Re: [PyMOL] pymol2 does not do the same thing as pymol<2
Hi Fabrice,
Interesting observation. PyMOL reads "metalc" bonds from mmCIF files and
represents them as "zero order" bonds. Apparently this breaks double bond
detection in your given example. This is something we need to fix.
Possible workarounds:
1) Load .pdb files instead of .cif files
2) Load .mmtf files, they have full bonding information, including bond orders
3) Load .cif files, but with connect_mode=4, which looks up all bond orders
from the chemical components dictionary
Relevant settings:
https://pymolwiki.org/index.php/Fetch_type_default
https://pymolwiki.org/index.php/Connect_mode
Cheers,
Thomas
> On Mar 15, 2018, at 5:55 PM, Fabrice Carles <carlesfabr...@gmail.com> wrote:
>
> Dear pymol users,
>
> I would like to know if there is a way to change pymol2 settings in order to
> fit older version.
>
> My problem is very simple. Pymol 2 and pymol 1.8 do not provide the same
> results.
>
> I download and select the ATP molecule in both pymol 1.8.6.0. and 2.0.7:
>
> cmd.fetch('1atp')
> cmd.select('lig','organic')
>
> Pymol 1.8.6.0 detect three double bonds between phosphate and oxygen of ATP
> molecule but pymol2 does not.
> Using the command below, I compare the differences between the two versions
> in sdf file format.
>
> cmd.save('atp.sdf',selection='lig')
>
> diff 1atp_pymol1.8.sdf 1atp_pymol2.sdf
> 2c2
> < PyMOL186 3D 0
> ---
> > PyMOL2.0 3D 0
> 18,19c18,19
> <11.10009.8800 -1.4300 O 0 5 0 0 0 0 0 0 0 0 0 0
> <13.92909.9200 -2.7000 O 0 5 0 0 0 0 0 0 0 0 0 0
> ---
> >11.10009.8800 -1.4300 O 0 0 0 0 0 0 0 0 0 0 0 0
> >13.92909.9200 -2.7000 O 0 0 0 0 0 0 0 0 0 0 0 0
> 24c24
> <15.74806.8350 -0.4270 O 0 5 0 0 0 0 0 0 0 0 0 0
> ---
> >15.74806.8350 -0.4270 O 0 0 0 0 0 0 0 0 0 0 0 0
> 38c38
> < 1 18 2 0 0 0 0
> ---
> > 1 18 1 0 0 0 0
> 41c41
> < 2 19 2 0 0 0 0
> ---
> > 2 19 1 0 0 0 0
> 47c47
> < 3 24 2 0 0 0 0
> ---
> > 3 24 1 0 0 0 0
>
>
>
> 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 et Analytique (ICOA)
>
> University of Orleans - France
--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.
--
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Re: [PyMOL] pymol.finish_launching(['pymol', '-qc']) causes 100% CPU usage
Hi Yang, With PyMOL 2.1, "finish_launching" should not be necessary to use the PyMOL API in jupyter notebook. PyMOL will now automatically start a backend process (without the GUI, like with "-c") in the main thread if you call any pymol.cmd function. Check out this screenshot: https://pymol.org/alpha/jupyter-notebook.png On the other hand, "finish_launching" will launch PyMOL in a new thread with an event loop, which will cause 100% CPU usage (at least with "-c"). Cheers, Thomas > On Mar 15, 2018, at 1:35 AM, Yang Su <s...@crystal.harvard.edu> wrote: > > Dear List, > > I would like to use some of the pymol capabilities with my other python code > in jupyter notebook. But after running > > import pymol > pymol.finish_launching(['pymol', '-qc']) > > CPU usage stays at 100% for the python 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 it a bug in pymol? > > Thanks, > > Yang -- 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! http://sdm.link/slashdot ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
[PyMOL] PyMOL 2.1 released
Greetings, We are happy to announce the release of PyMOL 2.1. Download ready-to-use installers from https://pymol.org/ or update your 2.0 installation with "conda update -c schrodinger pymol". We also have exciting news for those who prefer to compile PyMOL from source. We’ve pushed the PyMOL 2.0 and 2.1 user interface updates to the open-source repository at sourceforge (rev 4187). New features include (Incentive and Open-Source): - new selection keywords "polymer.protein" and "polymer.nucleic" - MMTF export - plugins initialized by default (can be suppressed with -k) Incentive PyMOL only: - "auto_copy_images" support on all platforms - SpaceNavigator support on all platforms (requires installation of additional drivers, see https://pymol.org/spacenavigator/ ) - colored errors and warnings in the feedback window - Stereo 3D auto-detection 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. -- Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] Has anybody had success installing Pymol 1.3 from source on MacOSX 10.13?
