Re: [PyMOL] Can i find a specific sequence in pymol?

2021-12-15 Thread Thomas Holder
Hi Ambbar, To select sequence "ACDEF", you can do: select mysele, pepseq ACDEF See also https://pymolwiki.org/index.php/Selection_Algebra Cheers, Thomas On Wed, Dec 15, 2021 at 7:54 PM Ambbar Aballay González wrote: > > Dear friends, > How can I find and select a specific sequence in

Re: [PyMOL] Loading chempy objects into PyMOL 2.4.0

2021-12-01 Thread Thomas Holder
Hi Raul, I suggest to use cmd.load_coords() to add trajectory frames to your model. https://pymolwiki.org/index.php/Load_coords Cheers, Thomas > On Nov 30, 2021, at 21:49, R Mera wrote: > > Dear all, > > I am trying to implement a reader for

Re: [PyMOL] APBS with ions

2021-11-03 Thread Thomas Holder
Hi Kamil, The "Selection" field uses "polymer & ..." by default, which excludes ions. You can use a selection which includes ions instead, for example "all", "not solvent", or something like "(polymer | name CAL) & ...". Here an example that works for me: fetch 1rx1 alter elem Ca, resn="CAL"

Re: [PyMOL] How to label on surface

2021-10-13 Thread Thomas Holder
Hi Yeping, Try something like this, it moves the label 6 angstrom towards the front: set label_position, [0,0,6] See also https://pymolwiki.org/index.php/label_position Cheers, Thomas > On Oct 11, 2021, at 05:52, sunyeping via PyMOL-users > wrote: > > Dear Pymol users, > > I wish to

Re: [PyMOL] Capping of multiple pdb file using python script in pymol

2021-10-13 Thread Thomas Holder
Hi Shivani, Your selection needs to be object-specific, e.g. like this: for filename in glob("*.pdb"): cmd.load(filename) obj = filename[:-4] editor.attach_amino_acid(obj + " and resi 10 and name N", 'ace') Hope that helps. Cheers, Thomas > On Oct 9, 2021, at 21:18, shivani sharma

[PyMOL] Farewell

2021-04-30 Thread Thomas Holder
it. They have some great plans and I'm excited to watch how they will take PyMOL to the next level. I don't think that my PyMOL journey is over yet. But for the next chapter in my career, I'll "just" be a user and a member of the community. See you around. Cheers, Thomas -- Tho

Re: [PyMOL] Running PyMOL on a headless machine

2021-04-30 Thread Thomas Holder
Hi Andras, Thanks for reporting this issue and for posting your solution/workaround. This issue will be fixed in PyMOL 2.5. Cheers, Thomas On Wed, Mar 24, 2021 at 10:25 AM András Ferenc WACHA wrote: > > Dear fellow PyMOL users, > > I have found a solution (at least a workaround): > > pymol

Re: [PyMOL] Problem with Pymol following update to Mac Big Sur

2021-04-30 Thread Thomas Holder
Hi Marc, The latest versions of PyMOL (e.g. 2.4) work fine on macOS Big Sur. Old versions of MacPyMOL (until 1.8.6) are not compatible, unfortunately, and we're not aware of any workarounds to make it work. Upgrading PyMOL is your only option. Cheers, Thomas On Mon, Apr 19, 2021 at 8:16 AM

Re: [PyMOL] Problem with pymol

2021-03-23 Thread Thomas Holder
> > ___ > PyMOL-users mailing list > Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net > Unsubscribe: > https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe -- Thomas Holder PyMOL Principal Developer Schröd

Re: [PyMOL] How to read the alignment object

2021-02-23 Thread Thomas Holder
Hi Pedro, Are you looking for cmd.get_raw_alignment()? https://pymolwiki.org/index.php/Get_raw_alignment Cheers, Thomas On Tue, Feb 23, 2021 at 9:33 PM Pedro Lacerda wrote: > > Hi, > > I aligned my structures with the align command and the object argument. So I > got an alignment object. >

Re: [PyMOL] representation of residue sidechain within a beta strand?

2021-01-29 Thread Thomas Holder
//sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe >> >> >> _______ >> PyMOL-users mailing list >> Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net >> Unsubscribe: >> https://so

Re: [PyMOL] Iterate over residue index

2021-01-27 Thread Thomas Holder
> Unsubscribe: > https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. ___ PyMOL-users mailing list Archives: http://www.mail-archive.com/pymol-users@lists.sourc

Re: [PyMOL] Mac Installation Question

2021-01-27 Thread Thomas Holder
rategies for installing open source pymol and rdkit I would really > appreciate the help. > > Thank you, > > Justine > > > ___ > PyMOL-users mailing list > Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.

