Re: [PyMOL] need suggestion

ligand with zero occupancy and keep the ligand there so now i want to show both map in my figure but i do not know how to do it . Any one help me to get it would be appreciated. Thanks Best Regards AFSHAN -- Thomas Holder PyMOL Developer Schrödinger, Inc

Re: [PyMOL] Distance or measurement labels Version 1.6 and 1.7 does not show

Hi Burkhard, bug fixed in SVN rev 4067. Let me know if it works for you. Cheers, Thomas On 27 Feb 2014, at 10:07, Thomas Holder thomas.hol...@schrodinger.com wrote: Hi Burkhard, this was a very strange ATI only bug which we already could fix in our Incentive PyMOL release. The fix

Re: [PyMOL] Yaw, Pitch and Roll of CGO

related to the camera position. Cone still rotates not about itself, but about axis of global coordinate system. Do you have any other ideas? Cheers, Paweł 2014-02-06 17:00 GMT+01:00 Thomas Holder thomas.hol...@schrodinger.com: Hi Pawel, have you tried using the camera=0

Re: [PyMOL] loading a cube file from the API

the files. Any ideas? Cheers, Raul -- Thomas Holder PyMOL Developer Schrödinger, Inc. -- Managing the Performance of Cloud-Based Applications Take advantage of what the Cloud has to offer - Avoid Common

Re: [PyMOL] generate solvent exclusive surface with scaled VDW radii

the protein to its vicinity. Thank you in advance. Ye -- Thomas Holder PyMOL Developer Schrödinger, Inc. -- Android apps run on BlackBerry 10 Introducing the new BlackBerry 10.2.1 Runtime for Android apps. Now

Re: [PyMOL] MacPymol + Missing Features (APBS?)

. Is there something I'm missing or was this an experimental feature that didn't make the cut? Cheers, João -- Thomas Holder PyMOL Developer Schrödinger Contractor -- Android apps run on BlackBerry 10 Introducing the new

Re: [PyMOL] apbs plugin

this is with pymol 1.7 ubuntu 12.04 using 1FAS fetched from the pdb thanks jpd -- Thomas Holder PyMOL Developer Schrödinger, Inc. -- Android apps run on BlackBerry 10 Introducing the new BlackBerry 10.2.1

Re: [PyMOL] Corrupted IDTF file from small molecule (sticks representation)

, Thomas -- Thomas Holder PyMOL Developer Schrödinger, Inc. -- Android apps run on BlackBerry 10 Introducing the new BlackBerry 10.2.1 Runtime for Android apps. Now with support for Jelly Bean, Bluetooth, Mapview and more

Re: [PyMOL] RNA stick depiction with filled-out rings

invisible? Thanks a lot. Claus -- Thomas Holder PyMOL Developer Schrödinger, Inc. -- Android apps run on BlackBerry 10 Introducing the new BlackBerry 10.2.1 Runtime for Android apps. Now with support for Jelly Bean

Re: [PyMOL] Yaw, Pitch and Roll of CGO

it's clear what I mean ;) Thank you Pawel -- Thomas Holder PyMOL Developer Schrödinger, Inc. -- Managing the Performance of Cloud-Based Applications Take advantage of what the Cloud has to offer - Avoid Common

Re: [PyMOL] Colorbyrmsd

want to change the scale and recolor the PBDs. Thanx in advance Monica -- Thomas Holder PyMOL Developer Schrödinger, Inc. -- Managing the Performance of Cloud-Based Applications Take advantage of what the Cloud has

Re: [PyMOL] Write map from list of coordinates.

, PyMOL needs to be compiled with numpy for chempy.brick support. Incentive PyMOL ships with numpy support, and open-source PyMOL has numpy support if it can import numpy during compilation. Cheers, Thomas -- Thomas Holder PyMOL Developer Schrödinger, Inc

Re: [PyMOL] List residues functionality ?

