Re: [PyMOL] regarding show_bumps

ents transition of a > domain from one orientation to the other. I tried using "show_bumps.py" to > bring up clashes during the transition but the cgo that is written out shows > clashes only for the first state. Am I doing something wrong or should we > pass additional commands t

Re: [PyMOL] iterate names in group

Cheers, > Jared > >> On Jan 25, 2016, at 2:34 PM, Jordan Willis 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 pymol app. >> >

Re: [PyMOL] Displaying sticks on RNA bases only

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

tiple aligned proteins with their electrostatic surfaces > simultaneously? I tried 'set grid_mode' 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'

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

cting 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)

Re: [PyMOL] Quick PyMOLWiki Update

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

t 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

gt;> 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 > comp

[PyMOL] PyMOL with Python 3

th 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] RMSD calculations for a group of structures

,'w') > rms2=cmd.align('structure_0002 and name ca','structure_0001 and name ca') > . > . (NOTE: I got all of these structures by the command split_states somename) > . > rms9=cmd.align('structure_0009 and name ca','structure_0001 and nam

Re: [PyMOL] MacPymol

te: > Hi, > By accident(!) I upgraded my Mac OS to El Captain. The problem is now I > cannot open my MacPymol that was fine up to previous or lion. > I downloaded XQuartz but still somehow doensn’t open my old MacPymol. Has > some one experienced or solved this problem? > &g

Re: [PyMOL] light reposition

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, > Darya -- Thomas Holder P

Re: [PyMOL] save_transformed.py

ion.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 Holder PyMOL Principal Developer Schrödinger, Inc.

Re: [PyMOL] save_transformed.py

gt;>>> -Spencer >>>>> >>>>> On Thu, Nov 26, 2015 at 8:33 AM, Smith Liu wrote: >>>>> Dear All, >>>>> >>>>> For get view, we get something like >>>>> >>>>> set_view (\ >>>>>

Re: [PyMOL] default fetch format

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] default fetch format

7, Albert wrote: > 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? > > tha

Re: [PyMOL] can we clone representation?

ello: > > I've shown an object as cartoon and displaced sticks with various > colors. I am just wondering, can we clone all representation from object > 1 to object 2 with some command in Pymol?

Re: [PyMOL] Pymol 1.8.0.0 requires ZLIB 1.2.3.5?

amp; 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

#x27; (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

Re: [PyMOL] problem of pymol 1.8

t; 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 ver

[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] 1.7.6.6 does not display a 1.7.4.4 .pse ifle.

ssor 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 Schrödinger, In

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

> > > > Hi Thomas e.a., > > Given two selections, would there be an easy way to > > 1. find the atoms which are both in selection 1 and 2, and the indices of > those in the selections > > and > > 2. find the matching atoms in the two selections

Re: [PyMOL] CGO segmentation fault

ntive, 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

Re: [PyMOL] pdbml

le "/usr/lib/python2.7/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: >>

Re: [PyMOL] Pymol Morph movie error

peg_encode_err = > os.popen3(_mpeg_encode_exe) > > WindowsError: [Error 2] The system cannot find the file specified: 'Ex: > C\\Temp /c "C:\\Program Files\\PyMOLPyMOL\\ext\\bin\\mpeg_encode.exe"' > > pro

Re: [PyMOL] Segmentation fault when I tried to load a pdb file

F pymol: line 3: 17889 Segmentation fault. Could you help me to fix > this please? Thanks. Beibei -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. -- ___ PyMOL-users

Re: [PyMOL] Atoms appears on cartoon at high resolution

em when zooming in. Cheers, Thomas On 07 Oct 2015, at 09:48, Thomas Holder wrote: > Hi Lucile, > > This picture looks unusual, can you give some details on how you created it? > E.g. is this a full-atom protein structure, or a CA-only or pseudo-atom > coarse grain model? Did you modi

Re: [PyMOL] GROMACS trajectories

ted and defunct now. > pymolwiki.org/index.php/User:Speleo3/VMD_plugins -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. -- Full-scale, agent-less Infrastructure Monitoring from a single dashboard Integrate with

Re: [PyMOL] Atoms appears on cartoon at high resolution

ion an helix cartoon? (see attached picture) > thanks in advance > Lucile > > -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. -- Full-scale, agent-less Infrastructure Monitoring from a single

Re: [PyMOL] Problems loading new mrc-format electron density files into pymol

e the .mrc files if someone would like to take a look at them. > They are too large to attach to this email (they bounced back from the pymol > mail server). > > > Thanks in advance for any help, > > > Mike > > Michael F.