on of 'Array1D'
> rowptr_(M, r), colind_(nz, c), dim1_(M), dim2_(N) {}
> ^
> modules/cealign/src/tnt/tnt_array1d.h:63:11: note: candidate
> constructor
> not
> viable: no known conversion from 'const int *' to 'const int'
> for
> 2nd
> argument; dereference the argument with *
> Array1D(int n, const T );
> ^
> modules/cealign/src/tnt/tnt_array1d.h:64:11: note: candidate
> constructor
> not
> viable: 2nd argument ('const int *') would lose const qualifier
> Array1D(int n, T *a);
> ^
> modules/cealign/src/tnt/tnt_array1d.h:62:11: note: candidate
> constructor
> not
> viable: requires single argument 'n', but 2 arguments were
> provided
> explicit Array1D(int n);
> ^
> modules/cealign/src/tnt/tnt_array1d.h:65:14: note: candidate
> constructor
> not
> viable: requires single argument 'A', but 2 arguments were
> provided
> 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();
> ^
> In file included from modules/cealign/src/ccealignmodule.cpp:32:
> In file included from modules/cealign/src/ccealignmodule.H:36:
> In file included from modules/cealign/src/tnt/tnt.h:55:
> modules/cealign/src/tnt/tnt_sparse_matrix_csr.h:97:18: error: no
> matching
> constructor for initialization of 'Array1D'
> rowptr_(M, r), colind_(nz, c), dim1_(M), dim2_(N) {}
>^ ~
> modules/cealign/src/tnt/tnt_array1d.h:63:11: note: candidate
> constructor
> not
> viable: no known conversion from 'const int *' to 'const int'
> for
> 2nd
> argument; dereference the argument with *
> Array1D(int n, const T );
> ^
> modules/cealign/src/tnt/tnt_array1d.h:64:11: note: candidate
> constructor
> not
> viable: 2nd argument ('const int *') would lose const qualifier
> Array1D(int n, T *a);
> ^
> modules/cealign/src/tnt/tnt_array1d.h:62:11: note: candidate
> constructor
> not
> viable: requires single argument 'n', but 2 arguments were
> provided
> explicit Array1D(int n);
> ^
> modules/cealign/src/tnt/tnt_array1d.h:65:14: note: candidate
> constructor
> not
> viable: requires single argument 'A', but 2 arguments were
> provided
> 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/ccealignmodule.cpp:588:5: warning: variable 'o' is
> incremented both in the loop header and in the loop body
> [-Wfor-loop-analysis]
> o++;
> ^
> modules/cealign/src/ccealignmodule.cpp:431:36: note: incremented here
> for ( int o = 0; o < bufferSize; o++ ) {
>^
> 3 warnings and 2 errors generated.
> error: command 'clang' failed with exit status 1
> === BUILD ERRORS END ===
>
> --
> Martin Plochberger
> **
> Max F. Perutz Support GmbH
> Dr. Bohr-Gasse 9, Room: 4.220
> A-1030 Vienna
> **
> Tel.: +43-1-4277-24041
--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.
--
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Re: [PyMOL] pymol comments
Hi Ulrike, > - Is there a command, which would be: select all residues, which are right > now shown as sticks ? Background : sometimes you analyze the protein a little > bit more empirically, that means you highlight some residues in sticks e.g. > at domain interfaces , then you undo this and take others. If there is not a > command like this, it would be convenient to have it. Yes you can select by representation: select mysele, rep sticks See "Style" selectors in the operator table: https://pymolwiki.org/index.php/Selection_Algebra > - the undo button (academic pymol version 2.0.5) is still not working (but I > guess you know this, would be nice to have an undo in the academic licence) Adding undo for styling etc. is on the roadmap! The already existing undo button only covers editing operations (stuff you can do in the builder, like adding bonds or fragments). > - Is there a command, which would give you all the image specific stettings. > Background: sometimes you create a figure you save the .png, but you don't > click the log command for the .pse file. After some month/years you want to > generate a similar figure, and then it looks pretty similar but not > identical. I guess it would be more complicated, to import the .png in pymol, > and retrieve all "figure" options (like ray trace mode, antialias, dash > width, transparency etc) . But still .. such a feature would be useful. If you want to list all settings which have been changed (have a non-default value) you can use this script: https://pymolwiki.org/index.php/Save_settings > - sometimes pymol (version 2.0.5) crashes, especially before ray-ing more > complex sceneries (but I guess this is a common bug. Still, would be nice to > have that fixed) It's possible that you run out of memory when ray tracing a very complex scene. You could try lowering the "hash_max" setting, which trades computing time for memory usage: https://pymolwiki.org/index.php/Hash_max If it's crashing for a different 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 tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] Installing Pymol API on linux for Anaconda Python 3.5
Hi Ahmad, We currently only provide packages for Python 2.7 and 3.6. Any chance you could upgrade to 3.6 or create a new environment with 3.6? This is how you would do it with a new environment: # create environment with PyMOL and Python 3.6 conda create -n py36 -c schrodinger pymol python=3.6 # activate environment and run PyMOL source activate py36 pymol Cheers, Thomas > On Mar 2, 2018, at 8:05 PM, Ahmad Abdelzaher <underoath...