(stored.resi_list)): print %s, % stored.resi_list[i], if ((i+1) % 10 == 0): print return stored.resi_list # End Script Thanks for any input Carsten -- Thomas Holder PyMOL Developer Schrödinger, Inc

Re: [PyMOL] Pymol 1.7 and measurement wizard problem

prompted to click on the first atom, and when I do so, nothing happens (nothing gets selected and no error msg on the command line). Ideas of what the problem may be? I have pymol 1.7 on my windows 7, 32 bit. Thank you in advance. -- Thomas Holder PyMOL Developer Schrödinger, Inc

Re: [PyMOL] Write map from list of coordinates.

via some fancy python code? Best Regards Esben Jannik Bjerrum -- Thomas Holder PyMOL Developer Schrödinger, Inc. -- WatchGuard Dimension instantly turns raw network data into actionable security intelligence

Re: [PyMOL] quiet copy

pymol import cmd pymol.finish_launching() cmd.copy('mol_copy','mol_ori') I get the message Executive: object mol_copy created. in the terminal. It is posible to keep the copy comand quiet? Thanks. -- Thomas Holder PyMOL Developer Schrödinger, Inc

Re: [PyMOL] PyMOL v1.7 Released

be generating a .map.ccp4 via FFT (in the CCP4 package) to use isomesh to do the job. Are there any updates/plans on this feature? And I was wondering if there will be a AxPyMOL version for Mac OS X coming at some point as well? Best, Matthias -- Thomas Holder PyMOL Developer

Re: [PyMOL] combining multiple objects into one multistate object

the objects end up in the first state (and the cartoon representation is a subset of what it should be (other representations are fine). I'm using incentive v1.6.0.0 on Windows 7. Jed -- Thomas Holder PyMOL Developer

Re: [PyMOL] Ray tracing with no GUI yields segmentation fault

and Physics Faculty of Pharmaceutical Sciences at Ribeirão Preto University of São Paulo - Brazil De: Thomas Holder thomas.hol...@schrodinger.com Para: Ricardo O. S. Soares rsoa...@fcfrp.usp.br Cc: pymol-users pymol-users@lists.sourceforge.net Enviadas: Terça-feira, 14 de Janeiro de 2014 18:18

Re: [PyMOL] Ray tracing with no GUI yields segmentation fault

Paulo - Brazil -- Thomas Holder PyMOL Developer -- CenturyLink Cloud: The Leader in Enterprise Cloud Services. Learn Why More Businesses Are Choosing CenturyLink Cloud For Critical Workloads, Development Environments

Re: [PyMOL] Color by conservation

in cmd.get_names(): cmd.align(x, 3efw and c. A, object=algn) # color color_by_conservation aln=algn, as_putty=1 everything went as it should but when it came to the last command pymol gave me this error: Bad or incorrectly specified alignment object How can I fix this problem? Thanks -- Thomas

Re: [PyMOL] How to automate RMSD calculation for large no of structures

I like to add that to get the ALL ATOMS RMSD you need to pass cycles=0 to cmd.align or to Rob's align_allfiles. Otherwise, the outlier rejection refinement might drop atoms from the alignment. Cheers, Thomas On 07 Jan 2014, at 13:58, Tsjerk Wassenaar tsje...@gmail.com wrote: If the

Re: [PyMOL] show atoms as circle

Hi Yeping, PyMOL show spheres, name CA PyMOL set sphere_mode, 3 an eventually (example numbers): PyMOL set sphere_point_max_size, 100 PyMOL set sphere_scale, 0.5 Hope that helps. Cheers, Thomas On 06 Jan 2014, at 09:34, sunyeping sunyep...@aliyun.com wrote: Dear all, I want to draw CA

Re: [PyMOL] Cylindrical helices don't show up

Hi HJ, this should help: PyMOL set cylinder_shader_ff_workaround Cheers, Thomas On 26 Dec 2013, at 04:11, HJ Lee hojunle...@gmail.com wrote: For some reasons, PyMOL (1.6.0.0, windows 64 bits) doesn't show the cylindrical helices in cartoon presentation. It just presents helices as an

Re: [PyMOL] sticks

Hi Ahmet, could be a shader problem (missing support by your graphics driver). Try: PyMOL set cylinder_shader_ff_workaround (see http://pymolwiki.org/index.php/Cylinder_shader_ff_workaround ) or: PyMOL set use_shaders, 0 Cheers, Thomas On 22 Dec 2013, at 00:39, Ahmet yıldırım

