Re: [PyMOL] Building of the Carbon lattice

er hand I want to build such 2D lattices > http://imageshack.us/photo/my-images/543/lattice.png/ > made from SP3 carbons as the nodes via some automatic script to > obtain lattices with desired dimensions. > > James -- Thomas Holder PyMOL Developer Schrödinger Contractor from num

Re: [PyMOL] Regarding electrostatic potential mapping

p > 3) ramp_new e_lvl, map, > 4) set surface_color, e_lvl, myfile > > I have attached the Delphi log file for reference also. I would really > appreciate any help in this regard. > > Thanks, > Soumya -- Thomas Holder PyMOL Developer Schrödinger Contractor -

Re: [PyMOL] Building of the Carbon lattice

e to write a simple TcL script and reorient > the whole > molecule by changing one parameter . I don't currently have a way to include > library > items, like say a methyl group, and I was debating about doing this in python > but I wanted to have easy access to lapack etc fo

Re: [PyMOL] Pymol visualization problem

the L1 and E2 (both chain A and B). >> Thirdly, i changed the docking software and generated a complex using >> another software, this time i still was unable to visualize complete complex >> in pymol. >> Any help will be much appreciated. >> Kind regards >> Abida

Re: [PyMOL] DNA measurement help require by sculptor

Briony Marshall - Sculptor > www.briony.com <http://www.briony.com/> > <http://www.briony.com/>join my mailing > list: www.briony.com/subscribe.html <http://www.briony.com/subscribe.html> > or like me on facebook: www.facebook.com/brionymarshallsculptor > <

Re: [PyMOL] Pymol visualization problem

of > E2 (both chain A and B are alike). Then in order to see if it is docking > error or visualization error, i rendered the complex in swiss pdb viwer and > saw the L1 and E2 (both chain A and B). > Thirdly, i changed the docking software and generated a complex using > another soft

Re: [PyMOL] Coloring molecule after color_ramp

(XX*) > > After that we would like to color defined residues for example in red > using the selection tool. Although the color is changed in the sequence > pane, the color is not applied to the molecule. > > Any suggestions? > &g

Re: [PyMOL] DNA ligand presentation in PyMOL

ions like (chain A and resi 34). http://pymolwiki.org/index.php/Single-word_Selectors http://pymolwiki.org/index.php/Selection_Algebra http://pymolwiki.org/index.php/Property_Selectors Cheers, Thomas -- Thomas Holder PyMOL Developer Schrödinger Contractor ---

Re: [PyMOL] get_dihedral for multiple files(states of a movie)

gt; I have generated a movie of 300 snapshots (MD simulation trajectory). > How can i calculate dihedral angles for same four atoms across the > trajectory (or a movie)?? > I mean "get_dihedral 58/n,58/c,58/ca,58/cb "values 300 times for each > snapshot. > >

Re: [PyMOL] Renumber Script problem

r right near the > beginning that is 6 residues down from the previous one. Needless to > say, this is screwing up the rest of the count. Is there any idea why? > I've provided a screenshot. > > Thanks, > Ale

Re: [PyMOL] Renumber Script problem

get_id() and not options.norestart): > chain_id = chain.get_id() > residue_id=int(options.start) > if(options.preserve): > hetero = residue.id[0] > insert = residue.id[2] > residue.id=(hetero,residue_id,insert) >

Re: [PyMOL] How do I get current selection name from python?

> > I read the sources, but couldn't find a single instance where current > selection would be a default one. -- Thomas Holder PyMOL Developer Schrödinger Contractor -- Master Visual Studio, SharePoi

Re: [PyMOL] echo colour

y > University of Otago > PO Box 56 Dunedin 9054 > New Zealand > > Skype: jtyndall > > Ph: +64 3 479 7293 -- Thomas Holder PyMOL Developer Schrödinger Contractor -- Master Visual Studio, SharePoint,

Re: [PyMOL] How do I get current selection name from python?

raryFile(dir=os.curdir, > prefix="{frame:03d}_{sel}_".format(frame=cmd.get_frame(), sel=Selection) , > suffix=".pdb") > print tempFile.name, Selection # prints righteous file name and selection > name (though not in quotes) > cmd.save(tempFile.name,

Re: [PyMOL] Hight-quality visualisation

set antialias, 2 > ray 800, 600 > > In particular I wounder to know how I could decrease width of contour > black line (appeared in set ray_trace_mode) ? > Also I'd like to show more examples besides those which I found here > http://www.pymolwiki.org/index.php/Ray_trace_mode#

