Re: [PyMOL] default water bond lengths in PyMOL

a hydrogen given a separate residue number). I > am assuming that PyMOL assigns bonds based on distance between atoms, is > there a way to minimize this? The RCSB doesn't like my current PDB file! > > Thanks, Tom Pochapsky -- Thomas Holder Py

Re: [PyMOL] aligned and cealign command

ve similar fold. I am interested to know, how much > degree the subunits move or rotate when we aligned the chain A with cealign > command. > best > Jiri -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc.

Re: [PyMOL] Middle mouse button in Mac Pymol does not work?

akes any sort of > docking much more difficult. > > Also, is there a guide to what all the Mouse Mode commands actually do? MvAZ? > MvSZ? PkTB? DrgM? > > -- > Jason D. Kahn > Dept. of Chemistry and Biochemistry > University of Maryland &g

Re: [PyMOL] difficulty opening EmrE protein (pdb: 3B5D) in Pymol

gt; opens up as many little cross signs seem to be corresponding to CA atoms. > When I try to preset it pretty or any other preset options, it disappears. > The command "show cartoon" is not doing anything on it. > > Cheers > Mohsen > > ___

Re: [PyMOL] PDB Format not correct for use in CHARMM

idue are mixed up. It also added >> addition TER's which I had to manually delete. >> >> So how would I specify the output PDB format to be the same as in the >> original im

Re: [PyMOL] selection coloring in ribbon

Hi Yuxing, We have released Incentive PyMOL 1.8.4.1, which fixes the ribbon coloring issue. Cheers, Thomas On 21 Nov 2016, at 15:57, Thomas Holder <thomas.hol...@schrodinger.com> wrote: > Hi Yuxing, > > Thanks for reporting this. Yes it's a bug, luckily with a simple fix. We

Re: [PyMOL] selection coloring in ribbon

due prior to the N-terminal of the selection). Is this a bug? > > Thanks. > > Yuxing > > UT Southwestern > > Medical Center > > The future of medicine, today. --

Re: [PyMOL] Adding a new internal GUI to Pymol for Leap motion support

nu or > adding > an external window that will run alongside Pymol representing a menu, > and adding in our own attributes? > > Thanks in advance, > > Casper Peters and Johan Shcneiders. > > P.S. > Here are our e-mail addresses for contacting us: > Casper P

Re: [PyMOL] Compile error svn 4162

; of member 'm_i' > layer3/CifDataValueFormatter.h:20:13: error: making 'm_i' static > layer3/CifDataValueFormatter.h:20:13: error: ISO C++ forbids in-class > initialization of non-const static member 'm_i' > > g++ version 4.5.1 > > Do you have any advise on how to get past this

Re: [PyMOL] pymol in pthyon get_wizard() problems

a python novice so please excuse me if this is something simple. Here is >> a line that I have in my script that is giving me an error, which is now >> quite long so I don't want to post it all here now: >> --- >> pymol.cmd.get_wizard(

Re: [PyMOL] problem of optirun in Pymol

ol > > Pymol doesn't start and I didn't get any error messages from terminal > either. > > I am just wondering how can we solve the problem? > > Thx a lot > > Albert -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc.

Re: [PyMOL] problem of internal_gui

.. > > I am just wondering how to solve this problem? I am using PyMOL-1.8.2.3. > > I also tested in the latest 1.8.4, it has the same issue. > > Thank you very much. > > Albert -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. -

[PyMOL] PyMOL 1.8.4 released

- display_scale_factor: Internal GUI scaling for 4K and Retina displays Find the complete release notes at: http://pymol.org/d/media:new184 We welcome any feedback and bug reports. Cheers, - The PyMOL Team at Schrödinger -- Thomas Holder PyMOL

Re: [PyMOL] regarding pymol plugin windows

ong and hence can not see the one listed > at the end. Is there a way to reorganise the list of plugins in the plugin > window of pymol or have a scroll bar to browse downwards. > > Thank you > > Best Regards > Priyan -- Thomas Hol