Re: [PyMOL] measuring wizard

you reply, Thomas. > > Invoking > > alter all, ID = index > > didn't help. > > Regards, > > Vaheh Oganesyan > www.medimmune.com > > > -Original Message- > From: Thomas Holder [mailto:thomas.hol...@schrodinger.com] > Sent: Friday, Oct

Re: [PyMOL] measuring wizard

ct1 is being chosen. Is it a bug in > program or am I doing something wrong? > > > Regards, > > Vaheh Oganesyan > MedImmune, ADPE > www.medimmune.com -- Thom

Re: [PyMOL] morphing with heteroatoms

sing the commercial version of > Pymol. Pymol looses heteroatoms (zinc in my case) while morphing. Is > there any way around this? > > (I tried replacing zinc with water and linking it to the protein using > CONECT - didn't work) > > Thanks for your help. > Kart

Re: [PyMOL] Pymol crash when deleting callback object

you can also crash many versions of pymol by making mistakes in > the callback, such as passing a different name for the callback and the cgo > object (yes, this is a silly thing to try, but it shouldn't crash). > > -Spencer -- Tho

Re: [PyMOL] pdbml

useful we can include that in the next PyMOL release. Cheers, Thomas ''' Adds a "load_pdbml" command to PyMOL. (c) Thomas Holder, Schrodinger, LLC ''' import os from pymol import cmd @cmd.extend def load_pdbml(filename, object='', discrete=0

Re: [PyMOL] Ploting coordinates

.471680.8 > #7278cc > > Where the first three columns are the x, y and z coordinates, the next three > are the size of the object, and the last is the colour (which isn’t so > important - neither is the size, reall

Re: [PyMOL] pymol fails to open (crash)`

menu. I can open the > program by double clicking on a pdb file and there are no issues. > > Current version is 1.7.6.2 > > Any idea how to fix this? Might be my hardware but just wondering if others > see this or there is a fix? > J

Re: [PyMOL] how can we display properties?

so on. I am just wondering is it > possible to display those properties in Pymol? > > Thank you very much > > Albert -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. -- ___

Re: [PyMOL] label

uld label the absolute > configuration (R/S) for a chiarity atom? > > Thank you very much. > > Albert -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. -- ___

[PyMOL] PyMOL Open-Source Fellowship - Call for Applications

develop free resources to help scientific progress and the community as a whole. Details and application instructions can be found on http://pymol.org/fellowship The application deadline is November 1st, 2015. We look forward to your submissions! Cheers, Thomas -- Thomas Holder PyMOL

Re: [PyMOL] any hotkey?

? For instance: > > If I press keyboard "L", Pymol zoom to ligand binding pocket > automatically > > Thanks a lot > > Albert -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc.

Re: [PyMOL] XYZ format - max size of the name field

oms > > However, at the same time if I do: > select H_100, name H100 > I get: > selection "H100" defined with 2 atoms > what means that the last character has been omitted. > > Of course I can work it out by naming atoms like: HH01 instead of H1000, but > I

Re: [PyMOL] how to copy color?

: > Hello: > > I've colored object1 in various color in different regions. I am just > wondering how can we copy the color scheme for object1 to object2? > Object 2 is the same protein with object1 but with different conformations. > > Thank you very much > >

Re: [PyMOL] python command to get b-factor and occupancy of a single atom?

t; Dirk Kostrewa > Gene Center Munich, A5.07 > Department of Biochemistry > Ludwig-Maximilians-Universität München > Feodor-Lynen-Str. 25 > D-81377 Munich > Germany > Phone: +49-89-2180-76845 > Fax:+49-89-2180-76999 > E-mai

Re: [PyMOL] Pymol crash when raytracing empty graphics

that there are some polygons in frame would > > also be appreciated. Say, if there was a way to detect that cartoon would > > fail so that I can switch to a lines or nonbonded representation (I wish > > that was the default fallback for cartoon). > >

Re: [PyMOL] How to name overfull chains in PDB file?