Re: [PyMOL] how to pass an argument to python in pymol

2020-12-01 Thread Thomas Holder
rrect way to pass arguments? > > Thank you vey much. > Michael > ___ > PyMOL-users mailing list > Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net > Unsubscribe: > https://sourceforge.net/projects/pymol/li

Re: [PyMOL] Suppressing text output message when writing a PNG image

2020-11-25 Thread Thomas Holder
, distribute or copy this e-mail. Please inform the sender and > delete the message and attachments from your system. No confidentiality or > any privilege regarding the information is waived or lost by any > mistransmission or malfunction". > > No me imprimas si no es necesario.

Re: [PyMOL] VdW radii

2020-11-17 Thread Thomas Holder
mail-archive.com/pymol-users@lists.sourceforge.net > Unsubscribe: > https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. ___ PyMOL-users mailing list Archives: h

Re: [PyMOL] Importing Pymol as library

2020-11-17 Thread Thomas Holder
mental)’? > > Thanks, > Yannis > > ___ > PyMOL-users mailing list > Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net > Unsubscribe: > https://sourceforge.net/projects/pymol/lists/pymol-users/unsubsc

Re: [PyMOL] cannot read the character in the registraton for education page

2020-11-12 Thread Thomas Holder
Just enter your best guess. If it was wrong, you'll get a new chance with a new code. The code is composed of upper case letters and numbers. Cheers, Thomas On Fri, Nov 13, 2020 at 8:32 AM PLOYPLOEN PHIKULSOD wrote: > > Hello, > > I am registering for permission to use Pymol for educational

Re: [PyMOL] How to get the object name from chempy.Atom

2020-11-09 Thread Thomas Holder
__ > PyMOL-users mailing list > Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net > Unsubscribe: > https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. _

Re: [PyMOL] How to edit a volume field?

2020-11-09 Thread Thomas Holder
gt; @pslacerda > +55 71 9 9981-1856 > http://lattes.cnpq.br/8338596525330907 > ___ > PyMOL-users mailing list > Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net > Unsubscribe: > https://sourceforge.net/projects/pymol/li

[PyMOL] Fwd: Join us: Augmenting PyMOL’s World-Class Visualisation with Cutting Edge Science Webinar on November 12th and 19th

2020-11-05 Thread Thomas Holder
CET > Date: Thursday, Nov. 19 > REGISTER  <https://go.schrodinger.com/har3L2O00E000UPOj030UN7> > > <https://go.schrodinger.com/a0300a03UE0700OUMOjO2rP> > <https://go.schrodinger.com/R00a273OUP0030r0ENUOPj0> > Copyright © 2020 Schrödinger, Inc. > Our address is 120 West 45

Re: [PyMOL] pref_get() on library mode

2020-10-26 Thread Thomas Holder
net > Unsubscribe: > https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. ___ PyMOL-users mailing list Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.ne

Re: [PyMOL] Formatted output

2020-10-26 Thread Thomas Holder
_ > PyMOL-users mailing list > Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net > Unsubscribe: > https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc.

Re: [PyMOL] [EXTERNAL] png command in Educational Pymol

2020-10-20 Thread Thomas Holder
See last question here ("Ray tracing does not work"): https://pymol.org/edu/faq.php Cheers, Thomas On Tue, Oct 20, 2020 at 1:18 PM Mooers, Blaine H.M. (HSC) wrote: > > Hi Jeff, > > I have the incentive version of PyMOL. > It too is saving draw images with ray tracing when using the batch mode

Re: [PyMOL] Pymol install on CentoOS7

2020-10-08 Thread Thomas Holder
> ___ > PyMOL-users mailing list > Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net > Unsubscribe: > https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe -- Thomas Holder PyMOL Principal Developer S

Re: [PyMOL] Rendering Unit Cell in API

2020-10-08 Thread Thomas Holder
cmd.rotate('z',-90) > cmd.ray(1024, 1024) > cmd.zoom(complete=1) > cmd.png(basename+'_X'+'.png', dpi=600) > > cmd.rotate('z',-90) > cmd.rotate('x',-90) > cmd.rotate('z', 90) > cmd.ray(1024) > cmd.zoom(complete=1) > cmd.png(basename+'_Y'+'.png', dpi=600) > > cmd.qui

