Re: [PyMOL] scenes and states

? If so, how is that set up? How is that then incorporated into a scene? Do CGO, measurements, mesh, and volume objects have states as well? Bob -- Thomas Holder PyMOL Developer Schrödinger Contractor -- Get 100

Re: [PyMOL] defer_builds_mode

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, Daniel -- Thomas Holder PyMOL Developer Schrödinger Contractor -- Try

Re: [PyMOL] Label by selection identifier

? Jordan -- Thomas Holder PyMOL Developer Schrödinger Contractor -- Try New Relic Now We'll Send You this Cool Shirt New Relic is the only SaaS-based application performance monitoring service that delivers powerful

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

)\DeLano Scientific\PyMOL/modules\psico\fullinit.py, line 10 from . import init ^ SyntaxError: invalid syntax What's wrong ? Thanks for your help Stephane -- Thomas Holder PyMOL Developer Schrödinger Contractor

Re: [PyMOL] Secondary structure labeling

Pymol. I have them defined in my header file using DSSP. Thank you in advance. Bishwa Subedi -- Thomas Holder PyMOL Developer Schrödinger Contractor -- Learn Graph Databases - Download FREE O'Reilly Book Graph

Re: [PyMOL] Pymol error

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 help. Rhitankar On Sat, May 4, 2013 at 6:21 AM, Thomas Holder wrote: Hi Rhitankar, looks like you installed the python3 version of Pmw which

Re: [PyMOL] Pymol error

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 PyMOL was always targeted to power-users who are familiar with compiling

Re: [PyMOL] Secondary structure labeling

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 Holder wrote: Hi Bishwa, can you be more precise what you mean by label? If the secondary structure

Re: [PyMOL] Pymol error

of Chemistry, Yale University New Haven, CT 06511 -- Thomas Holder PyMOL Developer Schrödinger Contractor -- Get 100% visibility into Java/.NET code with AppDynamics Lite It's a free troubleshooting tool designed

Re: [PyMOL] extra bonds

=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 Developer Schrödinger Contractor

Re: [PyMOL] Transparency of VASCo surfaces

2011 (Pymol Hybrid). Am I missing something? thanks and regards Gianluigi -- Thomas Holder PyMOL Developer Schrödinger Contractor -- Try New Relic Now We'll Send You this Cool Shirt New Relic is the only SaaS-based

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

], glycan* PyMOLiterate_state 1, glycan* and id 1, print x, y, z 2.96896576881 2.08610153198 -0.626740753651 IterateState: iterated over 1 atom coordinate states. -- Thomas Holder PyMOL Developer Schrödinger Contractor

Re: [PyMOL] CGO fixed in space

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 Holder PyMOL Developer Schrödinger Contractor

Re: [PyMOL] Reset Default Carbon Color

. -- Thomas Holder PyMOL Developer Schrödinger Contractor -- Precog is a next-generation analytics platform capable of advanced analytics on semi-structured data. The platform includes APIs for building apps and a phenomenal

Re: [PyMOL] conect records?

(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 -- Precog is a next-generation

Re: [PyMOL] export sequence alignment

alignment. Other tools maybe? I have mustang already Cheers Joel -- Thomas Holder PyMOL Developer Schrödinger Contractor -- Minimize network downtime and maximize team effectiveness. Reduce network management

Re: [PyMOL] movie for morphing

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 -- Minimize network

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

/index.php/Get_raw_distances See also: http://pymolwiki.org/index.php/Distance Hope that helps. Cheers, Thomas -- Thomas Holder PyMOL Developer Schrödinger Contractor -- Minimize network downtime and maximize team

[PyMOL] PyMOL Testing Framework

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 Contractor

Re: [PyMOL] loadDir script

? James -- Thomas Holder PyMOL Developer Schrödinger Contractor -- Minimize network downtime and maximize team effectiveness. Reduce network management and security costs.Learn how to hire the most talented Cisco Certified

