> How can I force pymol2 to write exactly the same sdf as before ?
> Is there new defaults settings in pymol2 that I can override ?
>
> Thanks,
>
> Fabrice
>
> Fabrice Carles - PhD student
> Structural Bioinformatics & Chemoinformatics,
> Institut de Chimie Organique
n process. After
>
> pymol.cmd.quit()
>
> CPU usage returns to normal. I see the same pattern when I run those
> commands in an interactive python shell. Tried pymol 2.0/2.1 with both python
> 2.7 and 3.6 on mac (anaconda) and linux.
>
> Did I do anything wrong or is
tion on Linux
Find the complete release notes at:
https://pymol.org/d/media:new21
We welcome any feedback and bug reports.
Cheers,
- The PyMOL Team at Schrödinger
--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.
-
inline Array1D(const Array1D );
> ^
> modules/cealign/src/tnt/tnt_array1d.h:61:11: note: candidate
> constructor
> not
> viable: requires 0 arguments, but 2 were provided
> Array1D();
> ^
> modules/cealign/src/ccealign
t reason, we should fix it. It would be great if
you can provide the exact steps which lead to a crash for you.
Cheers,
Thomas
--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.
--
Check out the vibrant
tps://repo.continuum.io/pkgs/free/noarch
> - https://repo.continuum.io/pkgs/r/linux-64
> - https://repo.continuum.io/pkgs/r/noarch
> - https://repo.continuum.io/pkgs/pro/linux-64
> - https://repo.continuum.io/pkgs/pro/noarch
>
> Regards.
--
Thomas Holder
PyMOL Principal
already tried saving as .wrl. but I cannot
> open it on Pymol and the file syntax is confusing)
>
> 3- Are there any other softwares or libraries to do such things? (output
> isomesh at one specific level (5), store it in a convenient way, etc)
>
> Thank
? For example, should I type “load
> session1.pse” first, hit enter and then type ‘load session2.pse, partial=1’ ??
>
> Many thanks for your help,
>
> Maria
--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.
; or "nucleic" are used as
names, we may want to add them as keywords in the future
The new keywords are available in SVN rev 4185 and in the latest alpha build
(https://pymol.org/alpha ). The PyMOLWiki selection algebra page has been
updated.
Cheers,
Thomas
> On Dec 18, 2017, at 7:41
ort the settings
> from a particular Pymol session to another different session.
>
> Thanks very much in advance!!
--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.
--
Check out the vibrant tech community on
This is my volume https://www.dropbox.com/s/x4ic7uvdlknk8us/volume.png?dl=0
>
>
> Thanks.
--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.
--
Check out the vibrant tech community on one of the
-visualization-software-engineer-0
Cheers,
The PyMOL Team at Schrödinger
--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.
--
Check out the vibrant tech community on one of the world's most
engaging tech sites
ms/physbiochem
>
> There may be confidential information within the contents of this email meant
> 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
bon atoms also. Is it a bug or issue associated with 'Byring'?
> carb_pos = cmd.select('e. C and Byring e. C and (pc.>0)')
> I am sharing the image for better understanding.
> Cheers
> Vijay
--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.
--
gn
> the residues shown in the sequence display?
>
> I would find this a very powerful feature.
>
> Many thanks for any help.
>
> Tony Lewis
--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.
--
format required:
>
> cmd.load_coords(coordinates, 'prot')
>
> I tried to use all the floats the ones after the other like [1.1, 2.2,
> 3.3,...] and I was close to making it work, but it said the numbers of atoms
> did not match. I read that I should probably used a numpy array but I
,
Thomas
> On Dec 18, 2017, at 7:57 PM, wtempel <wtem...@gmail.com> wrote:
>
> Speaking of atom selection, I wonder how many pymol and phenix users would
> benefit from a fully "standardized" selection syntax. Would this be a
> worthwhile design goal?
> Wolf
would load them as named
objects of the same name.
We are looking for new keywords that minimize the chance of such naming
conflicts.