Re: [PyMOL] Edu-PyMOL Bachelor Thesis

2020-09-24 Thread Thomas Holder
r my question. I look forward to your > response. > Vivian > > > > ___ > PyMOL-users mailing list > Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net > Unsubscribe: > https://sourceforge.net/proj

Re: [PyMOL] Command varargs

2020-07-30 Thread Thomas Holder
Hi Pedro, Add `_self=pymol.cmd` as a keyword argument, then it should work properly as a command. @pm.extend def func(*args, kw1=1, kw2=True, _self=pm): pass Cheers, Thomas On Thu, Jul 30, 2020 at 11:52 AM Pedro Lacerda wrote: > > Hi, > > How can I accept variable arguments in my command?

Re: [PyMOL] Reading Cell Dimensions from GROMACS XTC file

2020-07-14 Thread Thomas Holder
> Unsubscribe: > https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. ___ PyMOL-users mailing list Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge

Re: [PyMOL] choice of color in util.cbc

2020-07-14 Thread Thomas Holder
en-source pymol2.5.0a0 running on windows 10. > > Thanks! > > Charles > ___ > PyMOL-users mailing list > Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net > Unsubscribe: > https://sourceforge.net/projects/pymol/l

Re: [PyMOL] How to count the number of molecules in a selection?

2020-07-09 Thread Thomas Holder
net > Unsubscribe: > https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. ___ PyMOL-users mailing list Archives: http://www.mail-archive.com/pymol-users@lists.sourcefo

Re: [PyMOL] Which 3D setup for a new installation? (Since 3D Vision is discontinued)

2020-07-07 Thread Thomas Holder
PM, Oganesyan, Vaheh > wrote: > > Hi Thomas, > > Can you also mention appropriate graphics cards that pair well with the > Volfoni hardware? > > Thank you. > > From: Thomas Holder > Sent: Tuesday, July 7, 2020 10:03 AM > To: David Krause > Cc: pymol-users@l

Re: [PyMOL] cmd.get_fastastr()

2020-07-07 Thread Thomas Holder
0:59 PM, Pedro Lacerda wrote: > > I used the function to check if the fasta is smaller than 25 characters. If > it is then it is a peptide: > https://github.com/pslacerda/pymol-labimm/blob/master/scripts/peptbase/create.py#L186 > > There is another way to check for pept

Re: [PyMOL] Which 3D setup for a new installation? (Since 3D Vision is discontinued)

2020-07-07 Thread Thomas Holder
y > > +49 (0)69 6301 84971 (Phone) > +49 (0)69 6301 84975 (Fax) > kra...@biochem2.uni-frankfurt.de > > > > ___ > PyMOL-users mailing list > Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net > Unsubscribe:

Re: [PyMOL] cmd.get_fastastr()

2020-07-05 Thread Thomas Holder
___ > PyMOL-users mailing list > Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net > Unsubscribe: > https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. __

Re: [PyMOL] transparent electron density silhouette

2020-06-23 Thread Thomas Holder
_ > PyMOL-users mailing list > Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net > Unsubscribe: > https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc.

Re: [PyMOL] Python script with iterate_state and selection command

2020-06-23 Thread Thomas Holder
t; Thanks in advance for your help > > Stéphane > > > _______ > PyMOL-users mailing list > Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net > Unsubscribe: > https://sourceforge.net/projects/pymol/lis

Re: [PyMOL] Install license file from CLI

2020-06-22 Thread Thomas Holder
ol2 Cheers, Thomas -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. ___ PyMOL-users mailing list Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-us

Re: [PyMOL] Install license file from CLI

2020-06-19 Thread Thomas Holder
you said, but the warning message > keeps popping: > > > > > > > > > El jue., 18 jun. 2020 a las 20:16, Thomas Holder > () escribió: > Hi Antonio, > > Rename the file to "license.lic". > > Cheers, > Thomas > > >

Re: [PyMOL] Install license file from CLI

2020-06-18 Thread Thomas Holder
t; $HOME/miniconda3/share/pymol/ . But a warning text stating "No License File - > For evaluation Only (0 days remaining)" still appears when rendering PNG > files with PyMol. Any suggestions? > > El jue., 18 jun. 2020 a las 12:44, Thomas Holder > () escribió: > Hi Ant