@gmail.com> wrote: > > Hello, > > I'm trying to nstall the Pymol API on linux for Anaconda Python 3.5. > > I tried the commands here: https://anaconda.org/schrodinger/pymol, this is > what I got. > I would appreciate if someone helps me install it. > > [labusr@luxor Downloads]$ conda install -c schrodinger pymol > Fetching package metadata ... > Solving package specifications: . > > UnsatisfiableError: The following specifications were found to be in conflict: > - pymol -> freemol >=1.157 -> python 3.6* > - python 3.5* > Use "conda info " to see the dependencies for each package. > > [labusr@luxor Downloads]$ conda install -c schrodinger/label/alpha pymol > Fetching package metadata ... > Solving package specifications: > > PackageNotFoundError: Packages missing in current channels: > > - pymol -> freemol >=1.157 > - pymol -> glew >=2.0.0,2* > - pymol -> mtz2ccp4_px > - pymol -> pmw > - pymol -> rigimol > - pymol -> simplemmtf-python > > We have searched for the packages in the following channels: > > - https://conda.anaconda.org/schrodinger/label/alpha/linux-64 > - https://conda.anaconda.org/schrodinger/label/alpha/noarch > - https://conda.anaconda.org/salilab/linux-64 > - https://conda.anaconda.org/salilab/noarch > - https://repo.continuum.io/pkgs/main/linux-64 > - https://repo.continuum.io/pkgs/main/noarch > - https://repo.continuum.io/pkgs/free/linux-64 > - https://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 Developer Schrödinger, Inc. -- Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] On APBS, Isomesh generation and export
Hi Fernando, Can't find any bad english in your email :-) 1: https://en.wikipedia.org/wiki/Marching_cubes 2: To open the isomesh again in PyMOL, I suggest to save a PyMOL session file (.pse). Getting access to the actual geometry is more tricky. There is a script on the PyMOLWiki which can convert isomesh and isosurface objects to CGOs. The script could be a starting point for you to export a custom file. The data is rather simple, just a sequence of vertices and normals. https://pymolwiki.org/index.php/Dump2CGO 3: VTK? scikit-image? Cheers, Thomas > On Feb 5, 2018, at 4:24 AM, Fernando Oliveira <fll.oliveira...@gmail.com> > wrote: > > Hi! > > This is my first e-mail to this list. Sorry in advance for my bad english. > > I've been using APBS for the past month in order to build protein binding > sites representations for a artificial neural network I've been working on. > At first I used the OpenDX output file from APBS stand-alone but I wanted to > generate Isomesh files aswell, in order to store the files conveniently for > future analysis or even to use as data input at some order work. > > 1- When APBS finished calculation, it creates a map object. But how does > PyMol translate the .dx map into that beautiful Isomesh? (achievable using > the Isomesh command aswell) > > 2- How to save that isomesh in a way I could open it again with Pymol or > another Visualization tool? (I 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) > > Thanks for the attention. -- 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! http://sdm.link/slashdot ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] Load command to get two sessions together
Hi Maria, If the load command fails, then you don't have the correct "working directory". You can query PyMOL's working directory with the "pwd" command and change it with "cd". See: https://pymolwiki.org/index.php/Pwd https://pymolwiki.org/index.php/Cd Or more easily from the PyMOL 2.0 menu: "File > Working Directory > Change..." Loading session files "partially" has also become even easier in PyMOL 2.0. Just use "File > Open...", after browsing for your .pse file PyMOL will show a dialog where you can choose to load partial or not. Cheers, Thomas > On Feb 6, 2018, at 12:46 PM, COSTA Maria <maria.co...@i2bc.paris-saclay.fr> > wrote: > > Dear PyMOL users, > > I would like to combine two pymol sessions together to compare to different > conformations of a molecule that I have in two different pse files. > > One of you suggested me the following (and this works with others) > > load session1.pse > load session2.pse, partial=1 > > but in my case, when I open a new pymol session and type : load > nameofmysession.pse I get an error saying ‘can’t open nameofmysession.pse’ ? > Is this because pymol doesn’t find my pse file in my computer ? If yes, > where should I store my pse session files ? > > Also, regarding how to proceed: Should I open a new pymol session and type > the two command lines above successively ? 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. -- Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] Poll: new protein/nucleic selection keywords
We've closed the poll. Thanks to everyone who participated! The result wasn't quite what I was hoping for ;-) The clear winners are "protein" and "nucleic". But I also got direct feedback that adding "protein" as a keyword would introduce backwards incompatibility with exiting workflows, where "protein" is used as an object or selection name. So this is what's we'll do: 1) add "polymer.protein" and "polymer.nucleic" as the new keywords (place #2 in the poll) 2) let PyMOL print a deprecation warning if "protein" 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 PM, Thomas Holder <thomas.hol...@schrodinger.com> > wrote: > > We'd like to know your thoughts! > > How should we name the new selectors for protein and nucleic acid? > > Link to poll: > https://goo.gl/forms/r0Ck03VTytZQxN4A2 > > We will enhance the PyMOL selection language by adding a new selector for > protein, and a new one for nucleic acid. They will be subsets of the already > existing "polymer" selector. > > The obvious keyword choices seem to be "nucleic" and "protein". However, this > would likely introduce conflicts with existing workflows where e.g. files are > named "nucleic.pdb" or "protein.pdb", and PyMOL 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 Holder PyMOL Principal Developer Schrödinger, Inc. -- Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] Export Pymol session settings
Hi Martin, Check out this script: https://pymolwiki.org/index.php/Save_settings Cheers, Thomas > On Feb 7, 2018, at 12:09 PM, MARTIN ALCORLO PAGES <malco...@iqfr.csic.es> > wrote: > > Hi there! > > I am Martin, I would like to know if there is a way to export 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 one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] Color bar for volume?