For an overview of the current selection language, see
https://pymolwiki.org/index.php/Selection_Algebra
--
Thomas
st important issue)
> • If I hide all the hydrogens I can't make them appear again.
> For 3: there is no options unde rshow menu to show the hydrogens again. If I
> go to Action menu and add hyrodgens I get an error:
> AddHydrogens-Error: can't modify a discrete object.
>
> So how can i
ce switch, and get a meaningful
> model displayed in PyMOL. Has the mmcif format been suggested to the PDB2PQR
> developers?
> Many thanks.
> Wolfram
>
> On Thu, Dec 7, 2017 at 3:01 AM, Thomas Holder <thomas.hol...@schrodinger.com>
> wrote:
> Hi Wolfram,
>
> Do you ru
f this is answered somewhere else. I couldn't find the answer.
>
> How does one change the default view on startup/load (now cartoon in 2.0) to
> lines or sticks?
>
> Thanks,
>
> --paul
--
Thomas Holder
PyM
ther than trying to hack together a list of
> resn values.
>
> Many thanks for any help.
>
> Tony Lewis
--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.
--
Check out the vibra
> subsequently calculated APBS surfaces?
> Best regards.
> Wolfram Tempel
--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.
--
Check out the vibrant tech community on one of the world's most
e
unattached and randomly
> in the pdb. I simplified with a dipeptide AA instead. The file is attached
> here.
>
> Regards,
> Simon
>
> 2017-11-18 17:04 GMT+08:00 Thomas Holder <thomas.hol...@schrodinger.com>:
> Hi Simon,
>
> I think this is the code you're looking for
ersion 1.8.7.0. on my CentOS 7 OS.
> Everytime I try to launch it, it crashes with a message:
> /usr/bin/pymol: line 3: 19995 Segmentation fault (core dumped)
> "/usr/bin/python" "/usr/lib64/python2.7/site-packages/pymol/__init__.py" "$@"
>
> What shoul
> available? Like XAPAPAPAPY where X and Y are NME and ACE? The main point is
> to automize the process since I don't want to write NME / ACE manually
> everytime.
>
> I appreciate any suggestion and comment.
>
> Regards,
> Simon
--
Thomas Holder
PyMOL Principal
from aromatic ring
> aren't correct. From the input file, type is 'C.ar' but becomes 'C.2' in the
> output file. The right bond type is conserved (C.ar).
>
> So my question is: Is it a bug or an expected behavior ?
>
> Best regards
&g
w I have a folder called pymol with the following files / directories:
>
> data examples ext modules pymol pymol.exe scripts setup.sh
>
> How should I install and run it?
>
> Regards.
--
Thomas H
pen source version?
> If it is supported, where can I find more information on getting that setup?
>
>
> Any pointers in greatly appreciated Thank you....
>
> thanks
> -simon
>
>
> C
g something wrong here?
> I saved via command line „save filename.mtl“
>
> Would there be another option that the mtl-file is generated automatically
> during saving as .obj.
>
> Thanks in advance for the help!
>
> Verena
--
specific range of b-factor values, and show
> stricks for them. How can I use commands to do it?
>
> Many thanks.
>
> Li
>
> --
> Li Xue, Ph.D.
> Computational Structural Biology group
> Utrecht University, Faculty of Science - Chemistry
> Email: l@
quence Analysis Facility, Biology Division, Caltech
--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.
--
Check out the vibrant tech community on one of the world's most
engaging
whatever it is called in
> that system, when each patch is applied? I did not notice any numbers like
> that, not even in the "about" display, which shows "1.9.0.0".
>
> Thanks,
>
> David Mathog
> mat..
ized object "" of type 0.
> ExectiveSetSession-Error: after names.
> ExectiveSetSession-Warning: restore may be incomplete.
>
>
> Any help would be greatly appreciated!
>
> Many thanks,
>
4k resolution monitor and GeForce
> graphics.