Re: [PyMOL] sticks

but they are very similar. How can I color each residue with different colors? Thanks in advance 2013/12/22 Thomas Holder Hi Ahmet, could be a shader problem (missing support by your graphics driver). Try: PyMOL set cylinder_shader_ff_workaround (see http://pymolwiki.org/index.php

Re: [PyMOL] how to define vectors between pseudoatoms

Hi, to get the angle between 4 atoms, use get_dihedral. For angle between 3 atoms (lines intersect) use get_angle. http://pymolwiki.org/index.php/Get_Angle http://pymolwiki.org/index.php/Get_Dihedral Cheers, Thomas PS: it's nice to give your name in an email to a list like this one On 12

Re: [PyMOL] 答复： gradually changed colors with flexibility

-- 发件人：Thomas Holder spel...@users.sourceforge.net 发送时间：2013年12月10日(星期二) 04:50 收件人：孙业平 sunyep...@aliyun.com 抄　送：pymol-users pymol-users@lists.sourceforge.net 主　题：Re: [PyMOL] gradually changed colors with flexibility Hi Yeping, use the spectrum command: PyMOL

Re: [PyMOL] gradually changed colors with flexibility

Hi Yeping, use the spectrum command: PyMOL spectrum b, blue_white_red http://pymolwiki.org/index.php/Spectrum Cheers, Thomas On 09 Dec 2013, at 11:30, sunyeping sunyep...@aliyun.com wrote: Dear all, I want to show amino acids in a structure according to their flexibility (B factor)

Re: [PyMOL] AutoDock plugin

Hi James, is it recent version of PyMOL, or recent version of Windows which makes trouble? On Windows, the plugin tries to write to the PyMOL installation folder, which fails if you don't have write permissions there. This needs to be fixed, the plugin should write to the users folder also on

Re: [PyMOL] Error loading pymol libraries from a python script.

Hi David, incentive pymol builds have the python interpreter and the _cmd module built into the pymol.exe executable. This means running the script with your system python is not supported. Instead, run your script with pymol, without the GUI, like this: /opt/soft/pymol-v1.5.0.3/pymol -cqr

Re: [PyMOL] Windows 8 problem

Hi Giuseppe, plugin installation should work fine on Windows 8. Which version of PyMOL do you use? Since 1.5.0.5 plugins can be installed in the user's home folder. Older versions of PyMOL only did system level installation of plugins, which required admin write permissions. Cheers, Thomas

Re: [PyMOL] pdbml

Hi Jerome, I think the simple reason is that nobody ever wrote a PDBML parser for PyMOL. Is that a good reason? Cheers, Thomas On 28 Nov 2013, at 13:21, Jerome BENOIT g62993...@rezozer.net wrote: Hello List, is there any good reason why PyMOL can not read PDBML data files ? Cheers,

Re: [PyMOL] what is an object colored ?

Hi Jon, this will give you the A1 object color: s = cmd.get_session(A1, partial=1, compress=0) print cmd.get_color_tuple(s[names][0][5][0][2]) I use to query the color of the first atom instead of the object color, see psico.querying.get_color:

Re: [PyMOL] resubmitting vanderwaal bumps ?

Hi Suzanne, the showbumps.py script uses the sculpting mechanism, which is no real energy forcefield and thus those units are arbitrary. Calculating the stability of a mutant is a very advanced task, and PyMOL is not made for that. PyMOL can give you visual clues for your reasoning, like

Re: [PyMOL] Font problem

Hi, this is fixed now in the sourceforge SVN repository. Cheers, Thomas On 21 Nov 2013, at 15:36, Jason Vertrees jason.vertr...@schrodinger.com wrote: Justin, You're right, they are ugly! We're fixing that ASAP. Thanks for bringing this up. Cheers, -- Jason On Thu, Nov 21,