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

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. Thanks, Matt -- Thomas Holder PyMOL Developer Schrödinger Contractor

Re: [PyMOL] Color changes during a morph

,newcolor, resi 430:572, a) cmd.recolor() ugly, I know! this is 64 bit pymol 1.5.0.6 eval for linux. Thanks in advance, Max -- Thomas Holder PyMOL Developer Schrödinger Contractor -- Own the Future-Intelreg

Re: [PyMOL] PyMOL 1.6 pre-release announcement

, 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 improvements, this version should complete

[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 mba...@debian.org wrote: Hi, On Sun, Mar 24, 2013 at 11:02:08AM +0100, Thomas Holder

Re: [PyMOL] Mesh Cavity Mode?

with mesh? Thanks in advance for responses. Cheers, Jared -- Thomas Holder PyMOL Developer Schrödinger Contractor -- Everyone hates slow websites. So do we. Make your web apps faster with AppDynamics Download

Re: [PyMOL] (no subject)

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 web apps faster

Re: [PyMOL] Error while running a python script

if (thread.get_ident() == pymol.glutThread): AttributeError: 'module' object has no attribute 'glutThread' Bharat -- Thomas Holder PyMOL Developer Schrödinger Contractor -- Everyone hates slow websites. So do we. Make

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

.__init__() argument 1 must be string, not instance Error: unable to initialize plugin 'movs'. I guess there is something wrong with the code but this seems strange. It looks o.k. Thanks. -Yarrow -- Thomas Holder PyMOL Developer Schrödinger Contractor

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

system, or use it to clip a system multiple times from different sides. # Enjoy! # Cheers, # Tsjerk -- Thomas Holder PyMOL Developer Schrödinger Contractor -- Symantec Endpoint Protection 12 positioned

Re: [PyMOL] refinement in morph

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. --Jianghai -- Thomas Holder PyMOL Developer Schrödinger Contractor

Re: [PyMOL] running pse file in batch mode

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 Tel: (+44) - 1865 - 287561, FAX: (+44) - 1865 - 287547 -- Thomas Holder PyMOL

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

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 -- Everyone hates slow websites. So do

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

CHINESE ACADEMY OF SCIENCES NO.1 Beichen West Road,Chaoyang District,Beijing 100101,china -- Thomas Holder PyMOL Developer Schrödinger Contractor -- Everyone hates slow websites. So do we. Make your web apps faster

Re: [PyMOL] Increase sphere size for heavy element

is drawn with a very small radius. Can this radius be increased? Thanks Martin -- Thomas Holder PyMOL Developer Schrödinger Contractor -- Everyone hates slow websites. So do we. Make your web apps faster

Re: [PyMOL] Display style for partial bond

-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 -- Thomas Holder PyMOL Developer Schrödinger Contractor

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

atoms, but in different molecules. Cheers, Rob -- Thomas Holder PyMOL Developer Schrödinger Contractor -- Everyone hates slow websites. So do we. Make your web apps faster with AppDynamics Download AppDynamics Lite

Re: [PyMOL] constant distances over states

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 -- Everyone hates slow websites. So do we

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

:#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 -- The Go Parallel Website

[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

Re: [PyMOL] Path problem when running a script

obvious reason why it's not looking in the /opt/pymol/scripts directory, even when this is in the sys.path? Thanks, Jens -- Thomas Holder PyMOL Developer Schrödinger Contractor -- Free Next-Gen Firewall Hardware Offer

Re: [PyMOL] problem setting up morph under eMovie

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 -- Free Next-Gen Firewall Hardware Offer

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

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 -- Free Next-Gen Firewall Hardware Offer Buy your Sophos next-gen

Re: [PyMOL] default settings

: invalid syntax That's because you're using the wrong file name: On a linux-type system, this file will be located in /path/to/home/.pymolrc. -Nat -- Thomas Holder PyMOL Developer Schrödinger Contractor -- Everyone

Re: [PyMOL] Hight-quality visualisation

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#Modes James -- Thomas Holder PyMOL Developer