Hi Murpholino,
You could convert your volume colors to a ramp object with a Python script like
this:
# conversion function
def volume2ramp(volname, rampname='', mapname='none'):
v = cmd.volume_color(volname)
colors = []
for i in range(0, len(v), 5):
colors.append('0x%02x%02x%02x' % (
int(v[i + 1] * 0xff),
int(v[i + 2] * 0xff),
int(v[i + 3] * 0xff)))
cmd.ramp_new(rampname or cmd.get_unused_name('ramp'),
mapname, v[0::5], colors)
# apply to your volume object
volume2ramp('myvolume')
Hope that helps.
Cheers,
Thomas
> On Feb 6, 2018, at 3:36 PM, Murpholino Peligro <murpholi...@gmail.com> wrote:
>
> Is there a way to add a color bar to a volume?
> I am looking for something like the bar in the last picture here
> (https://pymolwiki.org/index.php/Ramp_New)
> This is my volume https://www.dropbox.com/s/x4ic7uvdlknk8us/volume.png?dl=0
>
>
> Thanks.
--
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PyMOL Principal Developer
Schrödinger, Inc.
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[PyMOL] Schrodinger is hiring for PyMOL!
The PyMOL team has an open position for a software engineer! We are looking for a highly qualified software engineer and would love to fill this position from within the community. The ideal candidate has a background in computational chemistry or biology and is an avid PyMOL users. Ability to write C++ and Python code that is well-designed, modular, maintainable, testable, and documented is essential. PyMOL has an amazing user base and your contribution will have a recognized impact. Details and how to apply: https://www.schrodinger.com/careers/software-engineers/3d-scientific-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, Slashdot.org! http://sdm.link/slashdot ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] viewport in pymol2
Hi Gary,
Which operating system do you use?
PyMOL 1.x was hard coded to place the window in the upper left corner of the
screen. PyMOL 2.x leaves window placement up to the operating system (window
manager). E.g. KDE on Linux places the window in the least occupied screen area
(my favorite), MacOS always puts it in the center of the screen.
If you're launching from the command line, you could also specify width and
height like this, which is applied before the window manager places the window:
pymol -W 1350 -H 950
PyMOL 2.1 will bring back the "window" command (it's non-functional in 2.0),
which hopefully will resolve the issue for you. It will allow you to fit the
window back onto the screen after resizing.
# pymolrc:
cmd.viewport(1350, 950)
cmd.window('fit')
A pre-release build of PyMOL 2.1 is available here: https://pymol.org/alpha/
Cheers,
Thomas
> On Jan 31, 2018, at 9:58 AM, Gary Hunter <gary.hun...@um.edu.mt> wrote:
>
> My pymolrc file contains a line: viewport 1350,950
> which nicely fills my screen when I start pymol 1.8. However in pymol2 the
> screen has the correct dimensions but the whole thing is offest to the right
> and down. What should be the top left corner of the window is placed about a
> quarter of the way from the left hand side and about one sixth of the way
> down from the top.
>
> Is it a bug or is there a new viewport command?
>
>
>
> --
> Prof. Gary J. Hunter,
>
> Laboratory 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/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 in error please inform the sender and remove it from your
> system.
--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.