Re: [PyMOL] Error whle running pymol

pen shared object > file: No such file or directory" > > I am using CentOS 7 running work station. I have tried sym linking and tried > copying the libXss.so.1 file to the pymol folder. > Please help me in solving the problem. > > Thanks in advance. > Vija

Re: [PyMOL] how to hide dashed artificial cartoon?

w my structure as cartoon, there would be a > "dashed loop" cartoon filling in the missing part of my structure. I am > just wondering how can we disable PyMol show the missing part automatically? > > Thank you very much > > Albert -- Tho

Re: [PyMOL] Pymol Command window not displaying

> in __init__ > self.tk = _tkinter.create(screenName, baseName, className, interactive, > wantobjects, useTk, sync, use) > TclError: invalid command na

Re: [PyMOL] pymol alignment help

ment. > Thanks in advance. > > Clarisa. -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. -- ___ PyMOL-users mailing list (PyMOL-users@lists

Re: [PyMOL] Plugin menu options and measuring protein cavity volumes in PyMol

s any info on how to > measure cavity volumes in a protein structure by PyMOL with standard > commands, I would appreciate it. > Thanks, > Tom Pochapsky -- Thomas Holder

Re: [PyMOL] dump_binary and PyMOL 1.8 PSE files

) > 119-120 (2 char for Chain) > 121 stereo > 123 chemFlag > 123 protekted > > I need this to end at 119, not 123, to be consistent with the pickle data. -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. -

Re: [PyMOL] dump_binary and PyMOL 1.8 PSE files

segi; > lexidx_t chain; > lexidx_t resn; > lexidx_t name; > lexidx_t textType; > lexidx_t custom; > lexidx_t label; > ... > > What am I missing? You're looking at the wrong struct. When doing the binary dump, structs from layer2/AtomInfoHistory.h are used. See https://

Re: [PyMOL] dump_binary and PyMOL 1.8 PSE files

I'm looking at a file that lists the dump version > as 1.8.1, but I don't even see how that would ever work, since in that > AtomInfo structure the ANISOU data is just a 64-bit pointer. That would end > up just a useless reference, wouldn't it? > > On Mon, Aug 8, 2016

Re: [PyMOL] dump_binary and PyMOL 1.8 PSE files

swer first what we want, > it is better to take what answer we get. > > -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. -- __

Re: [PyMOL] Color residue in cartoon mode

ticks and then change the color of the sticks. But that’s >> not what I need! >> >> Do you have any ideas how to display the desired nucleotide? >> >> Many thanks in advance, >> >> Maria > > H. Adam Steinberg > 7904 Bowman Rd >

[PyMOL] PyMOL 1.8.2.3 bugfix release

Greetings, PyMOL 1.8.2.3 fixes an annoying picking bug, where picking atoms with the mouse can select the wrong atoms. If you use Incentive PyMOL 1.8.x, we recommend to upgrade. Builds are available as usual from http://pymol.org/download Cheers, - The PyMOL Team at Schrödinger -- Thomas

Re: [PyMOL] Grammar for PyMOL selection algebra

he language available in for example as context-free grammar. > I was trying to find something in the source code rather unsuccessfully. > > All the best > > Lukas Pravda > > CEITEC | Central European Institute of Technology > http://webchem.ncbr.muni.cz/ -- Thomas Hold

Re: [PyMOL] Structural matching of Side-chain selection

ay &! n. n+ca+c+o > select md &! n. n+ca+c+o > > now trying to align both objects with any method I obtain error like > > PyMOL>super obj01, obj02 > ExecutiveAlign: invalid selections for alignment. >

Re: [PyMOL] Corrupted/too large MacPymol Files

ated. > > > Thanks, > > Angelica -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. -- Attend Shape: An AT Tech Expo July 15-16. Meet us at AT Park in San Francisco, CA to explore cutting-edge tech

Re: [PyMOL] Selective valency on bond

' onto a single > bond, or is it a global command which is not capable of this fine-tuning? I > am using MacPyMol if this makes a difference at all? > > Thanks for your help, > Patrick -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. --

Re: [PyMOL] Details of the morph interpolation?

as the single letter code. With the BLOSUM62 matrix, X matched to X has a score of -1 (penalty). In theory you could modify the file /Applications/MacPyMOL.app/Contents/pymol/data/pymol/matrices/BLOSUM62 and change the X/X score to 1, then PyMOL will align the FE atoms. > Thank you for your time,

Re: [PyMOL] Details of the morph interpolation?