Re: [PyMOL] Saving setting in PyMol

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 James -- Thomas Holder PyMOL Developer

Re: [PyMOL] echo colour

: jtyndall Ph: +64 3 479 7293 -- Thomas Holder PyMOL Developer Schrödinger Contractor -- Master Visual Studio, SharePoint, SQL, ASP.NET, C# 2012, HTML5, CSS, MVC, Windows 8 Apps, JavaScript and much more. Keep your skills

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

# prints righteous file name and selection name (though not in quotes) cmd.save(tempFile.name, Selection) # but still saves nothing cmd.extend(bk_saves_unique_pdb, bk_saves_unique_pdb) -- Thomas Holder PyMOL Developer Schrödinger Contractor

Re: [PyMOL] Renumber Script problem

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, Alex -- Thomas Holder PyMOL Developer Schrödinger Contractor

Re: [PyMOL] Renumber Script problem

: residue.id=(' ',residue_id,' ') residue_id +=1 io=PDBIO() io.set_structure(struct) io.save(args[1]) if __name__ == __main__: main() -- Thomas Holder PyMOL Developer Schrödinger Contractor

Re: [PyMOL] DNA ligand presentation in PyMOL

/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 -- Master Visual Studio

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

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. Regards Tasneem -- Thomas Holder PyMOL Developer Schrödinger Contractor

Re: [PyMOL] DNA measurement help require by sculptor

mobile: +44 (0)7956 107 893 Pangolin London Sculptor in Residence blog: www.a-n.co.uk/link/creative-year http://www.a-n.co.uk/link/creative-year -- Thomas Holder PyMOL Developer Schrödinger Contractor -- Master SQL

Re: [PyMOL] Pymol visualization problem

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 -- Thomas Holder PyMOL Developer Schrödinger Contractor

Re: [PyMOL] Building of the Carbon lattice

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 numpy import array s = 'HETATM %4d C03 UNK

Re: [PyMOL] Regarding electrostatic potential mapping

, 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 -- Master HTML5, CSS3

Re: [PyMOL] Building of the Carbon lattice

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 for later extensions. Thanks. -- Thomas Holder PyMOL Developer

Re: [PyMOL] which code actually executes to load axplor file? Debugstatements not executing.

some rendering (I have an old viewer I wrote with glut and thought I may be able to salvage parts of that for use here). Thanks. -- Thomas Holder PyMOL Developer Schrödinger Contractor -- Master Visual Studio

Re: [PyMOL] test for bonded atom

hbonds, all, all, mode=2 There is no direct way to list these pairs, but you can use get_raw_distances script from the PyMOLWiki: http://pymolwiki.org/index.php/Get_raw_distances Hope that helps. Cheers, Thomas -- Thomas Holder PyMOL Developer Schrödinger Contractor

Re: [PyMOL] can not label my selection, very weird

to 117.74000). Selector: selection t0 defined with 7 atoms. Executive: Colored 7 atoms. File string, line 1 label=test message; save t0.pse; ^ SyntaxError: invalid syntax Label: labelled 0 atoms. -- Thomas Holder PyMOL Developer Schrödinger Contractor

Re: [PyMOL] Memory not released after load and delete of structure

Modeling Product Management Schrödinger, Inc. (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- Thomas Holder PyMOL Developer Schrödinger Contractor -- LogMeIn Rescue: Anywhere, Anytime Remote support

Re: [PyMOL] setting the cutoff radius that determines when atoms are bonded

the entire movie, even if atoms move further apart than the cutoff. Is my perception correct here? If so, can I make the bonds be calculated for each frame? -- Thomas Holder PyMOL Developer Schrödinger Contractor

Re: [PyMOL] Possible (minor) bug

Skype: jtyndall Ph: +64 3 479 7293 -- Thomas Holder PyMOL Developer Schrödinger Contractor -- Keep yourself connected to Go Parallel: BUILD Helping you discover the best ways to construct your parallel projects