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Re: [PyMOL] PyMOL 2.0.7 is selecting wrong atoms
Hi Vijay,
All "by"-operators have a weak priority, so you'll need an extra set of
parenthesis there:
carb_pos = cmd.select('e. C and (byring e. C) and (pc.>0)')
See also the yellow highlighted note about "Entity expansion" here:
https://pymolwiki.org/index.php/Selection_Algebra
Cheers,
Thomas
> On Feb 1, 2018, at 4:16 AM, Vijay Masand <vijaymas...@gmail.com> wrote:
>
> Dear PyMOL users,
> Today, I used following command to select positively charged ring
> carbon atoms, surprisingly, PyMOL 2.0.7 selected negatively charged
> ring carbon 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
--
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PyMOL Principal Developer
Schrödinger, Inc.
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Re: [PyMOL] Can I easily specify an alignment to use in the sequence display?
Hi Tony, It's possible, but not out of the box. I wrote a script for this some time ago which uses biopython and emboss. If you're using Linux or MacOS, everything is prepackaged for you in Anaconda Cloud. For installation instructions and examples, see: https://pymolwiki.org/index.php/Load_aln Cheers, Thomas > On Jan 11, 2018, at 11:40 AM, Tony Lewis <tonyele...@gmail.com> wrote: > > Dear PyMOL people, > > Please can anyone tell me whether there's an easy way to use an alignment of > the residues in the displayed structures (say, from a FASTA file) to align > 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. -- Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] Record and load coordinates
Hi Ben,
The coordinates argument must have a Nx3 shape, that means:
len(coordinates) = number of atoms
len(coordinates[0]) = 3
You can use numpy's reshape() function:
import numpy
coordinates = numpy.asfarray(coordinates).reshape((-1,3))
cmd.load_coords(coordinates, '%prot')
I recommend to prefix the object name with "%" to unambiguously address a named
object or selection. I mention this because I just ran into a common selection
language ambiguity problem myself: I named my object "obj01" and then pasted
your code without changing the object name. The error message was "atom count
mismatch" instead of "invalid selection name". Why? Because "prot" was
evaluated as the selection keyword "protected", so it was a valid (but empty)
selection expression.
Cheers,
Thomas
> On Jan 11, 2018, at 7:43 AM, Benjamin Bailly <bbai...@gmail.com> wrote:
>
> Hi everyone,
>
> I have been scratching my head quite a bit on this one, I am sure there must
> be a simple solution but I can't seem to figure it out.
>
> In short, I would like to record the spacial coordinates of a protein so that
> when I run my script I can fetch it from the PDB and place it exactly where I
> would like it to be.
>
> I used this command to obtain the coordinates, and here is the output I get:
>
> PyMOL>print cmd.get_coords('prot')
> [[159.402 258.709 204.556]
> [159.932 259.514 204.223]
> [158.951 258.206 203.792]
> ...
> [117.662 263.108 309.314]
> [115.591 265.038 307.88 ]
> [116.386 259.713 306.195]]
>
> To load the position in my script I know that I should be able to use the
> following command however I can not figure out the 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 am not
> sure of its format.
>
> Your help would be much appreciated,
>
> Many thanks
>
> Ben
--
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PyMOL Principal Developer
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Re: [PyMOL] Poll: new protein/nucleic selection keywords
Hi Wolfram, That reminds me that I compiled a (very incomplete) selection language comparison table a long time ago. Finally managed to upload it to the PyMOLWiki: https://pymolwiki.org/index.php/Selection_Language_Comparison Phenix's and PyMOL's language are actually pretty close. Cheers, 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? > Wolfram Tempel -- 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! http://sdm.link/slashdot ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
[PyMOL] Poll: new protein/nucleic selection keywords
We'd like to know your thoughts! How should we name the new selectors for protein and nucleic acid? Link to poll: https://goo.gl/forms/r0Ck03VTytZQxN4A2 We will enhance the PyMOL selection language by adding a new selector for protein, and a new one for nucleic acid. They will be subsets of the already existing "polymer" selector. The obvious keyword choices seem to be "nucleic" and "protein". However, this would likely introduce conflicts with existing workflows where e.g. files are named "nucleic.pdb" or "protein.pdb", and PyMOL 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 Holder PyMOL Principal Developer Schrödinger, Inc. -- Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] Upgraded from 1.7 to 1.9: Different behavior
Hi Thomas, To have same stick size for hydrogens, set stick_h_scale to 1.0, see: https://pymolwiki.org/index.php/stick_h_scale I don't think that PyMOL's behavior for loading multi-entry .sdf files has changed. If get the same behavior in 1.7.2.1 and any other version. The entries are loaded into one object as discrete states, with the same (carbon) color. Adding hydrogens to discrete objects was never supported. Are you sure you didn't load .sdf files "multiplexed" in the past? This would split the states into individual objects. load targets.sdf, multiplex=1 If your example really behaves different in 1.9 and 1.7, then it would be great if you could send me the input files. Thanks, Thomas > On Dec 14, 2017, at 9:18 AM, Thomas Strunz <beginn...@hotmail.de> wrote: > > I've upgraded some of the users to version 1.9.0.0 due to moving to windows > 10. It's the build from Christoph Gohlke. > > We use it mainly for one purpose and to make it easier I created a short pml > script to load the data and apply settings. However pymol doesn't behave the > same anymore. > > The script: > > reference.sdf > targets.sdf > preset.pretty(selection='all') > set valence, 1 > set stick_radius, 0.2 > > In version 1.7.2.1 this would load the 2 files and all mols in file 2 had a > different coloring than in file 1. Also hydrogen hat the same stick size as > the other bonds. I could go to hide/show to remove/add the hydrogens. > > In Version 1.9.0.0 this is different: > > • all molecules have the same color. Changing color isn't applied > automatically anymore > • The hydrogen sticks are tiny. how do I make them the same size again? > (least 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 show hide hydrogens? > > Thanks for the help. > > Thomas -- 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! http://sdm.link/slashdot ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] loading PQR-format coordinates