> cheers, Marko
> --
>
> Marko Hyvonen
> Department of Biochemistry, University of Cambridge
>
> mh...@cam.ac.uk
>
> +44 (0)1223 766 044
> @HyvonenGroup
>
> http://hyvon
and workarounds:
https://pymol.org/2/support.html#known-issues
Cheers,
Thomas
> On Sep 21, 2017, at 8:31 PM, Thomas Holder <thomas.hol...@schrodinger.com>
> wrote:
>
> Hi again,
>
> 24h post-release feedback summary :) Thanks everyone who already tested the
> new version
need refresh if you had opened it before)
Cheers,
Thomas
> On Sep 20, 2017, at 8:18 PM, Thomas Holder <thomas.hol...@schrodinger.com>
> wrote:
>
> Dear PyMOL users,
>
> We are thrilled to announce the release of Incentive PyMOL 2.0!
>
> As the version number indic
and bug reports.
Cheers,
- The PyMOL Team at Schrödinger
--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.
--
Check out the vibrant tech community on one of the world's most
engaging tech sites, Slashdot.org
step, nor did it occur when I simulated 1TUB.pdb/1JFF.pdb Can you
> please help?
>
> Thank you and regards,
> Raag
>
--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.
--
Check out the vibr
oratory of Biochemistry and Protein Science,
>
> 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/physb
gt; It seems that the function sometimes does not return any result - any idea
> why this happens?
>
> Thank you and all the best,
> Gregor
--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.
--
Chec
:
>
> Hi All,
>
> I have a protein, which is colored by rmsd.
> The .pml coloring scripts have been produced by ProSmart.
> The color spectrum is white, yellow and red, where red denotes the
> highest rmsd value.
>
> Does anyone knows how to select only these AAs, which a
n and in general
> have not worked with cif files inside pymol.
>
> How do I select polymer 58 inside this cif structure.
> Thanks in advance
> Hari
>
>
> Chain Info
>
> Polymer: 58
> Length: 117 residues
> Chain
gt;
> Hi, I was trying to set assembly 1 and load 1C0K (and other structures) in
> pdb, cif and mmtf format. I noticed that when I split_states and get each
> model, model_0001 of cif and pdb format corresponds to model_0002 of mmtf
> format.
--
Thomas Holder
PyMOL Principal De
ve Product) and have been
> trying to install the Caver plugin.
> However, it gives an error saying that it has been installed but
> initialization failed. Please help!
>
> Regards,
> Raag
--
Thomas Holder
PyM
9', mmtfVersion: '1.0.0'
> Segmentation fault (core dumped)
>
> The strange thing is that if I try to normally load this file in bash doing
> pymol 4v99.mmtf the file is correctly loaded. Is there something I am missing?
>
> 2017-06-22 17:52 GMT+02:00 Gianluca Tomasello <gi
gt; (water).
>
> Thank you,
>
> Kelly
--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.
--
Check out the vibrant tech community on one of the world's most
engaging tech sites,
y and
> it was the following error:
>
> Glebs-MacBook-Pro:pymol-psico-master Own$ python setup.py
> File "setup.py", line 7
>
> ^
> SyntaxError: invalid syntax
>
> 2017-07-18 19:52 GMT+02:00 Thomas Holder <thomas.hol...@schrodinger.com>:
>&
r "license" for more information.
>>>>>
>> Glebs-MacBook-Pro:pymol-psico-master 2 Own$ ls -t
>> READMEpsicosetup.py
>> Glebs-MacBook-Pro:pymol-psico-master 2 Own$ python setup.py
>> File "setup.py", line 10
>>print 'Warni
several chains, some insertions like
> lyzocyme which were not aligned against reference), thus keeping only
> seven-transmembrane scaffold present in reference.pdb.
>
> I thanks so much for the help!
>
> Gleb
--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.
---
I have a protein and a ligand inside the pocket. I want to estimate
> the x, y and z
>
> Best Regards,
> Mohammad
--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.
--
Check out the vibrant
Hi Gianluca,
https://pymolwiki.org/index.php/nb_spheres
Cheers,
Thomas
> On Jul 10, 2017, at 1:31 PM, Gianluca Tomasello <giagi...@gmail.com> wrote:
>
> Hi, is it possible to render nonbonded atoms as small spheres using only
> stick representation?