-users@lists.sourceforge.net/msg00359.html > In other words, refinement is not done on the basis of energy differences, > Ramachandran plot, interatomic clashes, or other problems with geometry that > could arise at each interpolation step. > > Is that correct? If so, is there a way t

Re: [PyMOL] Numpy in incentive pymol

t; > -- > Filip Leonarski, PhD > IBMC/CNRS > 15 rue René Descartes > 67084 Strasbourg Cedex -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. -- What NetFlow Analyzer can do for you? Monitors n

Re: [PyMOL] post-processing of pdb ensemble

mation regarding chain letters (which was lost > > after some operations on pdbs) for all of those structures assuming > > that within each of these pdbs residues are ordered correctly e.g from > > (1-104 which > > should be chain A) than from 1-100 (it should be chain B), th

Re: [PyMOL] pymol plugins Problem

'tconcoord' (pmg_tk.startup.tconcoord). > > Unable to initialize plugin 'align_all' (pmg_tk.startup.align_all). > > Regards > > RP -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. -- Mob

Re: [PyMOL] High Resolution Ray Tracing

no difference. > > Is there anything else I can try to successfully output such a large image? > > ____ > From: Thomas Holder <thomas.hol...@schrodinger.com> > Sent: 10 May 2016 20:34:44 > To: harold steinberg > Cc: Stephen Kerry

Re: [PyMOL] High Resolution Ray Tracing

es the vertical dpi >> by four. > > H. Adam Steinberg > 7904 Bowman Rd > Lodi, WI 53555 > 608/592-2366 -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. -- Mobile security can be enabl

Re: [PyMOL] How to attach the command area to the viewing area in pymol for windows

. > > Please see images below for reference. > > In windows 7 > http://s32.postimg.org/mrhxqcox1/pymol_PNG_in_windows7.png > > In mac > http://s32.postimg.org/cbczjm1wl/pymol_macosx.png > > > Thanks for your help

Re: [PyMOL] query

t;> your problem. >> >> Cheers. >> >> On Wed, Apr 27, 2016 at 6:15 PM, ankita mehta <mehtaroad...@gmail.com> wrote: >> Hii, >> I want to save the image in pymol >> I am using white background but it gives me dull colouring of the protein >>

Re: [PyMOL] strange mouse button problem since version 1.8 with PyMOL for Linux

ia remote login > (X-windows-powered SSH), which might indicate a local graphics/mouse > driver problem? > > Any comments are welcome! > > Thanks, > Christoph -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. --

Re: [PyMOL] morph issues

>>>>>> Message: 6 >>>>>> Date: Mon, 25 Apr 2016 20:54:01 -0500 >>>>>> From: harold steinberg <h.adam.steinb...@gmail.com> >>>>>> Subject: [PyMOL] morph issues >>>>>> To: pymol-users <pymol-users@lists.sour

Re: [PyMOL] Autosave session Pymol

if this would be interesting/useful for anybody and a >> question to the developers if this can be implemented? >> >> Best regards, >> Matic -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. -

Re: [PyMOL] Dynamic reloading of plugin

rytime i save > it? > > Thanks and best regards > Martin > > -- > Martin R. Hediger, PhD > Mittlere Strasse 65 > 4056 Basel -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. -- Find

Re: [PyMOL] ccmutate

s/Python.framework/Versions/2.7/lib/python2.7/site-packages/pymol/importing.py", > line 1263, in _fetch > raise ValueError('type') > ValueError: type > > > What could be going on? The PyMOL mutagenesis wizard in any case works when I > do the mutation by hand. &g

[PyMOL] PyMOL 1.8.2 released

y feedback and bug reports. Cheers, - The PyMOL Team at Schrödinger -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. -- Find and fix application performance issues faster with Applications Manager Applicat