14 chains？ It > seems that they can not be named with repeated letters which have been used > because this cause abnormality in display function in pymol. And identifier > like "A1", "A2", etc, can not be used either because there is only one colum > (colum 22) for the

Re: [PyMOL] bonding nucleic acid bases

. Cheers, Thomas ''' (c) 2015, Thomas Holder, Schrodinger LLC License: BSD-2 ''' from pymol import cmd try: get_raw_distances except NameError: try: from psico.querying import get_raw_distances except ImportError: print 'please inst

Re: [PyMOL] test message

tserv? > Or if I’ve been blacklisted for some reason? > > Thanks, > > H. Adam Steinberg > 7904 Bowman Rd > Lodi, WI 53555 > 608/592-2366 -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc.

Re: [PyMOL] installing other libraries with pymol python

eers, Thomas On 23 Jun 2015, at 18:04, Jordan Willis wrote: > Wow that is so cool. Is there any drawbacks I can expect? > > >> On Jun 23, 2015, at 1:44 PM, Thomas Holder >> wrote: >> >> Hi Jordan, >> >> if you want to use MacPyMOL with other

Re: [PyMOL] installing other libraries with pymol python

compatible with pymol. Or more > generally, how would one install third party libraries for use with pymol. If > you don’t use pandas, I highly recommend it. It’s incredibly useful for > manipulating data and it would be very handy to have with pymol scrips. > > Jordan -- Thomas

Re: [PyMOL] Difficulty running RNA coloring program

ac PyMOL 1.7.4.4, and I have attempted to run the attached program. I > know the program works on older versions, but I get the following error: > > AttributeError: 'module' object has no attribute 'extend' > > Does anyone know how to fix this? &

Re: [PyMOL] Error: "NameError: name 'callback' is not defined"

PyMOL contains an incompatible import on PyMOL versions 1.7.3+. > Thanks to Thomas Holder this is now fixed in github. > > In the next weeks we are going to try to get out a new release of CMview that > contains the patch. In the meantime you can try using an older PyMOL version, >

Re: [PyMOL] efficiency assigning b-factors

; {}”.format(residue[‘resnum’]),”b={}”.format(residue[‘value’])) >> >> This executes the alter command for each residue. For some reason, its >> taking forever in my script. Is there something inherently inefficient about >> alter? And is there anyway to fix it? Perhaps,

Re: [PyMOL] PyMOL ray tracing errors

s, .05 > set valence, 2 > set valence_size, 0.2 > python > preset.ball_and_stick("r. STI") > python end > orient r. STI > and this is the PML script I use to render the model using POV-Ray: > > set ray_opaque_background, 0 > png 2HYY_img0001.png, dpi=500, ray=1, width

Re: [PyMOL] Unusual error after distance measurement

t; > _ > Joel Tyndall, PhD > > Associate Professor in Medicinal Chemistry > National School of Pharmacy > University of Otago > PO Box 56 Dunedin 9054 > New Zealand > Skype: jtyndall

Re: [PyMOL] SCWRL version with educational-use PyMOL?

> > > On Jun 1, 2015, at 1:32 PM, Emilia C. Arturo (Emily) > > wrote: > > > > Hello. > > > > Does anyone know which version of SCWRL (backbone-dependent rotamer > > library) is used in the educational-use-only version of PyMOL? > >

Re: [PyMOL] create bonds between selections within cutoff radius

there > anyone from the community with time and capability willing to take this up > and maintain this resource or are we just letting this wither away? > > Cheers, > > Carsten > > -Original Message- > From: Thomas Holder [mailto:thomas.hol...@schrod

Re: [PyMOL] citing pymol script in thesis--copyright issues?

appendix on the modified script make sure to note what modifications I > did versus what was there originally? Thanks. -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. --

Re: [PyMOL] MacPyMOL in command line mode

with X11 forwarding enabled), it fails with some errors about >> connecting to WindowServer And I can tell it actually tried to launch the >> GUI very briefly, then returned to the command line to process the scripts. >> Is this right? Can I run it remotely on another comp

Re: [PyMOL] What legal license does PyMOL's logo available under?