--
Thomas Hold
in batch mode (pymol -cq script.py).
> If i run it in batch mode, each atom with a double bond is rendered without
> the sphere in the atom center (only double bond is shown).
>
> Instead, if i try to execute the script in default mode the central atom
> sphere is correct
reen size - because I have a small computer) so i can get very high
> resolution images that i can combine together into a high resolution movie.
> Regards,
>
> AC Research
--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.
--
il.com> wrote:
>
> Hi, I am using read_pdbstr function to load a strucutres into pymol. Is there
> a way to do the same for mmtf file formats? (I mean without using temporary
> files)
--
Thomas Holder
PyMOL Principal Devel
so finded that set stick_ball, on is deprecated
>
> "This setting is deprecated in v1.5 and later as it is always enabled."
>
> so i tried to use only set stick_ball_ratio, 3 without luck..
>
> Is there something i am missing? I would like to make something lik
om the header to name
> the selections?
>
> Thank you in advance,
>
> Julian
--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.
import json
import urllib2
from pymol import cmd
@cmd.extend
def pdb_chain_selections(code):
'''
DESCRIPTION
Make selections for every mo
No such
> file or directory
> #include
>^
> compilation terminated.
>
> I then installed msgpack by yum command and tried to run the pymol install
> script again, but the same error still occurred.
>
> I googled thi
C1)F)CCN).
>>>> When I tried to select all Nitrogen atoms which are exclusively in the
>>>> ring only, I tried following command:
>>>> abc=cmd.select('byring elem N')
>>>> But, this selected not only Nitrogen atoms in the ring but Carbon
&
..@geisinger.edu> wrote:
>
> Hi Thomas,
> Thanks for the reply. Didn't work, it just gave the same error message but
> with "idlelib.TreeWidget" instead of "modules.idlelib.TreeWidget"
> Jon
> ____
> From: Thomas Holder &l
epo/plugins/annocryst.py", line 22, in
>
> from modules.idlelib.TreeWidget import TreeItem, TreeNode
> ImportError: No module named modules.idlelib.TreeWidget
>
> I see it exists at /opt/pymol/Pymol-script-repo/modules/idlelib/
Email: chi.celest...@phys.chem.ethz.ch
> tele: 004144 63 37510
>
>> On May 19, 2017, at 5:33 PM, Thomas Holder <thomas.hol...@schrodinger.com>
>> wrote:
>>
>> Hi Celestine,
>>
>> Did you run the "get_raw_distances.py" script first? Y
; distance iface_hbonds, chain A, chain B, mode=2
>
>
>
> # dump (model,index) information
> get_raw_distances iface_hbonds
>
>
> -
> Celestine Chi, PhD
> ETH Zürich
> Laboratory for Physical Chemistry
> Vladimir-Prelog-Weg 2 HCI F 222
ry edge).
>
> Cheers,
>
> Anke
>
>
> Am 19.05.2017 um 10:38 schrieb Thomas Holder:
>> Hi Anke,
>>
>> The obvious difference I can see in your two samples is that the first one
>> contains sticks and spheres representations, and the second one only ha
h...@gmail.com> wrote:
>
> I know I can can find the hydrogen bond interactions between a
> selection and surrounding residues within a certain radius. I would
> like to find a way to retrieve the actual count of those interactions
> per residue. How can I do it in the API?
>
lt;105726...@gms.tcu.edu.tw> wrote:
>
> Hi everyone !
> I want to calculate the b-factor for my protein . Can. Anyone tell me how to
> do b-factor or some tutorial about that.
>
> Thanks in advance :)
--
Thomas Holder
PyMOL Princi
ligns 1632 atoms and gives an RMSD of 7.538, whereas
> action -> align -> to molecule aligns 375 and gives an RMSD of 24.416.
> I have also seen such differences on other pairs of structures.
>
> Any explanation of this phenomenon will be most appreciated.