Re: [PyMOL] selecting faces and vertices in CGOs

EPSRC Research Fellow, > Department of Physics and Astronomy, > University of Leeds > Tel: +44 (0)1133 431451 -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. -- Find and fix application perform

Re: [PyMOL] Cryo Maps - gaussian isosurface

sosurface the cryo map with the following: > isosurface mapname, EMD-6413, 4 (any number between 1-6) > > but that doesn’t allow me to apply the gaussian to the map… > > How do I create an isosurface with a gaussian? > > Thanks for any help, > > H. Adam Steinberg >

Re: [PyMOL] How to add multiline labels

to the next line? Any suggestions would be > highly appreciated. > > Regards, > > Amin. -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. -- Find and fix application performance issues faster with A

Re: [PyMOL] Text Font size

> size (viewport) and always draw the pretty rendering (cartoon, ligands, ..) > > > Thanks, > Abhinav > > Abhinav Kumar, PhD > Senior Scientist, Bioinformatics > Intrexon, Inc. > 329 Oyster Point Blvd., South San Francisco, CA 94080 > (650) 597-4072 | aku...@in

Re: [PyMOL] Text Font size

>> >> Thanks, >> Abhinav >> >> Abhinav Kumar, PhD >> Senior Scientist, Bioinformatics >> Intrexon, Inc. >> 329 Oyster Point Blvd., South San Francisco, CA 94080 >> (650) 597-4072 | aku...@intrexon.com -- Thomas Holder PyMOL Princ

Re: [PyMOL] Problem with ribbon

; Double click on the endpoints (to see the residue number) > > The one that should be 25, displays residue 20. > > Labels do show the correct residue numbers. > > Mark -- T

Re: [PyMOL] Problem with isomesh without map

do that. > > Is it possible to fix this one? > > Best, > Filip > > > -- > Filip Leonarski, PhD > IBMC/CNRS > 15 rue René Descartes > 67084 Strasbourg Cedex -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. -

Re: [PyMOL] The Wiki appears outdated or in error

l > or proprietary information. Any unauthorized review, use, disclosure or > distribution is prohibited. If you are not the intended recipient, > immediately contact the sender by reply e-mail and destroy all copies of the > original message. > > -Original Message- > Fro

Re: [PyMOL] The Wiki appears outdated or in error

und box from >> default COLLADA output and make it optional via a new >> `collada_background_box` setting. >> >> Sorry for the confusion, hope this clears it up. >> >> Cheers, >> Jared >> >> -- >> Jared Sampson >> Columbia University >> > > -

Re: [PyMOL] Morph DNA?

oes it only work with proteins? Both nucleotides > strings are ATOM (no HETEROATOM) and both are in the AGCT format, no DA DG DC > DT format. > > Does anyone know a program or web site that will morph DNA? > > Thanks, > > Adam

Re: [PyMOL] Problem with feedback push

print anything unless I > specifically re-enable all feedback after starting pymol (or use the unwieldy > `print cmd.get("var")`). Removing the feedback manipulation from my pymolrc > restores the expected output from get. Is this a bug with the feedback stack? > > -Spencer --

Re: [PyMOL] How to store matrix settings for individual scenes?

ever once the matrices are applied this also affects > the matrices for the scenes created previous to the overlay and matrix_copy. > Any way I can store the matrices in each scene instead of having them applied &

Re: [PyMOL] Immediately crashing

> Bundesministerium für Bildung und Forschung > Stellvertreter: MinDirig Rüdiger Eichel, Niedersächsisches Ministerium für > Wissenschaft und Kultur > Geschäftsführung: Prof. Dr. Dirk Heinz; Franziska Broer > Gesellschaft mit beschränkter Haftung (GmbH) > Sitz der Gesellschaft: Brau

Re: [PyMOL] auto_show_cartoon or similar

both options (attached). If > I leave all lines on it’s still a bit of a mess. I think it looks better with > all lines off. > > > > PM.pdf> > > > >> On Feb 8, 2016, at 1:29 PM, Thomas Holder <thomas.hol...@schrodinger.com> >> wrote: >&g