Hi Wolfram, Yes, mmCIF has been suggested to PDB2PQR developers, see: https://github.com/Electrostatics/apbs-pdb2pqr/issues/471 Cheers, Thomas > On Dec 7, 2017, at 8:06 PM, wtempel <wtem...@gmail.com> wrote: > > Thomas, > how did you know? I removed the --whitespace 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 run pdb2pqr with the --whitespace option? If yes, remove that and see > if PyMOL is happy with the output. > > Some versions of PyMOL's APBS Tools plugin have the --whitespace option by > default (first page, "pdb2pqr command line options") but it seems that this > flag creates about as many problems as it solves. The correct solution would > be to retire the PQR format and replace it with mmCIF, which is not a fixed > column format. > > Cheers, > Thomas > > > On Dec 7, 2017, at 1:14 AM, wtempel <wtem...@gmail.com> wrote: > > > > Hello, > > loading a pqr (PDB2PQR version 2.1.1) file into pymol 1.7 … 1.9 garbles the > > model in some systematic way, whereas PDB2PQR version 1.8 output appears to > > be displayed correctly. After superficial inspection I concluded that in > > 2.1.1 output, columns from (and including) the atom number appear to be > > shifted to the right by one position. Indeed, when I apply > > sed 's/^ATOM /ATOM/', the so modified 2.1.1 output appears to be displayed > > correctly in PyMOL. My question to those familiar with pqr models and the > > pymol source: is the sed hack safe as in that it would not distort any > > 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 engaging tech sites, Slashdot.org! http://sdm.link/slashdot ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] default view on load (2.0)?
Hi Paul, Put this line in your pymolrc file (File > Edit pymolrc): set auto_show_classified, 0 See also https://pymolwiki.org/index.php/auto_show_classified Cheers, Thomas > On Dec 12, 2017, at 7:22 PM, Paul Paukstelis <shocksofmig...@gmail.com> wrote: > > Forgive me if 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 PyMOL Principal Developer Schrödinger, Inc. -- Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] How to select nucleic/protein separately
Hi Tony, Unfortunately, PyMOL knows only temporarily during cartoon generation what's protein and what's nucleic acid. It doesn't store this information with the atoms. Maybe the following is a more robust hack than using residue names: select protein, (byres polymer & name CA) select nucleic, (byres polymer & name P) select rna, (byres polymer & name O2') select dna, (nucleic & !rna) To update these selections with a single key press, put this in your pymolrc: set_key F1, \ select protein, (byres polymer & name CA) \ select nucleic, (byres polymer & name P) \ select rna, (byres polymer & name O2') \ select dna, (nucleic & !rna) Cheers, Thomas > On Nov 30, 2017, at 1:00 PM, Tony Lewis <tonyele...@gmail.com> wrote: > > Dear PyMOL people, > > Please can anyone tell me if there's a standard way to select either of > nucleic / protein separately? > > I can use `polymer` to get both together but I can't see a standard way to > distinguish nucleic / protein within that. > > I'm currently using something like `resn A+C+G+U+DA+DC+DG+DT` to identify > nucleic but that's inadequate because it misses out various resn values (eg > BRU, OMG etc) that are part of modified DNA/RNA. > > The thing is: PyMOL clearly *knows* which bits are protein versus nucleic > because it draws the cartoons accordingly. So it feels like I should be > accessing this info from PyMOL rather 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 vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] loading PQR-format coordinates
Hi Wolfram, Do you run pdb2pqr with the --whitespace option? If yes, remove that and see if PyMOL is happy with the output. Some versions of PyMOL's APBS Tools plugin have the --whitespace option by default (first page, "pdb2pqr command line options") but it seems that this flag creates about as many problems as it solves. The correct solution would be to retire the PQR format and replace it with mmCIF, which is not a fixed column format. Cheers, Thomas > On Dec 7, 2017, at 1:14 AM, wtempel <wtem...@gmail.com> wrote: > > Hello, > loading a pqr (PDB2PQR version 2.1.1) file into pymol 1.7 … 1.9 garbles the > model in some systematic way, whereas PDB2PQR version 1.8 output appears to > be displayed correctly. After superficial inspection I concluded that in > 2.1.1 output, columns from (and including) the atom number appear to be > shifted to the right by one position. Indeed, when I apply > sed 's/^ATOM /ATOM/', the so modified 2.1.1 output appears to be displayed > correctly in PyMOL. My question to those familiar with pqr models and the > pymol source: is the sed hack safe as in that it would not distort any > 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 engaging tech sites, Slashdot.org! http://sdm.link/slashdot ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] NME and ACE capping from script
Hi Simon,
My example works for me in PyMOL version 1.8.0 and later. Which version do you
use?
