain A and resi 55 select r 22 , chain A and resi 22 distance (r55) ,(r22) This creates the dist01

Re: [PyMOL] getting Residue environment distances and residue-residue distances programatically

-archive.com/pymol-users@lists.sourceforge.net/msg07745.html -David On Tue, Mar 23, 2010 at 3:48 PM, hari jayaram hari...@gmail.com wrote: Hi I want to write a python/pymol script that will give me residue -residue distances within a pdb file programmatically I know that within pymol I can get

[PyMOL] subversion 3897 compile error in Cmd.c

Hi , I generally track trunk on pymol , i.e I keep my Ubuntu 64 bit linux box updated with the latest subversion build. While compiling revision 3897. I had an error during the build while compiling Cmd.h saying it could not find ce_types.h That file does exist in

Re: [PyMOL] subversion 3897 compile error in Cmd.c

Sorry for crying wolf. Everything is working fine with svn 3897 . After Justins email I checked that my system python was suddenly set to a different python and things were probably not getting linked up correctly during building. Now I do get : 1) distutils builds fine 2) make , make install

Re: [PyMOL] Caution - 120 Hz LCDs: Not CRT killers yet...

  that allows me to get stereo on this setup. Monitor : Viewsonic FuHzion VX2265wm 120Hz Graphics card: Quadro FX 4600 OS: Ubuntu Linux X86_64 - Hardy Heron 8.04 Stereo glasses: Crystal Eyes 3 with 3pin mini din connector Thanks for your help in advance Hari Jayaram Brandeis University On Tue

[PyMOL] update mesh level to custom value after deleting map object

H I have an old pymol session file . I have a mesh object displayed whose level I can manipulate in predetermined ways using the Action-Level-menu. I however want to pick a level different from the menu options provided . A further complication is that I have deleted the original map object and

Re: [PyMOL] launch pymol from inside an IDLE ( python-ide)

the Mac idle2.5 goofs up. I read something about idle running on a tkinter thread and pymol wanting to do the same thing. Anyways I guess the solution to the problem is to install fink on all macs in cases where I want to use IDLE for pymol script writing. Thanks again Hari Jayaram On Tue, Jun 10

[PyMOL] launch pymol from inside an IDLE ( python-ide) interactive shell ?

completion.. But I was wondering if there is some way to have my cake and eat it too and interact with pymol from within an IDLE shell window. Hari Jayaram

Re: [PyMOL] load cgo into existing pymol session

more complicated, it's in fact quite easy to define as a function itself. Hmm, I think I'm gonna store my CGO objects just like that myself :) Hope it helps, Tsjerk On Thu, Feb 21, 2008 at 10:16 PM, hari jayaram hari...@gmail.com wrote: Hi I have a running pymol session with nothing loaded

[PyMOL] load cgo into existing pymol session

window. I can successfully load any cgo file using a python script . I want to learn how to inject a cgo object like the one given below into a running python session . Can someone tell me how to do this. Your help is greatly appreciated Thank You Hari Jayaram Brandeis University #Contents

[PyMOL] how to get pymol sec structure assignments printed out

... like helix from A1 to A50 .. Thanks for your help in advance Hari Jayaram Brandeis University

[PyMOL] how to get pymol sec structure assignments printed out to a file

. Thanks again Hari Jayaram Brandeis University On 6/17/05, Warren DeLano war...@delsci.com wrote: iterate name ca, print chain,resi,ss -- Warren L. DeLano, Ph.D. Principal Scientist . DeLano Scientific LLC . 400 Oyster Point Blvd., Suite 213 . South San Francisco, CA 94080 USA

[PyMOL] pymol 0.98 and r3d input and getting sec structure assignments info

Hello , I tried to open an r3d (raster3d) file in pymol version 0.98 and I get the following error Traceback (most recent call last): File /xtal2/pymol/modules/pymol/__init__.py, line 218, in exec_deferred cmd.load(a,quiet=0) File /xtal2/pymol/modules/pymol/importing.py, line 549, in load