Re: [PyMOL] Selections don't work on structures loaded using 'fetch' command

results in 'selection "sele" defined >> with 0 atoms'. >> System is Linux. PyMOL is 1.7.7.2 version from svn. -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. -- Site24x7 APM Insight: Get

Re: [PyMOL] how to get an atom coordinates information

nformation of a specific atom. I am just > wondering how can we do this? Is there any command line? > > thank you very much > > Albert -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. -- Site24x7 APM Insight

Re: [PyMOL] PyMOL split_states error on [PDB: 1hho]

This is fixed in SVN rev 4150. Cheers, Thomas On 22 Feb 2016, at 05:53, Thomas Holder <thomas.hol...@schrodinger.com> wrote: > Hi all, > > The bug seems to be that the "pdb_insure_orthogonal" setting is only applied > to the first model. Turning the setting of

Re: [PyMOL] Problem aligning two structures: ExecutiveAlign-Error: atomic alignment failed (mismatched identifiers?)

. Does anybody understands what is happening here? > > Thank you very much, > > Max > > PS: If you need the PDB files let me know. I don’t know if this list acceptes > files -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. ---

Re: [PyMOL] PyMOL split_states error on [PDB: 1hho]

>>>>> From: Ioannis Michalopoulos <imicha...@bioacademy.gr> >>>>> Sent: Monday, February 22, 2016 3:39 AM >>>>> To: pymol-users@lists.sourceforge.net >>>>> Subject: [PyMOL] PyMOL split_states error on [PDB: 1hho] >>>>> >>>>>

Re: [PyMOL] How to tell from within a script if a plugin is loaded?

> script and not have it execute before the plugin finishes loading? >>> >>> I've tried something like this: >>> >>> ``` >>> import time >>> from pymol import cmd >>> loaded = 0 >>> while not loaded: >>> try: &g

Re: [PyMOL] visualizing a transparent surface within a transparent surface

w ligand surfaces that go into the protein disappear. > > > > How do I get the Ray quality and keep the ligand surface that is within the > > protein from disappearing? > > > > Hope I explained this well. > > BTW, surface mode is set to 1 to include all atoms >

Re: [PyMOL] Can't build trans peptides ?

olécules > normales et pathologiques > Université d'Evry-Val d'Essonne > Bâtiment Maupertuis > Rue du Père Jarlan > 91000 EVRY > FRANCE > Tél: +33 1 69 47 76 64 > FAX: +33 1 69 47 02 19 > e-mail charbel.mar...@inserm.fr -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc

Re: [PyMOL] weird behavior with renitialize

quot; in fetch or theunix "&&". > > Best regards, > > Blaine > > Blaine Mooers, Ph.D. > Assistant Professor > Director of the Laboratory of Biomolecular Structure and Function > Department of Biochemistry and Molecular Biology > University of Oklahoma Heal

Re: [PyMOL] ignore_case in next PyMOL version

uld want case-insensitive element symbols (ignore_case=off) > but case-sensitive chains (ignore_case_chain=on)? Are there other places > where case is important in the selections or structures (e.g. insertion > codes)? > > -Spencer > > On Tue, Feb 9, 2016 at 4:18 PM, Thom

Re: [PyMOL] ignore_case in next PyMOL version

Hi all, Quick update on the "ignore_case" issue: - ignore_case=on default restored in PyMOL 1.8.0.5 and latest SVN - latest SVN introduces new "ignore_case_chain" setting Cheers, Thomas On 02 Feb 2016, at 14:38, Thomas Holder <thomas.hol...@schrodinger.com> wrote:

Re: [PyMOL] Ray tracing max_threads

t; > -- > Jesper Lykkegaard Karlsen > Scientific Computing > Centre for Structural Biology > Department of Molecular Biology and Genetics > Aarhus University > Gustav Wieds Vej 10C > 8000 Aarhus C >

Re: [PyMOL] auto_show_cartoon or similar

was some dicussion of this in 2010 > (link below) but I haven't found anything more recent that does what I'd like. > > http://www.mail-archive.com/pymol-users%40lists.sourceforge.net/msg07734.html > > Thanks > Ivan -- Thomas Holder PyMOL Principal Developer Schrödi