Thomas
> On Nov 18, 2017, at 3:59 PM, Simon Kit Sang Chu <simoncks1...@gmail.com>
> wrote:
>
> Hi Thomas,
>
> Thanks for your help! But the NME and ACE are added 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:
>
> from pymol import cmd, editor
> cmd.set('retain_order', 0)
> cmd.fab('APAPAPAP')
> editor.attach_amino_acid("last name C", 'nme')
> editor.attach_amino_acid("first name N", 'ace')
>
> Hope that helps.
>
> Cheers,
> Thomas
>
> > On Nov 17, 2017, at 8:26 AM, Simon Kit Sang Chu <simoncks1...@gmail.com>
> > wrote:
> >
> > Hi everyone,
> >
> > I am generating segments of peptide to be used in GROMACS. I might be using
> > amber which does not allow automatic capping. Therefore, I hope to solve it
> > with Pymol.
> >
> > Currently, I use a pml scipt to generate the pdb file automatically. The
> > script is simple.
> >
> > for aa in "APAPAPAP" : cmd._alt(string.lower(aa))
> > cmd.save("peptide.pdb")
> >
> > However, if I want to add NME and ACE caps, is there any residue code
> > 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 Developer
> Schrödinger, Inc.
>
>
>
--
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PyMOL Principal Developer
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Re: [PyMOL] Pymol crashes
Hi Davinder, Usually such crashes are related to the graphics driver. Does PyMOL 2.0 also crash on your machine? https://pymol.org/2/#download Thomas > On Nov 14, 2017, at 11:44 PM, Dhalla, Davinder <d.k...@uleth.ca> wrote: > > Hi, > > I am trying to launch Pymol version 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 should I do? > > Regards > Davinder -- 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! http://sdm.link/slashdot ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] NME and ACE capping from script
Hi Simon,
I think this is the code you're looking for:
from pymol import cmd, editor
cmd.set('retain_order', 0)
cmd.fab('APAPAPAP')
editor.attach_amino_acid("last name C", 'nme')
editor.attach_amino_acid("first name N", 'ace')
Hope that helps.
Cheers,
Thomas
> On Nov 17, 2017, at 8:26 AM, Simon Kit Sang Chu <simoncks1...@gmail.com>
> wrote:
>
> Hi everyone,
>
> I am generating segments of peptide to be used in GROMACS. I might be using
> amber which does not allow automatic capping. Therefore, I hope to solve it
> with Pymol.
>
> Currently, I use a pml scipt to generate the pdb file automatically. The
> script is simple.
>
> for aa in "APAPAPAP" : cmd._alt(string.lower(aa))
> cmd.save("peptide.pdb")
>
> However, if I want to add NME and ACE caps, is there any residue code
> 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 Developer
Schrödinger, Inc.