Re: [PyMOL] pymol contact_map_visualizer plugin

-compiled_PyMOL Cheers, Thomas Ban Arn wrote, On 11/26/12 18:10: Dear Thomas Which version of pymol has python 2.7. Is it free for academics or I have to purchase license from schrodinger. Kindly advice. Many Thanks Balaji -- Thomas Holder PyMOL Developer Schrödinger Contractor

Re: [PyMOL] morphing 3-states

to morph 3 conformations. Morpheasy works fantastic for two conformations, and this makes around 80 frames. I can then reinitialize and do the other two states. I have no idea how to link the two. Does anyone have any ideas or documentation on this? Thanks, Jordan -- Thomas Holder PyMOL

Re: [PyMOL] was: Mobile PyMOL Problem and Solution/ Now: pdb or related libraries

from various locations or do you just have an interface for pdb.org? Besides deciding on what to eat today, I was curious if pymol has more generalized means of finding structure files. Thanks. note new address Mike Marchywka 2295 Collinworth Drive Marietta GA 30062. -- Thomas Holder

Re: [PyMOL] MacPyMOL 1.4 vs 1.5 problem with color

- Thanks in advance for the help! H. Adam Steinberg 7904 Bowman Rd Lodi, WI 53555 608/592-2366 -- Thomas Holder PyMOL Developer Schrödinger Contractor -- Monitor your physical, virtual and cloud

Re: [PyMOL] Peptide location mapping onto protein 3D structure

these tasks with Pymol or is there any other software I could be using? Thanks very much for your help, Cheers Sri -- Thomas Holder PyMOL Developer Schrödinger Contractor -- Monitor your physical, virtual and cloud

Re: [PyMOL] Controlling colors in volume object

colors to different regions of density systematically (the Volume-GUI is great, but somewhat tricky to make quick changes with), and display the result on screen. Is such a thing possible? Thanks /Per -- Thomas Holder PyMOL Developer Schrödinger Contractor

Re: [PyMOL] assigning secondary strux to artificial AAs

! -Johnny -- Thomas Holder PyMOL Developer Schrödinger Contractor -- Monitor your physical, virtual and cloud infrastructure from a single web console. Get in-depth insight into apps, servers, databases, vmware, SAP

Re: [PyMOL] fuse two proteins by a peptide bond

, but I really don't know how to do this step. I really appreciate your help! -- Thomas Holder PyMOL Developer Schrödinger Contractor -- Monitor your physical, virtual and cloud infrastructure from a single web console

Re: [PyMOL] Field lines representation

/apbs/examples/visualization/apbs-electrostatics-in-vmd ) Thanks. -- Thomas Holder PyMOL Developer Schrödinger Contractor -- Monitor your physical, virtual and cloud infrastructure from a single web console. Get in-depth

Re: [PyMOL] selecting certain residues within X angs of a point/residue

Hi John, here is something to start with: # put everything in state 1 (convert states to objects) split_states capsid delete capsid # specify the fixed residue select fixedresidue, capsid_0001 and chain D and resi 30 # select residues of interest within given radius select s1, chain A+B+C and

Re: [PyMOL] Fwd: contact_map_visualizer pymol plugin

* * finally:* * ^* * SyntaxError: invalid syntax* Could you please help me to sort out this error. Kindly advice. Many Thanks Balaji -- Thomas Holder PyMOL Developer Schrödinger Contractor -- Monitor your

Re: [PyMOL] Angle between two structure upon alignment

Hi Appu, if I understand you correct then you have a structure with at least two domains. If you align two conformations of that structure, one domain does not get superposed nicely. Right? The psico module provides the command angle_between_domains, which is what you are looking for I guess.