Re: [PyMOL] Saving setting in PyMol

.pymolrc > own@starlight ~/Desktop $ locate *.pymolrc > > How I could locate it ? > Akso I'm looking for detailed options of the possible settings in that > file ( e.g I didnt find how to set maximum quality of images as the > default option ) > > Thanks for help >

Re: [PyMOL] default settings

Mol, it comes >>> back with: >>> >>> File "/Users/adam/pymolrc.pym", line 1 >>>set auto_zoom = 0 >>>^ >>> SyntaxError: invalid syntax >> >> That's because you're u

Re: [PyMOL] rainbow coloring from the N to C terminus of multiple backbones shown as ribbons

entries and select rainbow, but its not feasible to do for 2000 > entries. > > I was wondering if there is an automated way of coloring each ribbon end > to end in the same rainbow. > > Best Regards, > Ali -- Thomas Holder PyMOL Developer Schrödinger Contractor --

Re: [PyMOL] problem setting up morph under eMovie

.4). > Regardless I also need instructions for how to embed the morph in the > list of commands. Any help would be greatly appreciated. > > Thanks -- Thomas Holder PyMOL Developer Schrödinger Contractor -- Fr

Re: [PyMOL] Path problem when running a script

le "/opt/pymol/modules/pymol/parsing.py", line 455, in run_file > execfile(file,global_ns,local_ns) > IOError: [Errno 2] No such file or directory: 'align_all.py' > > If I run the full path to the script it wo

Re: [PyMOL] VMD module in Rev 4019-4020 break build

gt; moldenplugin.c:38:#include "qmplugin.h" > basissetplugin.c:43:#include "qmplugin.h" > gamessplugin.c:160:#include "qmplugin.h" > > Please fix =) > > Best, > Quyen -- Thomas Holder PyMOL Developer Schrödinger Contractor

[PyMOL] setup.py and VMD plugins updated

-path and --bundled-pmw Please report any bugs or problems that you encounter. Cheers, Thomas -- Thomas Holder PyMOL Developer Schrödinger Contractor -- The Go Parallel Website, sponsored by Intel - in partnership with

Re: [PyMOL] constant distances over states

tance of the first state shown. I could script > this but first would like to ask the users group if there is an > easier alternative. > > Jordan -- Thomas Holder PyMOL Developer Schrödinger Contractor -- Ev

Re: [PyMOL] About draw_links.py by Dr. Robert Campbell

hain C, name CA resi 15 and chain C >> draw_links name CA & resi 5 and chain C, name CA resi 12 and chain C >> >> Sorry that it doesn't quite do what you were expecting! I designed it for >> the situation where I have two structures that exhibit a conformational &g

Re: [PyMOL] Increase sphere size for heavy element

-4.417 -1.426 1.00 0.00 N > > using "Preset/Ball-and-stick", the tungsten atom is drawn with a very > small radius. Can this radius be increased? > > Thanks > Martin -- Thomas Holder PyMOL Developer Schrödinger Contractor --

Re: [PyMOL] Display style for partial bond

H LIG 1 -0.441 -2.597 -1.043 1.00 0.00 H > > you'll see that a bond between W and C is drawn. However, this is > supposed to be a transition state, so a dashed bond would be more > appropriate. Can this somehow be drawn? > > Thanks, > Martin --

Re: [PyMOL] symmetry operation to generate the whole virus particle

erations. Can pymol do > these or other software is needed? Please help. > > Yeping Sun > CAS Key Laboratory of Pathogenic Microbiology & Immunology > INSTITUTE OF MICROBIOLOGY CHINESE ACADEMY OF SCIENCES > NO.1 Beichen West Road,Chaoyang District,Beijing 100

Re: [PyMOL] [PyMol] How to visualize surface within a given radius

the protein. > > I guess you could create a new selection of residues around a ligand and > show this surface but I wondered if there are any other ways of doing > this. -- Thomas Holder PyMOL Developer Schrödinger Contractor

Re: [PyMOL] refinement in morph

ovalently bonded atoms > like metals and waters are moving around a lot. However, if I turn off the > refinement, there are some distortions in my protein. Is there a way to make > the non-covalently bonded atoms just move along the transition path? > > Thanks.