Re: [PyMOL] Install license file from CLI

2020-06-18 Thread Thomas Holder
t print me unless it's necessary. > > ___ > PyMOL-users mailing list > Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net > Unsubscribe: > https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe -- Thomas Hold

Re: [PyMOL] User data

2020-06-15 Thread Thomas Holder
> PyMOL-users mailing list > Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net > Unsubscribe: > https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. ___

Re: [PyMOL] APBS plugin for Sugars

2020-06-15 Thread Thomas Holder
welcome. > > Thank you in advance, > > Mario > ___ > PyMOL-users mailing list > Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net > Unsubscribe: > https://sourceforge.net/projects/pymol/lists/pymol-us

[PyMOL] Python 2 support removed from master branch

2020-06-06 Thread Thomas Holder
his legacy branch, but we will accept pull requests with bug fixes. Cheers, Thomas -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. ___ PyMOL-users mailing list Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net U

Re: [PyMOL] [EXTERNAL] protecting a group during subsequent aligment

2020-06-04 Thread Thomas Holder
that didn't seem to prevent the entries in there to be > moved/aligned again. > > Any clue how to fix my problem? > > Many thanks, -yong > > > _______ > PyMOL-users mailing list > Archives: http://www.mail-archive.com/pymol

Re: [PyMOL] volume representation is extremely dark colored

2020-05-27 Thread Thomas Holder
t; > > > _______ > PyMOL-users mailing list > Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net > Unsubscribe: > https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe -- Thomas Holder PyMOL

Re: [PyMOL] [EXTERNAL] How to compute the interface surface between ligand and protein?

2020-05-22 Thread Thomas Holder
mprove the scoring. > It remains to be seen in practice which of these two types (molecular surface > or SASA) are more useful for my purpose. I also use other molecular > descriptors, but I don't want to elaborate on this because it's out of topic. > > Best, > Thomas > > >

Re: [PyMOL] [EXTERNAL] How to compute the interface surface between ligand and protein?

2020-05-21 Thread Thomas Holder
, while the opposite happens with the protein. > Could someone please explain this to me and verify that I am computing the > interface surfaces correctly? > > I thank you in advance. > Thomas > > > > -- > > == > > Dr. Thomas Evangelidis > >

[PyMOL] PyMOL 2.4 released

2020-05-20 Thread Thomas Holder
. Cheers, - The PyMOL Team at Schrödinger -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. ___ PyMOL-users mailing list Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net Unsubscribe: https://sourceforge.net/projects/p

Re: [PyMOL] How to inspect contents of 's' and 'p' for an atom?

2020-05-19 Thread Thomas Holder
ary if I don't know what is in > it? > PyMOL>iterate 4zho//A/26/CA, print(p) > > > Same question for 's': > PyMOL>iterate 4zho//A/26/CA, print(s) > > > Better still, where would I find documentation for this? > > Thanks, > > Mungo > > > Mu

Re: [PyMOL] Capturing scene pixels without writing image to disk

2020-05-07 Thread Thomas Holder
for your quick response, Thomas. Please, could you elaborate the previous > example a little bit further? I'm a little confused about what you can > accomplish using the callback function you posted. Thx -- Thomas Holder PyMOL Principal Devel

Re: [PyMOL] Capturing scene pixels without writing image to disk

2020-05-06 Thread Thomas Holder
> PyMOL-users mailing list > Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net > Unsubscribe: > https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. _

Re: [PyMOL] For set.view(), there's a Wiki example for the GUI, but not the PyMol API

2020-04-30 Thread Thomas Holder
ven ray-tracing doesn’t need that level of precision. > ___ > PyMOL-users mailing list > Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net > Unsubscribe: > https://sourceforge.net/projects/pymol/lists/pymol-users/unsub

Re: [PyMOL] incomplete secondary structure

2020-04-16 Thread Thomas Holder
ers@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/pymol-users > Unsubscribe: > https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe > > -- > > End of PyMOL-users Digest, Vol 167, Issue 5 > ******* > _

Re: [PyMOL] How to hide dihedral angle labels in mdo animation using set_dihedral

2020-02-25 Thread Thomas Holder
k you very much in advance! > > Best, Nanna H. List > > ___ > PyMOL-users mailing list > Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net > Unsubscribe: > https://sourceforge.net/projects/pymol/lists/pym

Re: [PyMOL] Accessing vertex normals from surface representation within PyMOL session

2020-02-25 Thread Thomas Holder
chive.com/pymol-users@lists.sourceforge.net > Unsubscribe: > https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. ___ PyMOL-users mailing list Archives: http://w

Re: [PyMOL] Pymol Rendering

2020-02-25 Thread Thomas Holder
list > Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net > Unsubscribe: > https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. ___ PyMOL-us

Re: [PyMOL] How to compile pymol with --glut?