Hi Justin, the logo that Brenton is referring to isn't included in the Open-Source repo or tarballs. It's only used with Mobile PyMOL and Incentive PyMOL. Cheers, Thomas On 28 May 2015, at 14:16, Justin Lecher wrote: > On 28/05/15 19:26, Thomas Holder wrote: >> Hi Brent

Re: [PyMOL] What legal license does PyMOL's logo available under?

f PyMOL's logo (i.e., this one), as > I would like to upload it to Wikimedia Commons. > > Thanks for your time, > Brenton -- Thomas Holder PyMOL

Re: [PyMOL] white background

the sequence will > appear only after clicking inside the viewer window. I don’t think either of > the mentioned are special features. Can it be fixed, please? > > Thank you. > Regards, > > Vaheh Oganesyan > MedImmune, ADPE > www.medimmune.

Re: [PyMOL] create bonds between selections within cutoff radius

m. This yields a weired > structure with very long, unwanted bonds. > I tried to iterate over the first selection, to draw only > bonds between an Pd atom and Si atoms which are within > range to that Pd atom like > >iterate (n. pd),

Re: [PyMOL] Handling of scene specific global settings?

for different scenes. > Right now I am using 1.7.3, but was wondering if anything has changed in > 1.7.6 in that regard? The issue is not new, but it would be nice if there > would be a feature like this implemented. > > Cheers, > Carsten -- Thomas Holder PyM

Re: [PyMOL] regarding theseus wrapper

Hi Priyan, I updated the wrapper, it now supports THESEUS 3.x: https://github.com/speleo3/pymol-psico Cheers, Thomas On 15 May 2015, at 07:26, Thomas Holder wrote: > Hi Priyan, > > the wrapper fails because THESEUS 3.0.0 changed the output. I suggest to use > THESEUS 2.x

Re: [PyMOL] regarding theseus wrapper

, in theseus > translations, rotations = _run_theseus(args, tempdir, preserve, quiet) > File "/media/XTAL/pymol/modules/psico/fitting.py", line 648, in _run_theseus > handle = open(os.path.join(tempdir, 'theseus_transf2.txt')) > IOError: [Errno 2

Re: [PyMOL] Logging commands errors

gt; > It seems to not be getting the right name for the background setting and > is just putting in '6' instead. > > > Thanks for your help, > Matt Baumgartner -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc.

Re: [PyMOL] Someone interested in writing a DSSR plugin for PyMOL?

.I. > > Department of Cell and Molecular Biology > > Uppsala University > > Phone Number: (+46)073-678-5334 > > mesguerra.org > > mauricio.esgue...@i

[PyMOL] Someone interested in writing a DSSR plugin for PyMOL?

o has experience with Python and the PyMOL API for writing an extension or plugin. Please contact me if this sounds appealing to you. Get DSSR from http://x3dna.org/ See it hooked up with JSmol: http://chemapps.stolaf.edu/jmol/jsmol/dssr.htm Cheers, Thomas -- Thomas Holder PyMOL Principal Deve

Re: [PyMOL] Delete all but one object

dl Lab > Sanford-Burnham Medical Research Institute > 10901 North Torrey Pines Road > La Jolla, CA 92037, USA > Phone: 858.646.3100 x 4216 > Email: blechtenb...@sanfordburnham.org -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc.