Re: [PyMOL] running pse file in batch mode

imes, > NDM Senior Reseach Fellow > University Research Lecturer > Division of Structural Biology > Wellcome Trust Centre for Human Genetics > University of Oxford > Roosevelt Drive, > Oxford OX3 7BN, UK > > Email: jonat...@strubi.ox.ac.uk, Web: www.strubi.ox.ac.uk >

Re: [PyMOL] How to ray trace clipped image without clipping spheres.

t; # the scene and cut out a spherical region. > > # Note that you can change the view after this operation and have a > nice sideview > # of a clipped system, or use it to clip a system multiple times from > different sides. > > # Enjoy! > > # Cheers, > > # Tsjer

Re: [PyMOL] [Pymol] plugins won't intitialize

odules/pmg_tk/PMGApp.py", > line 320, in initializePlugins > mod.__init__(self) > TypeError: module.__init__() argument 1 must be string, not instance > Error: unable to initialize plugin 'movs'. > > I guess there is something wrong with the code but

Re: [PyMOL] (no subject)

version of pymol incompatible with windows 8? Or is > there something I can do to get it working on my computer? -- Thomas Holder PyMOL Developer Schrödinger Contractor -- Everyone hates slow websites. So do we. Make your

Re: [PyMOL] Error while running a python script

; in load > _self.unlock(r,_self) > File "/usr/lib/python2.7/site-packages/pymol/locking.py", line 79, in > unlock > if (thread.get_ident() == pymol.glutThread): > AttributeError: 'module' object has no attribute 'glutThread' > > --

Re: [PyMOL] Mesh Cavity Mode?

urface_cavity_mode, 1` except with mesh? > > Thanks in advance for responses. > > Cheers, > Jared -- Thomas Holder PyMOL Developer Schrödinger Contractor -- Everyone hates slow websites. So do we. Make y

[PyMOL] PyMOL 1.6 pre-release announcement

Team at Schrödinger -- Thomas Holder PyMOL Developer Schrödinger Contractor -- Everyone hates slow websites. So do we. Make your web apps faster with AppDynamics Download AppDynamics Lite for free today: http://p.sf.net

Re: [PyMOL] PyMOL 1.6 pre-release announcement

Hi Michael, I haven't tagged that commit. It's svn revision 4025. For the final 1.6.0 version we will upload a tar.gz archive to sourceforge. Cheers, Thomas On Mar 24, 2013, at 1:18 PM, Michael Banck wrote: > Hi, > > On Sun, Mar 24, 2013 at 11:02:08AM +0100, Thomas Holde

Re: [PyMOL] Color changes during a morph

","+str(g)+","+str(b)+"]" > cmd.set_color("newcolor",col) > print "COL state "+str(a+1)+": "+col > cmd.set("surface_color", "newcolor", "resi 430:572", a) &

Re: [PyMOL] PyMOL 1.6 pre-release announcement

heers, Thomas Christoph Gohlke wrote, On 03/25/13 18:11: > On 3/24/2013 3:02 AM, Thomas Holder wrote: >> Dear PyMOL users, >> >> The pre-release version of PyMOL 1.6 has been pushed to the open >> source repository on SourceForge. Besides several minor fixes and >

Re: [PyMOL] Problem with h_add hydrogens in sequence viewer

er > programs (babel, chimera, namd, etc). > > I am using Pymol 1.5.0.1. (I will be updating to 1.6 soon). > > Any suggestions for settings to change or a workaround (possibly > involving other programs, if necessary), would be greatly appreciated.

Re: [PyMOL] loadDir script

name(c).split(".")[0], "add" ) > > what should I change here to sort files correctly? > > > James -- Thomas Holder PyMOL Developer Schrödinger Contractor -- Minimize network downtime a

[PyMOL] PyMOL Testing Framework

them with the PyMOL community. So, please feel free to jump in and contribute! The code and basic directions can be found on Github: https://github.com/schrodinger/pymol-testing Happy testing! Cheers, Thomas -- Thomas Holder PyMOL Developer Schrödinger Contr

Re: [PyMOL] movie for morphing

ith rocking the last > state for a few seconds. How do I do that? Can I rock or nutate a > state in the middle for a few seconds as well? > > Thanks. > > --Jianghai -- Thomas Holder PyMOL Developer Schrödinger Contractor --

Re: [PyMOL] How do you list H-bonds in pymol?

t the H-bond pairs to the console output. If you need that, use this script: http://pymolwiki.org/index.php/Get_raw_distances See also: http://pymolwiki.org/index.php/Distance Hope that helps. Cheers, Thomas -- Thomas Holder PyMOL Developer Schrödinger Contractor -