>
> Thanks i
45710 1.051540 -1.083943,
> 1.840800 1.307029 -0.904629,
> 2.165471 0.781700 -1.754629,
> 1.301289 0.550209 -1.380068,
> 1.840800 1.307029 -0.904629,
> 2.693056 1.515260 -1.343787,
> 2.165471 0.781700 -1.754629,
> 1.840800 1.307029 -0.904629,
> [...]
> #
ue
> selection along specific z-axis coordinates, for example from 6,377-7,139 on
> the z-axis, etc..Like that it selects all residues in that plane.
>
> Marko Sever, PhD student
--
Thomas Holder
PyMOL Pri
zero by using the following alter command:
>alter (resi 84 and name CE1), reps=0
> It seems the reps do changed to 0, but that atom is not being hidden. My
> question is: do we need to refresh the representation after altering one
> atom's reps? if yes, how to do that?
>
m by a H atom and also
> modify the C-H bond to the correct length).
> I know how to make it work by clicking the build panel. But is there a way I
> can write a script to make this happen? Thanks?
--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.
--
ssible that this feature will
> appear in future pymol versions?
>
> Best regards, Mykola Dimura.
>
>>> Unfortunately, the graphics window fonts can't be changed.
>>> But you could increase the size of the buttons in the object menu panel:
>>> set internal_g
olecule), the message: " Extrude-Warning: invalid putty
> settings (division by zero)", appears right after the command:
> cmd.spectrum('b','blue_white_red','yesfit_ALL and name CA')
>
> I really don't know what the problem is. Has anyone had a similar problem and
> cou
le to do so. I can't find the plugin
> manager. In the menu, after the wizard I have 'help' not 'plugins'.
>
> I installed the educational version of MacPyMOL in around Aug/Sep 2015.
>
> Looking forward to your help,
> Regards,
> Raag
--
Thomas Hol
3 session...
>> ./pymol: line 3: 29221 Segmentation fault "/usr/bin/python2.7"
>> "/data/joao/maindisk/software/pymol-svn/modules/pymol/__init__.py" "$@"
>> ```
>>
>> Any clues? Am I doing something wrong?
>>
>> Thanks,
about the python
> api here to be a bit lacking.
>
> https://pymolwiki.org/index.php/Centerofmass
> <https://pymolwiki.org/index.php/Centerofmass>
>
> I would appre
ly=1),chain,resi,resn)
>
> Thanks,
> Abhinav
>
> -Original Message-
> From: Thomas Holder [mailto:thomas.hol...@schrodinger.com]
> Sent: Wednesday, March 22, 2017 1:15 PM
> To: Kumar, Abhinav
> Cc: pymol-users@lists.sourceforge.net
> Subject: Re: [PyMOL] select
Kumar, PhD
> Senior Scientist, Data Science & Computational Biology
> Intrexon, Inc.
> 329 Oyster Point Blvd., South San Francisco, CA 94080
> (650) 597-4072 | aku...@intrexon.com
--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.
://pymolwiki.org/index.php?title=Special:RecentChanges=2017022000=30
We welcome any feedback and bug reports.
Cheers,
- The PyMOL Team at Schrödinger
--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc
xecutive: object "1okyVol" created.
> Volume: created "1okyVol"
> PyMOL>set ray_volume, 1
> Setting: ray_volume set to on.
> PyMOL>png volume.png, ray=0
> ScenePNG: wrote 640x480 pixel image to file "volume.png".
>
>
>
>
> --
&g
PymolString, 1, 1)
cmd.rotate([1, 0, 0], i * angle, currentName, 1, 0, None, [0, 0, 0])
cmd.alter(currentName, "chain='%s';rank=-1" % currentChain)
cmd.create(newPymolString, newPymolString + ' or ' + currentName, 1, 1)
cmd.delete(currentName)
Cheers,
; Em ter, 28 de fev de 2017 às 14:25, Thomas Holder
> <thomas.hol...@schrodinger.com> escreveu:
> Dear João,
>
> The Mobile (iPad) PyMOL interface is rather limited and does not expose these
> options, unfortunately. The only way to display a "grid_mode=on"
er scripts it
> was much easier to make everything one color so each bond was a single
> cylinder. I can use an older version, but I was wondering if there is
> perhaps a new setting I haven't seen yet that might let me revert this
> behavior.