2020-02-11 Thread Thomas Holder
; Best regards. > > > ___ > PyMOL-users mailing list > Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net > Unsubscribe: > https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe -- Thomas Holde

Re: [PyMOL] floating external gui

2020-02-11 Thread Thomas Holder
e to start pymol with floating external gui? > > Thanks, Tamas > > ___ > PyMOL-users mailing list > Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net > Unsubscribe: > https://sourceforge.net/projects/pymol/lists/pym

Re: [PyMOL] Getting session file name

2020-02-11 Thread Thomas Holder
n > > Cheers, > Jason M. > ___ > PyMOL-users mailing list > Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net > Unsubscribe: > https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe -- Thomas H

Re: [PyMOL] How to print the time stample on each frame of the movie for molecular dynamics trajectory in Pymol?

2020-01-20 Thread Thomas Holder
ing Sun > ___ > PyMOL-users mailing list > Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net > Unsubscribe: > https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe -- Thomas Holder PyMOL Principal De

Re: [PyMOL] diaplay actural sizes in Pymol

2020-01-20 Thread Thomas Holder
hives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net > Unsubscribe: > https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. ___ PyMOL-users mailing list Arc

Re: [PyMOL] click and select bug in 2.2

2020-01-10 Thread Thomas Holder
chive.com/pymol-users@lists.sourceforge.net > Unsubscribe: > https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. ___ PyMOL-users mailing list Archives: http://www

Re: [PyMOL] Performance of extended commands vs python function

2019-12-18 Thread Thomas Holder
which resulted - it seems - in all these calls piling up. > > Still, I don't know if it's intended behaviour for `sync` to be so much > slower if it's called as a pymol function. Attached you will find a minimal > working example to show the difference. > > > Il giorno lun 16 dic

Re: [PyMOL] Performance of extended commands vs python function

2019-12-16 Thread Thomas Holder
and ewual graphical representation. > > On Mon, Dec 16, 2019, 17:37 Thomas Holder > wrote: > Hi Lorenzo, > > When you say "run from a python script", is that with the graphical GUI? That > "instant update", does that include instant update of visual represe

Re: [PyMOL] Performance of extended commands vs python function

2019-12-16 Thread Thomas Holder
; performance of func even when I call it from within pymol? > > Thank you, > Lorenzo > > ___ > PyMOL-users mailing list > Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net > Unsubscribe: > https://sourcefo

Re: [PyMOL] [EXTERNAL] Differentiate between bond types by color and representation

2019-12-11 Thread Thomas Holder
t; > Am I trying to do this the wrong way? Is it just unfeasible? > > > ___ > PyMOL-users mailing list > Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net > Unsubscribe: > https://sourceforge.net/projects/

Re: [PyMOL] ModuleNotFoundError: No module named 'pymol._cmd'

2019-11-28 Thread Thomas Holder
gt; Markus > > > > ___ > PyMOL-users mailing list > Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net > Unsubscribe: > https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe -- Thomas Holder PyMOL Pr

Re: [PyMOL] Autosave

2019-11-28 Thread Thomas Holder
//pastebin.com/TNSuA0fH > > Thanks, > -Jason > ___ > PyMOL-users mailing list > Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net > Unsubscribe: > https://sourceforge.net/projects/pymol/lists/pymol-users/uns

Re: [PyMOL] Problem loading Amber trajectory

2019-11-28 Thread Thomas Holder
tin > > > ___ > PyMOL-users mailing list > Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net > Unsubscribe: > https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe -- Thomas Holder PyMOL Prin

[PyMOL] Admins for Pymol-script-repo needed

2019-11-15 Thread Thomas Holder
So if you want to become a Pymol-script-repo admin, please send me an email. Thanks, Thomas -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. ___ PyMOL-users mailing list Archives: http://www.mail-archive.com/pymol-users