Re: [PyMOL] movie, ~1700 residues, out of memory

Hi Christian, set defer_builds_mode to 3, this will prevent caching the geometry for all states. http://pymolwiki.org/index.php/Defer_builds_mode Cheers, Thomas On 09 Nov 2013, at 13:58, Christian Becke christian.be...@fu-berlin.de wrote: Dear pymol users, I'm trying to create a movie,

Re: [PyMOL] alter atom coordinates sequentially

Hi Pawel, sorry that you didn't get a reply. Some hints: - it looks like IDs are always reset with cmd.create, but with cmd.copy there are not http://pymolwiki.org/index.php/Copy - ID is neither necessarily unique nor contiguous (for example the TER record in a PDB file has it's own ID). You

Re: [PyMOL] change dihedral angles using the mouse

Hi Steve, in edit mode, right-mouse double click on the bond, then double click on any atom to drag it. Cheers, Thomas On 13 Nov 2013, at 10:47, Steve Grafton stevegrafto...@yahoo.com wrote: Does anyone know the method to change the phi/psi/omega angles using the mouse in pymol? I know

Re: [PyMOL] default values in pymol?

Hi Neshatul, have you looked at AtomInfoAssignParameters in layer2/AtomInfo.c ? Cheers, Thomas On 09 Nov 2013, at 17:17, neshat haq neshat...@gmail.com wrote: Can anyone tell where can I get the default values of van der wall radii (or other radii) used in pymol, for atoms and

Re: [PyMOL] puckering of ribose

Hi Priyadarshan, sorry that you didn’t get a reply on this question so far. It’s a good question, not native at all. This is a perfect task for sculpting in PyMOL. You should fix the atoms which should not move, and limit the terms to bond length and angles (no torsion or VDW). The steps to

Re: [PyMOL] Zoom option within the movie panel?

Hi Nick, unfortunately such a zooming feature is still missing on the movie panel. I absolutely agree that it would be a much appreciated addition. Cheers, Thomas On Oct 23, 2013, at 11:14 PM, Noinaj, Nicholas (NIH/NIDDK) [E] noin...@niddk.nih.gov wrote: Hi, I am wondering if it is

Re: [PyMOL] pymol crashes on xyz files with about 6000 atoms (slightly more).

for this task and this baffle me. Is there a way for me to de-bug this? Perhaps my input file is faulty. On Tue, Oct 22, 2013 at 1:32 AM, Thomas Holder spel...@users.sourceforge.net wrote: Hi Yotam, 6000 atoms should be absolutely no problem, even with much less memory. There were

Re: [PyMOL] pymol crashes on xyz files with about 6000 atoms (slightly more).

Hi Yotam, 6000 atoms should be absolutely no problem, even with much less memory. There were few known memory leaks that have been fixed since 1.4, so could you try to compile the latest code from SVN? http://pymolwiki.org/index.php/Linux_Install Cheers, Thomas On Oct 21, 2013, at 4:58 PM,

Re: [PyMOL] Loading pdbs with a non-standard load function?

Hi Chris, put something like this in your ~/.pymolrc.py script: from pymol import cmd def customload(*args, **kwargs): print do stuff cmd.load = customload cmd.extend('load', cmd.load) Make sure your customload function doesn't call cmd.load itself, but rather pymol.importing.load if you

Re: [PyMOL] make movies containing morph, zoom-in, and rotation

Hi Mengbin, it's all about the mview command. It can associate states, camera positions and object positions with movie frames. # store state 5 with frame 100 mview store, 100, state=5 # store camera position with current frame mview store # store all object positions with current frame mview

Re: [PyMOL] How to visualize coarse-grained pdb file with CONECT ?