>
>
de to save a screenshot to
> Photos.
>
> When I download two PDB codes, they appear one inside the other...
>
> Is that possibe using the PyMOL app?
>
> Best regards!
--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.
--
'm thinking about executing
> cmd.color for each color (255 times), which should be faster. However
> I'd still prefer to apply cmd.color per residue, so I don't have to
> define bulky selections per color.
>
> Is there some way to accomplish
File
> > Save molecule command. However I have thousands of ligand files to convert.
> May I know if there's a way or script that could do this in a faster way?
>
> Thank you for your time.
>
> Best Regards,
> Ng Kar Weng
> School of Pharmacy
> Taylor's University
he ones in mutagenesis wizard)?
--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.
--
Check out the vibrant tech community on one of the world's most
engaging tech sites, SlashDot.
vity data stored somewhere whilst the file is in use? I ask with the
> aim to extract that data into a python object.
>
> Thanks
> Laurie
--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.
-
ayer.kw_args)
> File "/home/albert/install/pymol/Pymol-script-repo/pymol2glmol.py", line
> 152, in dump_rep
>int(255 * float(bgcolor[1])), int(255 * float(bgcolor[2])))
> IndexError: tuple index out of range
>
>
> Do you have any idea what's the problem?
>
&
3D detected and enabled.
> Executive: Loading version 1.600 session...
> Unable to initialize plugin 'mtsslDockGui' (pmg_tk.startup.mtsslDockGui).
> Unable to initialize plugin 'mtsslWizard' (pmg_tk.startup.mtsslWizard).
> Unable to initialize plugin 'mtsslPlotter' (pmg_tk.startup.mtssl
.pse file and I am just wondering how can we convert it
> with a Linux command line directly to a .html file without opening pymol
> GUI?
>
> Thank you very much.
>
> Albert
--
Thomas Holder
PyMOL Pri
one help
> me out with the same.
>
> Thanks a lot,
>
> Himesh
>
> --
>
> Thanks & Regards,
>
> Himesh Makala
--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.
--
Che
(PDBe uses "" and "_diff" as map names), so scripts are
> backward compatible?
>
> Thanks,
> Filip
--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.
--
Check out the vibrant
e many of you will find it useful. If you come across any bugs or have
>> any feature requests or other suggestions, please feel free to email me
>> directly or create a new issue on Github.
>>
>> Happy PyMOLing!
>>
>> Cheers,
>> Jared
--
Thomas Ho
sliced, and the others are
> for cartoons, spheres and sticks. I couldn't find one for lines.
>
> Anyone have any ideas?
>
> Thanks!
--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.
--
Deve
;>>
>>>
>>>
>>> On 01/13/2017 10:34 AM, Academic Research wrote:
>>>> Pymol Professionals I need your help,
>>>>
>>>> I have the following command:
>>>>
+41 44 632 57 63, http://www.id.ethz.ch/
> samuel....@id.ethz.ch
>
>
> Von: Thomas Holder [thomas.hol...@schrodinger.com]
> Gesendet: Mittwoch, 11. Januar 2017 17:07
> An: Fux Samuel (ID SIS)
> Cc: pymol-users@lists.sourceforge.net
> Betreff: Re: [P
After the "rebuild" command, the isosurface just stays gray while the color
> ramp is shown correctly. Do you have any idea how this problem could be
> solved (is OpenGL2 required for coloring an isosurface) ?
>
> The cluster is running u
Erratum: Of course I meant "solvent accessible", not "excluded".
On 05 Jan 2017, at 09:52, Thomas Holder <thomas.hol...@schrodinger.com> wrote:
> Hi Vincent,
>
> Coloring the cartoon with a color ramp is not possible unfortunately.
> Incentive PyMOL sinc
imie des Protéines
> Drug Resistance and Membrane Proteins Laboratory
> 7 passage du Vercors
> 69007 LYON
> FRANCE
> +33 4 37 65 29 01
> http://www.ibcp.fr
--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.
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