Re: [PyMOL] export sequence alignment

ows) and I need the structural alignment based sequence alignment. > > Other tools maybe? I have mustang already > > Cheers > Joel -- Thomas Holder PyMOL Developer Schrödinger Contractor -- Minimize net

Re: [PyMOL] Reset Default Carbon Color

ded to > force this functionality, but I would rather avoid that if possible. -- Thomas Holder PyMOL Developer Schrödinger Contractor -- Precog is a next-generation analytics platform capable of advanced analytics on se

Re: [PyMOL] conect records?

ms (it is > initially a gromacs' gro file). Is there a way I can display conections > correctly in PyMOL? > > -- > With great respect, > Boris. -- Thomas Holder PyMOL Developer Schrödinger Contractor --

Re: [PyMOL] CGO fixed in space

Cheers, Thomas Soisson, Stephen M wrote, On 04/16/13 14:43: > Is there a way to associate a wizard message with stored scenes so that the > message changes with each scene? > > Thanks- > > Steve -- Thomas H

Re: [PyMOL] Fwd: Translate command seems to translate along an arbitrary axis

Second time: > > PyMOL>iterate_state 1, glycan* and id 1, print x, y, z > 3.3945341 1.4326853 -0.0 > IterateState: iterated over 1 atom coordinate states. > PyMOL>translate [1, 0, 0], glycan* > PyMOL>iterate_state 1, glycan* and id 1, print x, y, z > 2.9689

Re: [PyMOL] Distance between atoms on the interface

ow distances between two objects > (two chains) and filter them; for instance to display distnaces between > atomes of two interacting protein chains which are less than 6 A. > > Any help would be much appreciated, > > Mehdi -- Thomas Holder PyMOL De

Re: [PyMOL] Problems with H_add when theres alternate conformations present

1zw9 >> zoom resi 12 >> h_add 1zw9 >> >> the hydrogen on the nitrogen in the backbone peptide bond doesn't make a >> planer configuration, and if I save the object, the oxygen is assign

Re: [PyMOL] Transparency of VASCo surfaces

e before. > I am on pymol 1.5.0.3 on a Macbook pro 2011 (Pymol Hybrid). > > Am I missing something? > > thanks and regards > > Gianluigi -- Thomas Holder PyMOL Developer Schrödinger Contractor -- Try

Re: [PyMOL] morpheasy

s > its helicity. When I do morpheasy, the secondary structure of this helix > from the starting conformation is still preserved and not converted into > the loop conformation at the end of the movie. How can I depict this > change of secondary structure with the morpheasy? > >

Re: [PyMOL] extra bonds

ry pdb file use discrete=1, extra > bonds would be shown in sticks in those slightly distorted residues. > Is there is way to avoid those extra bonds? Thanks a lot. > > --Jianghai -- Thomas Holder PyMOL Devel

Re: [PyMOL] Pymol error

iven) > > As a result it never opens the "The Pymol Molecular Graphics System" > window. Can anyone help to find out what might be wrong. > > Thanks > Rhitankar > > -- > Rhitankar Pal > Postdoctoral Researcher, > Dept of Chemistry, Yale University > New H

Re: [PyMOL] Secondary structure labeling

the secondary structures (helices and strands) using Pymol. > I have them defined in my header file using DSSP. > > Thank you in advance. > > Bishwa Subedi -- Thomas Holder PyMOL Developer Schrödinger Contractor -

Re: [PyMOL] Pymol error

._initialise() > File > "/Library/Python/2.7/site-packages/Pmw/Pmw_2_0_0/lib/PmwLoader.py", line > 89, in _initialise > raise ImportError(msg) > > This is preventing it from opening the GUI. Do you have any idea what > should I do to avoid this. > > Thanks for your

Re: [PyMOL] Pymol error

Thanks again > Rhitankar > > > On Wed, May 8, 2013 at 12:34 PM, Thomas Holder wrote: > > Dear Rhitankar, > > I should point out that Schrödinger also sells pre-compiled PyMOL with > easy to use installers. http://pymol.org/academic.html > > Open-Source

Re: [PyMOL] Secondary structure labeling

ructure. But I would like to label/name the > alpha helices as alpha1...and beta strands as Beta1 and so on. Can that > be done using Pymol. > > Best > > Bishwa Subedi, M.Sc Bioinformatics > University of Turku > Finland > > On May 8, 2013, at 5:33 PM, Thomas Hol