Hi Tsjerk Aiqun, very good find, puzzled me as well. There is a setting pdb_unbond_cations which seems to be implemented a bit buggy, I think it should only prevent distance-based connectivity of cations, and not interfere with explicit CONECT records. Cheers, Thomas On Oct 15, 2013, at

Re: [PyMOL] using morph where only one state contains a small molecule

Hi Claus, going from the example on the PyMOLWiki, which uses also one structure with ligand and one without: fetch 1akeA 4akeA, async=0 align 1akeA, 4akeA morph mout, 1akeA, 4akeA extract ligand, 1akeA and organic hide everything show cartoon, mout show sticks, ligand The ligand can't be part

Re: [PyMOL] set stick_transparency

Hi Yeping, it's a bond setting, so use set_bond instead of set. Cheers, Thomas On Oct 5, 2013, at 1:16 PM, sunyeping sunyep...@aliyun.com wrote: Dear all, I want to set transparecy of selected residues which are shown as sticks and I use the command: set stick_transparency,

Re: [PyMOL] unable to change phi angle of proline

Hi Osvaldo, unfortunately PyMOL doesn't handle to set dihedrals in rings, so you have to break the ring first. Consider this: def set_phi(resi, phi, state=1, quiet=1): x = cmd.index('(first (resi %s and guide)) extend 2 and name C+N+CA' % resi) try: a = cmd.get_model(x[2],

Re: [PyMOL] Structural Allignment in PyMol

Hi Syeda, you have a lot of options in PyMOL to do this. For full-atom RMSD fit on topologically identical molecules (since it's MD, I guess this is the case), use the fit command: PyMOL fit mobile, target Otherwise, use align or super: PyMOL align mobile, target, cycles=0 From a python

Re: [PyMOL] Background colors in PyMOL 1.6

Hi Nils, getting hex colors from settings is fixed in SVN rev 4043. Cheers, Thomas On Sep 20, 2013, at 10:14 AM, Jason Vertrees jason.vertr...@schrodinger.com wrote: Hi Nils, Thomas will soon fix the return values of the get command for color to properly contain the 0x prefixes. In the

Re: [PyMOL] Guessing bonds for a chempy model.

cmd.load_model, and I could not find a way of doing it. Does anyone know how can I achieve this? Thanks! Raul -- Thomas Holder PyMOL Developer Schrödinger Contractor -- LIMITED TIME SALE - Full Year of Microsoft

Re: [PyMOL] Trouble with saving mol2 format

intel graphics) -- Thomas Holder PyMOL Developer Schrödinger Contractor -- LIMITED TIME SALE - Full Year of Microsoft Training For Just $49.99! 1,500+ hours of tutorials including VisualStudio 2012, Windows 8, SharePoint

Re: [PyMOL] new metals keyword

nonbonded and covalently bonded hetatms. Although I'm not sure how non-standard amino acids would fit in to those terms. -Spencer -- Thomas Holder PyMOL Developer Schrödinger Contractor -- How ServiceNow helps IT people

Re: [PyMOL] Object motions and Camera Motions not in sync

Willis Vanderbilt Medical Center jwillis0...@gmail.com mailto:jwillis0...@gmail.com -- Thomas Holder PyMOL Developer Schrödinger Contractor -- How ServiceNow helps IT people transform IT departments: 1. Consolidate

Re: [PyMOL] interpolate vs. reinterpolate

this is what's causing some issues with my complex movie. Does anyone have a simple explanation of when to use one or the other? J -- Thomas Holder PyMOL Developer Schrödinger Contractor -- How ServiceNow helps IT people

Re: [PyMOL] C-aplha c-alpha distances

it. Please help me in this regard I am very new to this field. Thank u in advance, Ananya -- Thomas Holder PyMOL Developer Schrödinger Contractor -- How ServiceNow helps IT people transform IT departments: 1. Consolidate

Re: [PyMOL] white background text color problem (was:Re: Sequence numbers in MacPyMOL 1.6.0.0 with background set to white)

this helps to narrow-down the issue. Thanks, Christoph -- Thomas Holder PyMOL Developer Schrödinger Contractor -- Learn the latest--Visual Studio 2012, SharePoint 2013, SQL 2012, more! Discover the easy way to master current

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

as it is starting, which may be related: libpng warning: iCCP: known incorrect sRGB profile Working on a Mac 10.6.8. Best, Engin -- Thomas Holder PyMOL Developer Schrödinger Contractor -- Learn the latest--Visual Studio 2012

Re: [PyMOL] new metals keyword

for those since they previously only considered protein atom names. Cheers, Thomas Thomas Holder wrote, On 08/13/13 17:56: Greetings, this is a quick announcement that we added the metals keyword to the selection language (SVN code revision 4039). Since PyMOL's selection language is one