[PyMOL] ignore_case in next PyMOL version

different from resn, name and elem. See also: http://pymolwiki.org/index.php/ignore_case Any kind of feedback regarding the planned change will be appreciated. Cheers, Thomas -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. --

Re: [PyMOL] drawing trajectory files

> all bonded atoms connected as solid lines. I couldn’t find an explanation on > the WIKI (earlier versions of pymol didn’t behave this way). Everything else > works fine (movie plays as it normally would). Any advice would be > appreciated. > > Thanks, > > Mike -- Th

Re: [PyMOL] ColorByRMSD script

>>> However, I'm getting the following error >>> message, when I initialize PyMOL after installing the plugin: >>> >>> >>> Exception in plugin 'colorbyrmsd' -- Traceback follows... >>> >

Re: [PyMOL] regarding show_bumps

shows > clashes only for the first state. Am I doing something wrong or should we > pass additional commands to show clashes for all states. Kindly post your > replies with help/suggestions in this regard. > > Thank you > > Best Regards > Priyan -- Thomas Holder PyMOL Princ

Re: [PyMOL] iterate names in group

red > >> On Jan 25, 2016, at 2:34 PM, Jordan Willis <jwillis0...@gmail.com> wrote: >> >> Hi, >> >> Is there a way to iterate through the names that have been grouped? >> >> iterate >> >> doesn’t seem to do it because it kills my pymo

Re: [PyMOL] Displaying sticks on RNA bases only

the riboses and phosphates which makes my drawings 'overloaded'. I hope I was > clear enough. > > Many thanks in advance for your answers, > > Maria > > CNRS > France -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc.

Re: [PyMOL] PyMOL + APBS plugin

de' and it works but not if I do an > alignment after loading the pqr structure and the APBS map. I suppose I > could/should align them before doing the calculations but since I didn't it > would be great if it is possible to do this during visualization. > Hopefully somebody can lo

Re: [PyMOL] OBJECT argument in ALIGN command - color

each end of the connecting line. I haven’t > discovered a way to make these bi-colored lines in ALIGN. Any ideas? > > I have tried the open source version 1.8.0, plus several earlier versions > from various origins (all on Macs) wit

Re: [PyMOL] Quick PyMOLWiki Update

ously, today my provider let me know that the PyMOLWiki was being > DDoS'd. I can imagine more productive use of one's time. If you encounter > issues, please let me know. > > Happy New Year! I hope everyone enjoyed their holiday(s). > >

Re: [PyMOL] Version question -- PSE session file format

nature does not answer first what we want, > it is better to take what answer we get. > > -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. -

[PyMOL] Announcing Julian Heinrich as PyMOL Open Source Fellow

nger -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. -- ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/list

Re: [PyMOL] PyMOL with Python 3

reviews. >> >> Justin > > Hi, > > I updated all scripts except of two for python2 and 3 compatibility. > > isoslider.py and frame_slider.py are using tk. Although 2to3 is able to > convert the code I am not familiar with implementing it in a cross ABI >

Re: [PyMOL] RMSD calculations for a group of structures

e > rmsd.txt? What other way can I use to do so? > > Thanks in advance, > D. -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. -- Go from Idea to Many App Stores Faster with Intel(R) XDK Give your u

[PyMOL] PyMOL with Python 3

with Python 2, we will check it in to SVN. Cheers, Thomas -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. -- Go from Idea to Many App Stores Faster with Intel(R) XDK Give your users amazing mobile app expe

Re: [PyMOL] MacPymol

solved this problem? > > Thanks in advance. > Young-Jin -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. -- Go from Idea to Many App Stores Faster with Intel(R) XDK Give your users amazing mobi

Re: [PyMOL] light reposition

t to reposition the light source, e.g., #2: > >set light2, [x, y, z] > > The problem is - I see no changes to the scene. > > The question: How to use the "set light(2-8)" command or is there any > other way to reposition light sources? > > Thank you, > D

Re: [PyMOL] save_transformed.py

> withneworientation.pdb has the all atom orientations (x,y,z) exactly same as > those of the original PDB I initially input to the pymol for the process I > obtained the withneworientation.pdb. > > Smith -- Thomas Hold