Re: [PyMOL] visualise NOEs

that it is recognised? Thanks in advance, regards, Krisztina -- Thomas Holder MPI for Developmental Biology Spemannstr. 35 D-72076 Tübingen plot_noe.py Description: application/chimera -- Everyone hates slow websites. So

Re: [PyMOL] visualise NOEs

Feher wrote: Sure, thanks for looking at it! Krisztina --- On *Mon, 10/29/12, Thomas Holder wrote: From: Thomas Holder spel...@users.sourceforge.net Subject: Re: [PyMOL] visualise NOEs To: Krisztina Feher feher_kriszt...@yahoo.com Date: Monday, October 29, 2012, 4:04 PM Hi

Re: [PyMOL] red_white_blue palette color bar

for red_white_blue? Thank you very much! yamei -- Thomas Holder MPI for Developmental Biology Spemannstr. 35 D-72076 Tübingen -- The Windows 8 Center - In partnership with Sourceforge Your idea - your app - 30 days. Get

Re: [PyMOL] Custom menus and shortcuts?

bk_toggles_W (): Hides W molecules. if stored.bk_toggles_W: cmd.hide(all) cmd.show(spheres, not (resn W)) stored.bk_toggles_W = 0 else: cmd.show(spheres, resn W) stored.bk_toggles_W = 1 Cheers, Thomas -- Thomas Holder MPI

Re: [PyMOL] How to rotate entire section of structure relative to rest

swing that section out and away from its current position? I'll deal with the positions of those individual residues if this cannot method cannot resolve my problem. Thanks, Alex -- Thomas Holder MPI for Developmental Biology Spemannstr. 35 D-72076 Tübingen

Re: [PyMOL] Tab completion using object names, not filesystem files?

, it would do what I'm looking for. Any ideas on the best way to do that? Best, -Ron -- Thomas Holder MPI for Developmental Biology Spemannstr. 35 D-72076 Tübingen -- Everyone hates slow websites. So do we. Make your

Re: [PyMOL] Make sure zoom is viewed from surface

, is viewed from outside the protein for each residue/.png file? Best Troels Emtekær Linnet Ved kløvermarken 9, 1.th 2300 København S Mobil: +45 60210234 -- Thomas Holder MPI for Developmental Biology Spemannstr. 35 D-72076 Tübingen from pymol import cmd, CmdException def zoomoutside(selection, ref

Re: [PyMOL] bond connection file

multiple frame (using MODEL and ENDMDL), the connections which i specified in the first frame is retained for rest of the frames. Am I doing some mistake in the way I wrote my PDB file? Regards Vishwas 2012/10/4 Thomas Holder spel...@users.sourceforge.net mailto:spel

Re: [PyMOL] bond connection file

some example .mol file), but particles are overlapping on each other. Can somebody suggest me a better way to feed in coordinates and bonding information to pymol. Regards Vishwas -- Thomas Holder MPI for Developmental Biology Spemannstr. 35 D-72076 Tübingen

Re: [PyMOL] PyMOL Model player

:31 PM, Martin Hediger wrote: Dear PyMOL Users Is it possible to let the PyMOL model player go back and forward, instead of jumping from the end to the start, once it reached the last loaded model of an object? Thanks for hints. Martin -- Thomas Holder MPI for Developmental Biology

Re: [PyMOL] Doubt with using APBS electrostatics in PyMOL

, On 10/02/12 18:36: Hi When I load the pqr file of the structure in PyMOL for creating the electrostatic surface using APBS, I see the distorted structure. I have generated this site using the PDB2PQR module at http://nbcr-222.ucsd.edu/pdb2pqr_1.8/ Can someone explain why it is so. -- Thomas

Re: [PyMOL] Adding hydrogens

to the beginning of the PDB file. Can PyMOL be configured such that the hydrogens are placed at the intuitively appropriate place in the PDB file? Thanks for any hints. Martin -- Thomas Holder MPI for Developmental Biology Spemannstr. 35 D-72076 Tübingen

Re: [PyMOL] Label entire movie

Hi Anke, Rasbach, Anke wrote, On 09/24/12 13:08: [...] Is it also possible to change font and box color? no, that's not possible. The colors are hard-coded. Cheers, Thomas -- Thomas Holder MPI for Developmental Biology Spemannstr. 35 D-72076 Tübingen