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

. Thanks. Yeping Sun Institute of Microbiology, Chinese Academy of Sciences -- Thomas Holder PyMOL Developer Schrödinger Contractor -- Learn the latest--Visual Studio 2012, SharePoint 2013, SQL 2012, more! Discover

Re: [PyMOL] color change upon ray-tracing

. Cheers, Thomas Oganesyan, Vaheh wrote, On 09/03/13 19:47: PyMOLers, Upon ray-tracing PyMOL v1.6.0.0 (Linux 64 bit) changes the color and the mesh line width of the electron density maps. How can I disable this metamorphosis? Thank you. Vaheh -- Thomas Holder PyMOL Developer

Re: [PyMOL] Mapping picture to CGO object in PyMOL?

Hi Florian, this is not possible, sorry. Cheers, Thomas Florian Nachon wrote, On 09/01/13 12:48: Hi, Probably a fancy request, but is there any way to map a picture to a cgo object in PyMOL, like a plane or a sphere? Best, Florian -- Thomas Holder PyMOL Developer Schrödinger

Re: [PyMOL] Alpha carbon pairwise distances

or is there another script to use? Thanks - Alicia -- Thomas Holder PyMOL Developer Schrödinger Contractor -- Introducing Performance Central, a new site from SourceForge and AppDynamics. Performance Central is your source for news

Re: [PyMOL] ray-tracing cones

, 1.0,# RGB Color 2 0.0, 0.0, # Caps 1 2 ] ) cmd.load_cgo(o, name) cmd.extend('cone', cone) -- Thomas Holder PyMOL Developer Schrödinger Contractor -- Introducing

Re: [PyMOL] Load pse file crash on Ubuntu

/18 -- Thomas Holder PyMOL Developer Schrödinger Contractor -- Introducing Performance Central, a new site from SourceForge and AppDynamics. Performance Central is your source for news, insights, analysis and resources

Re: [PyMOL] Newline character in labels: 2nd request :)

-3.0 ... Y 1.0 For this it would be most useful if I could use newline in my label definition. Hope you can help! Thanks, Chris -- Thomas Holder PyMOL Developer Schrödinger Contractor -- Get 100% visibility

[PyMOL] new metals keyword

. For example selecting by x,y,z coordinates, or selecting by secondary structure element. If you have a good idea for a new keyword or operator, please file a feature request on sourceforge. Cheers, Thomas -- Thomas Holder PyMOL Developer Schrödinger Contractor

Re: [PyMOL] ColorByRMSD autoscaling colors?

-- Thomas Holder PyMOL Developer Schrödinger Contractor -- Get 100% visibility into Java/.NET code with AppDynamics Lite! It's a free troubleshooting tool designed for production. Get down to code-level detail for bottlenecks

Re: [PyMOL] How to move/turn CGO

/cgo_axes.py, which has comments for all the CONE parameters? https://sourceforge.net/p/pymol/code/4038/tree/trunk/pymol/examples/devel/cgo_axes.py Cheers, Thomas -- Thomas Holder PyMOL Developer Schrödinger Contractor

Re: [PyMOL] varying label positions

labeling commands now: label c. A and n. CA and i. 52, (%s, %s) % (resn, resi) label c. A and n. CA and i. 144, (%s, %s) % (resn, resi) Is there a way to do this? Thanks! -- Thomas Holder PyMOL Developer Schrödinger Contractor

Re: [PyMOL] Bind reset to a key?