Re: [PyMOL] Pymol Qt Wayland

2019-11-05 Thread Thomas Holder
Hi Quyen, This works for me: export QT_QPA_PLATFORM=xcb pymol Hope that helps. Cheers, Thomas On Sun, Nov 3, 2019 at 6:15 AM RDirective wrote: > > Dear all, > > I have a slight problem with Pymol on Fedora 31. The vanilla distribution > runs Gnome on Wayland. Pymol complains that

Re: [PyMOL] Get surface coordinates

2019-10-30 Thread Thomas Holder
chive.com/pymol-users@lists.sourceforge.net > Unsubscribe: > https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. ___ PyMOL-users mailing list Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe

[PyMOL] Open position for PyMOL Software Engineer

2019-10-23 Thread Thomas Holder
/schrodingercom/view/P_AADAADpO9VyJDPz7O7 Cheers, The PyMOL Team at Schrödinger -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. ___ PyMOL-users mailing list Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net Unsubscribe: https

Re: [PyMOL] dots with/without ray tracing

2019-10-17 Thread Thomas Holder
> https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. ___ PyMOL-users mailing list Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe

Re: [PyMOL] feature request

2019-10-17 Thread Thomas Holder
did I know about the `set_object_color` > command. > > Thanks for the explanation, Thomas! > > Cheers, > > Jared > -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. ___ PyMOL-users mailing list Archives: http://www.m

Re: [PyMOL] feature request

2019-10-02 Thread Thomas Holder
From: Jared Sampson > Sent: Tuesday, October 1, 2019 2:45 PM > To: Oganesyan, Vaheh ; Thomas Holder > > Cc: pymol-users > Subject: Re: [PyMOL] feature request > > Hi Thomas and Vaheh - > > This is indeed an interesting idea. I was thinking about this in terms of &

Re: [PyMOL] feature request

2019-10-01 Thread Thomas Holder
ne Way, Gaithersburg, MD 20878 > T: 301-398-4640 M: 240-398-0046 > vaheh.oganes...@astrazeneca.com -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. ___ PyMOL-users mailing list Archives: http://www.mail-archive.com/pymol-users@lists.s

Re: [PyMOL] "Qt not available" error from compilation with python2 but not python3

2019-09-19 Thread Thomas Holder
-rf build python2 setup.py --glut install --prefix=~/pymol-install-py2 Hope that helps. Cheers, Thomas -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. ___ PyMOL-users mailing list Archives: http://www.mail-archive.com/pymol-users@lists

Re: [PyMOL] PyMol: incomplete replacement of b- and q-factors

2019-09-13 Thread Thomas Holder
iter(alldist) > alter all, b = next(di) > spectrum b > > Thank you, > Joe > ___ > PyMOL-users mailing list > Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net > Unsubscribe: > https://sourcef

Re: [PyMOL] amino acids displayed for mutagenesis. Hyp? PTMs? (Bruce Onisko)

2019-09-05 Thread Thomas Holder
ing the > SwissModel plugin...) > > Has anyone done this recently? If so maybe point me to a working link, or > step me through the process please? > > Thanks! > > Bruce -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. ___

Re: [PyMOL] aberrant behavior of mouse clicks in PyMOL

2019-08-22 Thread Thomas Holder
om > > > > ___ > PyMOL-users mailing list > Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net > Unsubscribe: > https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe -- Thomas Holder PyMO

Re: [PyMOL] How to calculate rmsd between each state of a MD simulation trajectory and a reference structure?

2019-08-21 Thread Thomas Holder
st > Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net > Unsubscribe: > https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe > > ___ > PyMOL-users mailing list > Archives: http://www.mail-archiv

Re: [PyMOL] HELIX and SHEET records not read by Pymol

2019-08-21 Thread Thomas Holder
eforge.net > Unsubscribe: > https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. ___ PyMOL-users mailing list Archives: http://www.mail-archive.com/pymol-users@lists.s

Re: [PyMOL] count_atoms and states

2019-08-15 Thread Thomas Holder
n-source/commit/c09ce287d447e6c703e57d31ae3e5d53f8359ee1 Cheers, Thomas -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. ___ PyMOL-users mailing list Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net Unsubscribe: https://sourceforge.net/projects/py

Re: [PyMOL] Label volume

2019-08-15 Thread Thomas Holder
t; Laboratório de Bioinformática e Modelagem Molecular > Faculdade de Farmácia / UFBA > > @pslacerda > +55 71 9 9981-1856 > ___ > PyMOL-users mailing list > Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net >

Re: [PyMOL] Plugin upload.