Re: [PyMOL] save_transformed.py

t;>0.999876618, -0.000452542, -0.015699286,\ >>>>>0.000446742,0.99821, -0.000372844,\ >>>>>0.015699454,0.000365782,0.999876678,\ >>>>>0.0,0.0, -150.258514404,\ >>>

Re: [PyMOL] can we clone representation?

representation from object > 1 to object 2 with some command in Pymol? As far as I known, this is > possible in VMD: > > http://www.ks.uiuc.edu/Research/vmd/plugins/clonerep/ > > Thank you very much > > Albert --

Re: [PyMOL] default fetch format

gt; Hello: > > I noticed that if we run command: > > fetch 2ac1 > > to get PDB into pymol in Version 1.8.0, it downloaded .cif file by > default. I am just wondering is it possible to change the default format > as .pdb file? > > thanks a lot > > Albert

Re: [PyMOL] default fetch format

vor of the mmCIF format, which is the new standard since 2014. See also http://mmcif.wwpdb.org/docs/faqs/pdbx-mmcif-faq-general.html Cheers, Thomas -- Thomas Holder PyMOL Principal Developer Schrödinger,

Re: [PyMOL] Pymol 1.8.0.0 requires ZLIB 1.2.3.5?

; Roger S. Rowlett > Gordon & Dorothy Kline Professor > Department of Chemistry > Colgate University > 13 Oak Drive > Hamilton, NY 13346 > > tel: (315)-228-7245 > ofc: (315)-228-7395 > fax: (315)-228-7935 > email: rrowl...@colgate.edu > > ---

Re: [PyMOL] problem of pymol 1.8

xPyder' (pmg_tk.startup.xPyder). > No module named backend_wxagg > Unable to initialize plugin 'mtsslPlotter' (pmg_tk.startup.mtsslPlotter). > > I google it, and cannot find any helpful information > > > thanks again > > ALbert > > > On 11/18/2015 11:16 PM,

[PyMOL] PyMOL 1.8.0 released

” command now by default downloads mmCIF files (type=cif). This release fixes the issues with ATI R9 graphics cards on OS X. Find the complete release notes on: http://pymol.org/features We welcome any feedback and bug reports. Cheers, - The PyMOL Team at Schrödinger -- Thomas Holder PyMOL Principal

Re: [PyMOL] problem of pymol 1.8

med wx > Unable to initialize plugin 'mtsslTrilaterate' > (pmg_tk.startup.mtsslTrilaterate). > > I am just wondering how can we solve the problem? I've already installed > python PMW in my machine. > > thank you very much. > > Alber

Re: [PyMOL] 1.7.6.6 does not display a 1.7.4.4 .pse ifle.

essor of Biological Chemistry, University of Michigan > Currently on sabbatical: > Laboratory of Susan Buchanan, Ph.D. > NIDDK, National Institutes of Health, Bethesda, MD 20892-8030 > sa...@umich.edu mobile (734) 276-6505 -- Thomas Holder PyMOL Principal Developer

Re: [PyMOL] Common atoms in two selections (and their indices)

svaldo. > > On Mon, Oct 26, 2015 at 10:33 AM, Tsjerk Wassenaar <tsje...@gmail.com> wrote: > > > > > Hi Thomas e.a., > > Given two selections, would there be an easy way to > > 1. find the atoms which are bo

Re: [PyMOL] CGO segmentation fault

es, Pymol (1.7.4.0 incentive, Mac) halts > with a segmentation fault. I know it's my bad for feeding a still nested > list, but a segmentation fault is a harsh way of complaining :) > > Cheers, > > Tsjerk > > -- > Tsjerk A. Wassenaar, Ph.D. -- Thomas Hold

Re: [PyMOL] pdbml

ython2.7/dist-packages/chempy/__init__.py", line 59, > in __getattr__ > raise AttributeError(attr) > AttributeError: properties > > Any help would be appreciated. > > > Regards, > Arthur > > > On 25.09.2015 01:50, Thomas Holder wrote: >> Hi Arthur &

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