Re: [PyMOL] Label entire movie

,z position? Or an easy way to move the pseudoatom accordingly? Thanks Anke -- Thomas Holder MPI for Developmental Biology Spemannstr. 35 D-72076 Tübingen -- Got visibility? Most devs has no idea what

Re: [PyMOL] question

in the peptide structure in pymol? you can add labels to atoms. So to label each residue with its name (resn), just label all CA atoms: PyMOL label name CA, resn Cheers, Thomas -- Thomas Holder MPI for Developmental Biology Spemannstr. 35 D-72076 Tübingen

Re: [PyMOL] movie help, rotating around an objects own center of mass.

understand you can supply an axis vector, but I have no idea how to do this. Essentially I want to do what movie.roll would do, but just to one object independently of the entire scene. Jordan -- Thomas Holder MPI for Developmental Biology Spemannstr. 35 D-72076 Tübingen

Re: [PyMOL] movie help, rotating around an objects own center of mass.

be much appreciated! Thanks, Jordan -- Thomas Holder MPI for Developmental Biology Spemannstr. 35 D-72076 Tübingen reinitialize set matrix_mode, 1 set movie_panel, 1 set scene_buttons, 1 set cache_frames, 1 set movie_auto_interpolate, off config_mouse three_button_motions, 1 python import glob, os

Re: [PyMOL] Question about mutagenesis wizard

Biociências Universidade Federal do Rio Grande do Sul - Campus do Vale Av. Bento Gonçalves, 9500 - Bairro Agronomia - Prédio 43323 M CEP:91501-970 Caixa Postal 15053 Porto Alegre, RS, Brasil Tel: +55 51 3308 9938 tel:%2B55%2051%203308%209938 -- Thomas Holder MPI

Re: [PyMOL] how to create a custom rainbow according to residue number

of residue number in Pymol ? Best Afonso ### Afonso Duarte ITQB-UNL Portugal -- Thomas Holder MPI for Developmental Biology Spemannstr. 35 D-72076 Tübingen -- Live Security Virtual Conference Exclusive

Re: [PyMOL] PyMOL Visualization Query

any patterns in the occurrence of charge throughout the transmembrane region of receptor proteins. Many thanks in advance. Regards, Spyros Charonis -- Thomas Holder MPI for Developmental Biology Spemannstr. 35 D-72076 Tübingen

Re: [PyMOL] colouring states independently

) cmd.scene(name,store) cmd.mview('store',name) One last thing, the number of particles is not the same for every state. I hope somebody can help me. Thanks, John -- Thomas Holder MPI for Developmental Biology Spemannstr. 35 D-72076 Tübingen

Re: [PyMOL] APBS problem

would be solved. Has anyone ever encountered this problem, and is there a simple solution in PyMol to adjust the coordinates and then save a simple PDB file with the corrected values? Thanks, Warren Gallin -- Thomas Holder MPI for Developmental Biology Spemannstr. 35 D-72076 Tübingen

Re: [PyMOL] pymol plugin with subprocess thread

you again for your help, Ed' On Tue, Aug 28, 2012 at 5:48 PM, Thomas Holder spel...@users.sourceforge.net mailto:spel...@users.sourceforge.net wrote: Hi Ed, this is possible. Example: def foo(a, b, c): command = ./myprogramm arg1 arg2 process

Re: [PyMOL] Ca sphere size from b-factor value

size) and also color the sphere based on the b-factor value. Is there an easy way to adjust the sphere size according to b-factor value? Thanks, Doug -- Jason Vertrees, PhD PyMOL Product Manager Schrödinger, LLC (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- Thomas

Re: [PyMOL] weird distance measurements when pdb file contains symmetric atoms

activated. Any ideas ? Thanks a lot, Pascal -- Thomas Holder MPI for Developmental Biology Spemannstr. 35 D-72076 Tübingen -- Live Security Virtual Conference Exclusive live event will cover all the ways today's

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