Re: [PyMOL] How to install Psico module for pymol with window 7

the following error > > File "C:\Program Files (x86)\DeLano > Scientific\PyMOL/modules\psico\fullinit.py", line 10 > from . import init > ^ > SyntaxError: invalid syntax > > What's wrong ? >

Re: [PyMOL] Label by selection identifier

t possible to label selections by their name? >> >> If I have a selection named "foo" and I say label foo, "foo", it >> of course labels all the atoms. Is it possible to get one label >> for the entire selection without using pseudoatoms? &g

Re: [PyMOL] defer_builds_mode

t; command doesn't get rid of the cache, whatever > is cached to RAM there... > This doesn't seem to happen in lines-representation, but also for sticks. > (PyMOL 1.5.0.4, Ubuntu 12.04 64-bit) > > Regards, &g

Re: [PyMOL] internal cavity lighting

uniq/5669624 > >> -- >> Yarrow Madrona >> >> Graduate Student >> Molecular Biology and Biochemistry Dept. >> University of California, Irvine >> Natural Sciences I, Rm 2403 >> Irvine, CA 92697 -- Thomas Holder PyMOL Developer Schrödinger Contra

Re: [PyMOL] settings

ond and then apply the sort of script that > Sid recently was interested 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

Re: [PyMOL] scenes and states

wrote: > Questions: > > Can two objects be in two different states -- object1 in state 3 and object2 > in state 10, for instance, at the same time? If so, how is that set up? How > is that then incorporated into a scene? > > Do CGO, measurements, mesh, and volume objects ha

[PyMOL] PyMOL 1.6 final release

age PyMOL sponsors to check out the internal documentation: http://pymol.org/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 T

Re: [PyMOL] PyMOL 1.6 final release

ons/PyMOLX11Hybrid.app/pymol/modules/pymol/parser.py", > line 260, in parse > exec(layer.com2+"\n",self.pymol_names,self.pymol_names) > File "", line 1, in > File "/MYPATH/Pymol/pymolplugins/__init__.py", line 65, in > x__initializePlugins

Re: [PyMOL] Pymol 1.6.0.0 setup.sh issue

untu > 12.04 LTS. > > Any ideas? > > Cheers, > > ___ > Roger Rowlett > Gordon & Dorothy Kline Professor > Department of Chemistry > Colgate University > 13 Oak Drive > Hamilton, NY 133

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 Schröding

Re: [PyMOL] Visualizing sp3-hybridized electron orbital

know > if it is possible 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 --

Re: [PyMOL] Isomesh plot in Pymol vs Coot

;>> # find example residue >>> orient i. 78 >>> # color >>> color magenta, e. N >>> color tv_yellow, e. C > >>> In Coot: >>> * Fetch 1CLL and its map from EDS >>> * zoom to residue 78 >>> * scroll to 1.06 sigma -

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

a distorted helix. How do I correct it? > > Thanks, > Ritu -- Thomas Holder PyMOL Developer Schrödinger Contractor -- This SF.net email is sponsored by Windows:

Re: [PyMOL] PyMOL 1.6 pre-release announcement

earlier) with a red >> background >> >> These are run on openSUSE 12.3 with SVN rev 4028 . On a side note, >> others who would like to beta test can use devel:languages:python repo >> in openSUSE: >> ht

Re: [PyMOL] Anaglyph colours

; Department of Physiology and Biochemistry > University of Malta, Msida, 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 --

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 wi

Re: [PyMOL] problem with "distance"

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 Holder PyMOL Developer Schrödinger Contractor --

Re: [PyMOL] Problems with Pymol v 1.6.0.0

uares). > > Is there some setting that I accidentally set somewhere? > > Thanks, > Matt -- Thomas Holder PyMOL Developer Schrödinger Contractor -- This SF.net email is sponsored b

Re: [PyMOL] Problems with Pymol v 1.6.0.0

aver plugin would be: Caver2_1_2 |-- Caver2_1.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] Ch

Re: [PyMOL] Averaging a pdb file

gt; duplicate of the first structure we opt. > > Anyways any suggestion will be appriciated. -- Thomas Holder PyMOL Developer Schrödinger Contractor -- This SF.net email is sponsored by Windows: Build for Wi

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

color changes. > >> Any idea why using modern shaders does not work with anaglyph and might this >> be improved later? > > Again, modern shaders do indeed work with PyMOL–I use them all the > time–your video card just has to be good enough and you need to be > using