2019-07-12 Thread Thomas Holder
est regards, > > Wael Azzam > B.S in Bioinformatics > Lebanese American University, Beirut -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. ___ PyMOL-users mailing list Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe

Re: [PyMOL] Plugin upload.

2019-07-12 Thread Thomas Holder
;> Will >> >> >> Wael Azzam via PyMOL-users 于2019年7月9日周二 >> 上午3:11写道: >> To whom it may concern, >> >> I am writing to you in the hopes of knowing how to upload a PyMol plugin >> that I developed on the page PyMolW

Re: [PyMOL] The 'select' command for complex residue selection

2019-07-09 Thread Thomas Holder
or resi > 116-119)) or (protein_A and chain C and resi 87-95) > > but it returns syntax error. So what is the correct command for this? > > Thank you in advance -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. ___

Re: [PyMOL] Errors in "Label" page on PyMOL Wiki

2019-07-08 Thread Thomas Holder
Hi Jared, I can confirm this. There is a tag in the page, if I remove the tag the page loads fine. I've sent an email to SBGrid to let them know. Cheers, Thomas On Mon, Jul 8, 2019 at 4:53 AM Jared Sampson wrote: > > Hi PyMOLers - > > I'm currently not able to access the label page on

Re: [PyMOL] `selection` argument in load_traj

2019-06-26 Thread Thomas Holder
ing? > > Thanks, > Lorenzo > ___ > PyMOL-users mailing list > Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net > Unsubscribe: > https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe -- Thoma

Re: [PyMOL] Thermal ellipsoid plot

2019-06-26 Thread Thomas Holder
Hi Koji, Yes it is my understanding that sphere_scale 1.1932 would correspond to 30% probability. Cheers, Thomas > On Jun 25, 2019, at 12:26 PM, koji naka wrote: > > Dear Mr. Thomas Holder, > > Thank you very much for your kind reply. > I am very happy to know the scale

Re: [PyMOL] set transparency for selected elements of secondary structure

2019-06-26 Thread Thomas Holder
list >Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net >Unsubscribe: > https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe > > > > ___ > PyMOL-users mailing list > Archives: http:/

Re: [PyMOL] PDB post-processing and TER records

2019-06-25 Thread Thomas Holder
; # save output as pdb > # I need to add something in the name of output indicating how much > chains have been renamed > # like output_withoutAB.pdb > cmd.save('output_' + '.pdb') > > thanks in advance for help! -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. ___

Re: [PyMOL] PDB post-processing and TER records

2019-06-25 Thread Thomas Holder
> > Thanks in advance! > > вт, 25 июн. 2019 г. в 14:50, James Starlight : >> >> I have got the idea! >> thank you so much Thomas! >> One question: generally if I integrate a pymol silent script inside my >> bash script, I do not need to use cmd.* s

Re: [PyMOL] Thermal ellipsoid plot

2019-06-25 Thread Thomas Holder
hive.com/pymol-users@lists.sourceforge.net > Unsubscribe: > https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. ___ PyMOL-users mailing list Archives: http://www.mail

Re: [PyMOL] PDB post-processing and TER records

2019-06-25 Thread Thomas Holder
Unsubscribe: > https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. ___ PyMOL-users mailing list Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe

Re: [PyMOL] possible bug mouse coordinates

2019-06-14 Thread Thomas Holder
Hi Arnaud, This should be fixed now, see https://github.com/schrodinger/pymol-open-source/commit/af28e453c6 Cheers, Thomas > On Jun 13, 2019, at 5:46 PM, Thomas Holder > wrote: > > Hi Arnaud, > > I can reproduce both issues, at least with "sticks" represe

Re: [PyMOL] Advice on plugin creation

2019-06-14 Thread Thomas Holder
of Biochemistry Tel: ++44 (0)1865 (2)75392 > University of Oxford > Oxford UK, OX1 3QU > > > ___ > PyMOL-users mailing list > Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net > Unsubscribe: > https://sour

Re: [PyMOL] possible bug mouse coordinates

2019-06-13 Thread Thomas Holder
X-ray facilities manager > Newcastle Structural Biology Laboratory > University of Newcastle > Medical School > ICAMB > Framlington place > NE2 4HH Newcastle upon tyne > Phone 0191 208 8931 > > > > ___ > PyMOL

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