API way: cmd.set_key('ALT-r', cmd.reset()) and PyMOL commad way: cmd.set_key('ALT-r', cmd.do(reset) But it doesn't work. I bind various things to keys, so I'm certain of the procedure. How could I bind reset to a key? I'm using 1.6.0.0 _ With respect, Boris. -- Thomas

Re: [PyMOL] importing openGL stream into Pymol

that using a CGO helps import an OpenGL object into the Pymol GUI. But does anyone know if it is possible to integrate an OpenGL stream like say, glxgears into the Pymol viewer? Thanks Suhas -- Thomas Holder PyMOL Developer Schrödinger Contractor

Re: [PyMOL] caver plugin

But this is wrong and does not work. Could someone give me some tutorial? Thanks. Yeping Sun -- Thomas Holder PyMOL Developer Schrödinger Contractor -- See everything from the browser to the database

Re: [PyMOL] Residue numeration problem

-- Thomas Holder PyMOL Developer Schrödinger Contractor -- See everything from the browser to the database with AppDynamics Get end-to-end visibility with application monitoring from AppDynamics Isolate bottlenecks

Re: [PyMOL] Residue numeration problem

by pymol. cheers, Gianluigi Da: Thomas Holder thomas.hol...@schrodinger.com A: Gianluigi Caltabiano chimic...@yahoo.it Cc: pymol-users pymol-users@lists.sourceforge.net Inviato: Martedì 23 Luglio 2013 9:27 Oggetto: Re

Re: [PyMOL] get coordinate

? Regards, Yeping Sun -- Thomas Holder PyMOL Developer Schrödinger Contractor -- See everything from the browser to the database with AppDynamics Get end-to-end visibility with application monitoring from AppDynamics Isolate

Re: [PyMOL] Pymol and load_traj

occurred as for my first attempts at loading a trajectory I was attempting to select a small portion using the start and stop options. Are there known issues with load_traj - I was not able to find any hints using Google. Thanks David -- Thomas Holder PyMOL Developer Schrödinger

Re: [PyMOL] Stereo (quad-buffered) and fixed object (Sequence, Sidebar) are suboptimal

effects due to one eye seeing different things as the other when having stereo switched on. Is it possible to render those objects for both eyes? Thanks Justin -- Thomas Holder PyMOL Developer Schrödinger Contractor

Re: [PyMOL] How Pymol reads a dcd file

or a script. Thank you Hira Batool Student of BS-Bioinformatics Biosciences Department COMSATS Institute of Information Technology Islamabad, PAKISTAN -- Thomas Holder PyMOL Developer Schrödinger Contractor -- See

Re: [PyMOL] pymol movie

the structure in both open and closed conformation. Now i want to make the movie of showing a series of change in going from open to close conformation. please tell me how to mkae movie. Thank you Appu -- Thomas Holder PyMOL Developer Schrödinger Contractor

Re: [PyMOL] restricting selection to the current frame

flag? E.g. the given example of selecting molecules when you got waters? Is there an easy workaround for the ID rolling? Regards, Daniel Am 01.07.13 21:38, schrieb Thomas Holder: Matthew Baumgartner wrote, On 07/01/13 21:34: I removed the byres command because I have more

Re: [PyMOL] trouble with sym exp

instead? -- Thomas Holder PyMOL Developer Schrödinger Contractor -- This SF.net email is sponsored by Windows: Build for Windows Store. http://p.sf.net/sfu/windows-dev2dev

Re: [PyMOL] Odd issue with control and shift keys in pymol

. It appears to be pymol specific as coot and other programs work fine. Has anyone seen this before or have some sort of explanation? Thanks, --paul -- Thomas Holder PyMOL Developer Schrödinger Contractor -- This SF.net email

Re: [PyMOL] Anaglyph colours sorted (kind of)

enough and you need to be using PyMOL v1.5 or later. Cheers, -- Jason -- Thomas Holder PyMOL Developer Schrödinger Contractor -- This SF.net email is sponsored by Windows: Build for Windows Store. http://p.sf.net/sfu

Re: [PyMOL] problem with distance

and atom o. For a proof, I'm pasting the top screen where the names of the atoms I clicked is: You clicked /molA//A/SER`53/O Selector: selection sele defined with 1 atoms. You clicked /molA//D/GLY`8/N) I was previously under 1.3 and didn't have this problem. Can you help me? Vincent -- Thomas

Re: [PyMOL] Problems with Pymol v 1.6.0.0

, Matt -- Thomas Holder PyMOL Developer Schrödinger Contractor -- This SF.net email is sponsored by Windows: Build for Windows Store. http://p.sf.net/sfu/windows-dev2dev ___ PyMOL