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

gt;> to use the control or shift keys for selection or editing in the gui. I >> dug out an older version (1.4.1) and it behaved properly. It appears to >> be pymol specific as coot and other programs work fine. Has anyone seen &g

Re: [PyMOL] Label problems (PyMOL ver. 1.6)

; Then, a yellow broken line was produced between the selected atoms. > However, the label of distance (i.e. 2.2 Å) was not shown though the > older versions (including v1.6-beta2) correctly showed. Label of > angle is the same. It is also ineffective to select "Show -> label" >

Re: [PyMOL] restricting selection to the current frame

is, please let me know, I would like to > select whole water molecules for making figures. use "bymol". Cheers, Thomas -- Thomas Holder PyMOL Developer Schrödinger Contractor -- This SF.net email is sp

Re: [PyMOL] Accessing progress bar

ers feedback on progress. > > Thanks, > 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 _

Re: [PyMOL] restricting selection to the current frame

could you elaborate on the "bymol" 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 Bau

Re: [PyMOL] trouble with sym exp

; I wonder if this is a problem of pymol? Can I feed it the symmetry > operators instead? -- Thomas Holder PyMOL Developer Schrödinger Contractor -- This SF.net email is sponsored by Windows:

Re: [PyMOL] pymol movie

substrate. I have solved 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 Holde

Re: [PyMOL] How Pymol reads a dcd file

ng me some helping material or a script. > Thank you > > Hira Batool > Student of BS-Bioinformatics > Biosciences Department > COMSATS Institute of Information Technology > Islamabad, PAKISTAN -- T

Re: [PyMOL] Pymol Library Script: findSurfaceResidues

x27;findSurfaceResidues3' >>>> PyMOL>run findSurfaceResidues3.txt >>>> Traceback (most recent call last): >>>> File >>>> "/Volumes/Data/scm/vikki/bld/MacPyMOL.app/pymol/modules/pymol/parser.py", >>>> line 338, in parse >

Re: [PyMOL] Pymol and load_traj

ding code is essentially taken from VMD). > > The issue 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 > usin

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

e unpleasant optical 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 De

Re: [PyMOL] Graphically attaching particles to proteins

cript, that already does something > along these lines? > > Thanks, M.A. -- Thomas Holder PyMOL Developer Schrödinger Contractor -- See everything from the browser to the database with AppDynamics Get end

Re: [PyMOL] Reducing the surface rendering load for JSmol export

he settings without success. >> >> Any advice would be most welcome. >> Best regards >> Nick -- Thomas Holder PyMOL Developer Schrödinger Contractor -- See everything from the browser to the data

Re: [PyMOL] get coordinate

ate of a selected atom? > > 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 applicat

Re: [PyMOL] caver plugin

> should I input the following command? > > chain A and resid 21 and CA > > But this is wrong and does not work. > > Could someone give me some tutorial? Thanks. > > Yeping Sun -- Thomas Holder PyMOL Developer Schrödinger Contractor -

Re: [PyMOL] Residue numeration problem

ainging to Hybrid) often, but not always, works. > Still is a pain in the back. > > Any clues? > > cheers, > > Gianluigi -- Thomas Holder PyMOL Developer Schrödinger Contractor -- See ever

Re: [PyMOL] Residue numeration problem

t; some reason it have been kept by pymol. > > cheers, > > Gianluigi > > -------- > Da: Thomas Holder > A: Gianluigi Caltabiano > Cc: pymol-users > Inviato: Martedì 23 Luglio 2013 9:27 > Oggetto:

Re: [PyMOL] pymol fails to compile

‘normalValsDA’ may be used uninitialized in > this function > layer1/CGO.c:3372: warning: ‘pickColorValsDA’ may be used uninitialized > in this function > layer1/CGO.c: In function ‘CGORenderRay’: > layer1/CGO.c:6185: warning: ‘vertexVals’ may be used uninitialized in > this fu

Re: [PyMOL] pymol fails to compile

numpy issue fixed in svn r4036. Cheers, Thomas Thomas Holder wrote, On 07/23/13 11:18: > Hi Andreas, > > I recently made a small change regarding numpy support. Can you please > send me the output of the following command: > > ls /usr/lib64/python2.6/site-packages/numpy/

Re: [PyMOL] importing openGL stream into Pymol

sing 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 S

<    1   2   3   4   5   6   7   8   9   10   >