Re: [PyMOL] Difficulty with Pymol segfault in CentOS 7 VM

oad any XYZ file without segfault. However, the view keeps > blinking during movement. It may also be of interest to note that I have used > opencascade without any problems as a 3d rendering and cad visualization > software on this same VM. >

Re: [PyMOL] RMS over a MD trajectory.

that PyMOL does compute the RMS along the trajectory if I >> simply: >> align trj, pdb1 >> as it is told in: >> http://www.pymolwiki.org/index.php/Align >> However, I am unable to get the list of RMS values printed out. How cou

[PyMOL] PyMOL 1.7.6 released

s. Cheers, - The PyMOL Team at Schrödinger -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. -- One dashboard for servers and applications across Physical-Virtual-Cloud Widest out-of-the-box monitoring suppor

Re: [PyMOL] rms_cur

with 72 atoms. > PyMOL>alter all,segi="" > Alter: modified 6110 atoms. > PyMOL>alter all,chain="" > Alter: modified 6110 atoms. > PyMOL>rms_cur sel1,sel2 > ExecutiveRMS-Error: No atoms selected. > PyMOL>rms_cur sel1,sel2 > ExecutiveRMS-Err

Re: [PyMOL] Raw map access

electron density) at a particular coordinates? I > would like to know sigma value for a particular atom. Is there any way, using > python, to achieve that? > > Best regards, > Filip -- Thomas Holder PyMOL Prin

Re: [PyMOL] How to use vmd molfile_plugin in pymol?

.ac.at/vasp/vasp/POSCAR_file.html;http://cms.mpi.univie.ac.at/vasp/vasp/CHGCAR_file.html > > Thanks very much for your help again. > > Best wishes > > On 24/04/2015, Thomas Holder wrote: >> Hi Wei-Bing, >> >> support to load topology files with the vmd plugins was added

Re: [PyMOL] How to use vmd molfile_plugin in pymol?

186 73108538 > E-mail: zhan...@csust.edu.cn, weibingzhang...@gmail.com > ------ -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. -- One dashboard for servers and applications across Physical-

Re: [PyMOL] 3D mouse

> only for the person addressed. This email must not be forwarded to third > parties without the express consent of the sender. If you believe you have > received this email in error please inform the sender and remove it

Re: [PyMOL] Interleaved atoms when creating from two objects

lows (Using MacPyMOL 1.7.4): > > fetch 4rp9, type=pdb1 > split_states 4rp9 > alter 4rp9_0002, chain = 'B' > create joined, 4rp9_* and resi 282 > > I've tried various combinations of the rebuild and sort commands, as well as > man

Re: [PyMOL] Problem with How do I change the font in the Tck/Tk external GUI window?

elf.font,8) > ./python2.7/dist-packages/pmg_tk/skins/normal/__init__.py:427: > self.my_fw_font=(self.font,10) > ./python2.7/dist-packages/pmg_tk/skins/normal/__init__.py:429: > text.configure(font = self.my_fw_font) > Il file binario ./python2.7/dist-packages/pmg_tk/skin

Re: [PyMOL] Backwards compatibility error: ExectiveSetSession-Error: after names .

rt_version, 1.74 save session.pse There are limitations. For details, see: http://pymolwiki.org/index.php/pse_export_version Cheers, Thomas On 08 Apr 2015, at 15:12, Thomas Holder wrote: > Hi Matt, > > there might be room for improvement regarding our versioning scheme. > Nev

Re: [PyMOL] Beginning with PyMol

Mol package is > perhaps broken. > I will do an extensive testing and be back with information. > Is there a self-sustaining package in your website that can run on its > own, just like Geogebra independent package? > Regards, > Rajib & Yuktimmana > > On 04/20/2

Re: [PyMOL] Beginning with PyMol

n do this, then this, ... to build > one molecule from scratch. > Regards, > Rajib & Yuktimmana > > On 04/19/2015 07:28 PM, Thomas Holder wrote: >> Hi Rajib & Yuktimmana, >> >> you can interactively build molecules using the builder: >> >>

Re: [PyMOL] Beginning with PyMol

ride, or butylene? > Eagerly awaiting your reply, > Rajib & Yuktimmana -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. -- BPM Camp - Free Virtual Workshop May 6th at 10am PDT/1PM EDT Develop your own