Re: [PyMOL] Problems with Pymol v 1.6.0.0

.jar |-- __init__.py(was: Caver2_1_2.py) `-- lib |-- dt3d.jar |-- j3dcore.jar |-- j3dutils.jar |-- ujmp-complete-0.2.4.jar `-- vecmath.jar And in Caver2_1_2/__init__.py, change: PYMOL_LOCATION = sys.modules[__name__].__path__[0] Cheers, Thomas -- Thomas Holder PyMOL

Re: [PyMOL] Anaglyph colours

, MSD 2080, Malta. phone: +356 2340 2917 phone: +356 21316655 (secretary), Fax: +356 21310577 http://www.um.edu.mt/ms/physbiochem -- Thomas Holder PyMOL Developer Schrödinger Contractor -- This SF.net email

Re: [PyMOL] PyMOL 1.6 pre-release announcement

This is fixed in SVN rev 4032. Cheers, Thomas Thomas Holder wrote, On 06/15/13 10:45: Hi Rob, this has not been fixed yet, I'm really sorry. We'll look into this ASAP. It only affects the open-source code, apparently we missed something when syncing with the incentive codebase. Cheers

Re: [PyMOL] PyMOL 1.6 pre-release announcement

who would like to beta test can use devel:languages:python repo in openSUSE: https://build.opensuse.org/package/show?package=pymolproject=devel%3Alanguages%3Apython -David -- Thomas Holder PyMOL Developer Schrödinger Contractor

Re: [PyMOL] Visualizing sp3-hybridized electron orbital

to accomplish with PyMOL??? Any comments or suggestions would be valuable! Thanks a lot in advance! Best regards, Yury -- Thomas Holder PyMOL Developer Schrödinger Contractor -- This SF.net email is sponsored by Windows

Re: [PyMOL] Isomesh plot in Pymol vs Coot

sigma -- Thomas Holder PyMOL Developer Schrödinger Contractor -- This SF.net email is sponsored by Windows: Build for Windows Store. http://p.sf.net/sfu/windows-dev2dev

Re: [PyMOL] Distorted secondary structure using 'alter' command

-- Thomas Holder PyMOL Developer Schrödinger Contractor -- This SF.net email is sponsored by Windows: Build for Windows Store. http://p.sf.net/sfu/windows-dev2dev ___ PyMOL-users

Re: [PyMOL] PyMOL 1.6 final release

,self.pymol_names) File string, line 1, in module File /MYPATH/Pymol/pymolplugins/__init__.py, line 65, in module x__initializePlugins = pmg_tk.PMGApp.initializePlugins Any idea? thank you Gianluigi -- Thomas Holder PyMOL Developer Schrödinger Contractor

Re: [PyMOL] Pymol 1.6.0.0 setup.sh issue

tel: (315)-228-7245 ofc: (315)-228-7395 fax: (315)-228-7935 email: rrowl...@colgate.edu -- Thomas Holder PyMOL Developer Schrödinger Contractor setup.sh Description: application/shellscript -- This SF.net email

Re: [PyMOL] Pymol 1.6.0.0 setup.sh issue

Thomas Holder wrote, On 06/13/13 18:43: Find a fixed setup.sh attached. I'll fix this ASAP in SVN. my mistake, doesn't affect open-source, no fix in SVN, sorry ;) -- Thomas Holder PyMOL Developer Schrödinger Contractor

[PyMOL] PyMOL 1.6 final release

/dsc/dokuwiki/doku.php?id=media:new16 http://pymol.org/dsc/dokuwiki/doku.php?id=properties http://pymol.org/dsc/dokuwiki/doku.php?id=media:morphing_updates We welcome any feedback and bug reports. Cheers, - The PyMOL Team at Schrödinger -- Thomas Holder PyMOL Developer Schrödinger Contractor

Re: [PyMOL] settings

in, that might change stick_color, would that unique bond setting be overridden? If a state's color is set using Spectrum_states.py, does that override already-set scene colors? Or is it incorporated into defined scenes then? -- Thomas Holder PyMOL Developer Schrödinger Contractor

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