Re: [PyMOL] MacPyMol working dir

nual I loose plugin control. > Just wondering if there is a way to have the “open” file starting from the > working directory with the fancy interface of MacPyMol, rather than the basic > Unix interface. > > Thanks, > gg-kawa -- Thomas Holder PyMOL Principal Developer Schröding

Re: [PyMOL] working on mmCIF assembly support

to > select all equivalent chains with a simple statement. > > Cheers, > > Tsjerk > On Thu, Apr 9, 2015 at 6:48 PM, Thomas Holder > wrote: > Hi all, > > I'm working on reading biological assemblies from mmCIF files. The patch > against the latest SVN

Re: [PyMOL] Cartoon visualization of per-residue txt data

name CA+C1*+C1' and ( byres ( ss )<-- > Selector-Error: Misplaced ). > Selector-Error: Malformed selection. > ( ss )<-- > > > James -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. -

Re: [PyMOL] when number of atoms changes, colors change in an uncontrolled manner

ions in which the number of atoms remains constant, I've never had > this problem. > > This occurs both when I run on Linux (Version 1.7.0.0) or on a Mac (Version > 1.7.2.1). > > Any help would be greatly appreciated. Both pdb files are attached. > > Efrem Braun --

Re: [PyMOL] Backwards compatibility error: ExectiveSetSession-Error: after names .

s a clear difference and I can inform my collaborators not > to update past 1.7.4. > > > On 4/8/15 2:38 PM, Thomas Holder wrote: >> Hi Matt, >> >> PyMOL session files are in general not "forward compatible". >> >> See for example: >> ht

Re: [PyMOL] Backwards compatibility error: ExectiveSetSession-Error: after names .

ognized object "1ycr" of type 10613678. > ExectiveSetSession-Error: after names. > ExectiveSetSession-Warning: restore may be incomplete. > > > Any idea what is wrong, or do I need to downgrade back to 1.7.4?

Re: [PyMOL] Zoom animation

t (the original script had > cmd.rotate('y',6) instead of cmd.zoom...) I have created based on input from > others on this mailing list. > > Thanks for your time, > Brenton -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc.

[PyMOL] Educational-Use-Only PyMOL Updated

not a full version of PyMOL and is not intended as a free replacement for academic PyMOL licenses. Cheers, Thomas -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. -- Dive into the World of Parallel Progra

Re: [PyMOL] Compile Errors on SVN 4111

d go there. The --std=c++11x flag as the name suggests is > only for CXX code. So adding --std=c++11x to CXXFLAGS would be more > appropriate. Works here on Gentoo systems flawlessly. > > Justin -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. ---

Re: [PyMOL] green rings

Incentive PyMOL 1.7.4.4 fixes this problem. Cheers, Thomas On 13 Mar 2015, at 23:55, Thomas Holder wrote: > The latest update to SVN fixes the ring color problem. > > Cheers, > Thomas > > H. Adam Steinberg wrote, On 03/10/15 10:39: >> Thank you! >> >>&

Re: [PyMOL] Assign secondary structure on group

The latest update to SVN fixes this. Cheers, Thomas Thomas Holder wrote, On 03/06/15 15:35: > Hi Matt, > > thanks for the bug report. If you use the command line instead, it > works if you put the group name in parenthesis, which forces PyMOL to > treat it as an atom select

Re: [PyMOL] green rings

The latest update to SVN fixes the ring color problem. Cheers, Thomas H. Adam Steinberg wrote, On 03/10/15 10:39: > Thank you! > >> On Mar 10, 2015, at 9:07 AM, Thomas Holder >> wrote: >> >> Hi Quentin, Adam, David, Francis, >> >> I just looked at t

[PyMOL] Recent changes to SVN

, so to compile, you might need: export CPPFLAGS="-std=c++0x" Cheers, Thomas -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. -- Dive into the World of Parallel Programming The Go Parallel W

[PyMOL] Announcing Jared Sampson's fellowship renewal

Open Source Fellowship Program and the fellows here http://pymol.org/fellowship. Cheers, Thomas & the PyMOL Team at Schrödinger -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. -- Dive into the World of

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