--
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Re: [PyMOL] Wrong atomic type when molecules are saved into mol2
Hi Célien, In my understanding, since every aromatic carbon is sp2 hybridized, PyMOL's output is not wrong. The problem is that PyMOL only knows about delocalized bonds, it doesn't have a proper concept of aromaticity (doesn't implement Hückel's rule). For example you sometimes also see PyMOL's "aromatic" bonds on carboxyl groups. There is actually some code to classify atoms with delocalized bonds as aromatic for MOL2 output, but it's disabled: https://sourceforge.net/p/pymol/code/HEAD/tree/trunk/pymol/layer2/Mol2Typing.cpp#l35 Bonds are exported as aromatic (ar) because the MOL2 format doesn't have a "delocalized" type, so "ar" is still the best match for PyMOL's classification. Hope that helps. Cheers, Thomas > On Nov 14, 2017, at 12:10 PM, Célien Jacquemard - Employé > <jacquem...@unistra.fr> wrote: > > Hello, > > I'm using PyMOL 1.8.6.1 (64 bits) on a Linux distribution (CentOS 7). I used > PyMOL API for CE alignment (protein and ligand) with a reference (target) > protein. Then, I saved the aligned protein and ligand. Input and output > format are mol2. However, I noticed that atomic types 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 > > Célien Jacquemard -- 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! http://sdm.link/slashdot ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] Installing Edupymol on centos 7
Hi Ahmad, Inside the pymol directory, run: ./pymol In case the external window does not open, install the LibXScrnSaver package on your system. Is there a reason why you don't use PyMOL 2.0 instead? We do provide an edu license file for PyMOL 2.0 on the Edu PyMOL download page. Cheers, Thomas > On Nov 5, 2017, at 11:49 PM, Ahmad Abdelzaher <underoath...@gmail.com> wrote: > > I just downloaded the free Edupymol version, > EduPyMOL-v1.7.4.5-Linux-x86_64.tar.bz2. > > I untarred using tar -xvjf EduPyMOL-v1.7.4.5-Linux-x86_64.tar.bz2. > > Now 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 Holder PyMOL Principal Developer Schrödinger, Inc. -- Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] running pymol on zSpace (UNCLASSIFIED)
Hi Simon, zSpace support was never in any official PyMOL release (neither Open-Source nor Incentive PyMOL). The zSpace company had their own custom patched version of Open-Source PyMOL which they deployed to some customers. I don't know if they still support it. Cheers, Thomas > On Oct 25, 2017, at 2:26 PM, Su, Simon M CIV USARMY RDECOM ARL (US) > <simon.m.su@mail.mil> wrote: > > CLASSIFICATION: UNCLASSIFIED > > Hello, > > While googling for "zspace molecular visualization", I came across > http://zspace.com/about/press-releases/zspace-announces-platform-support-for > -pymol-and-avogadro released back in 2013. However, when I tried to google > for information on how to run either PyMOL or Avogadro on zSpace, I am not > able to find anything useful. > > Is the support for zSpace in PyMOL not available in the open 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 > > > CLASSIFICATION: UNCLASSIFIED -- 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! http://sdm.link/slashdot ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] exporting/saving .obj and .mtl
Hi Verena, You're not doing anything wrong. Generation of .mtl output is not implemented. Of course saving an empty file is useless and confusing. We should remove the (non-functional) .mtl export and raise a warning if someone tries to save an .mtl file. Cheers, Thomas > On Oct 26, 2017, at 4:02 PM, Verena Resch <verena_re...@gmx.net> wrote: > > Hi all, > I was wondering if there is an option to export both the .obj and .mtl file > from pymol. > Saving as .obj works perfectly fine, however when I save as .mtl the file is > empty. > > Am I doing 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 -- 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! http://sdm.link/slashdot ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] how to iterate over residues with specific range of b-factors
Hi Li, Showing sticks: show sticks, b > 20 and b < 50 Iterating over residues: iterate byca (b > 20 and b < 50), print(resi) Cheers, Thomas > On Nov 1, 2017, at 6:18 PM, Li Xue <me.li...@gmail.com> wrote: > > Hello, > > I want to select residues with a 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@uu.nl -- 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! http://sdm.link/slashdot ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] drand48 in ply_c.h
Hi David, ply_c.h is part of the VMD molfile plugins. Would the following patch fix it for you? --- a/contrib/uiuc/plugins/molfile_plugin/src/ply_c.h +++ b/contrib/uiuc/plugins/molfile_plugin/src/ply_c.h @@ -3121,7 +3121,7 @@ void *get_new_props_ply(PlyFile *ply) } /* in case we need a random choice */ -#if defined(_MSC_VER) +#ifndef _XOPEN_SOURCE random_pick = 0; #else random_pick = (int) floor (rules->nprops * drand48()); If this works for you, I will also suggest this change upstream to the VMD authors. drand48() returns a float in [0,1) whereas rand() returns an integer in [0,MAX_RAND]. Cheers, Thomas > On Oct 24, 2017, at 2:08 AM, mathog <mat...@caltech.edu> wrote: > > Trying to build in mingw (have done this a couple of times before). > > Somebody introduced a file ply_c.h which references drand48() since the last > time this was built. That function isn't found in mingw, at least not with > the compile line setup.py produced. I can patch around this but wonder why > drand48() was used instead of rand() in the first place. > > Thanks, > > David Mathog > mat...@caltech.edu > Manager, Sequence 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 tech sites, Slashdot.org! http://sdm.link/slashdot ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] svn version number is ... ?
Hi David, Thanks for pointing out that the splash screen is out of date, we will fix that of course. Everything else says 1.9.0.0, that is the SVN log, the ChangeLog file, the "get_version" command (given a clean build), etc. Like Michael already pointed out, the PyMOL 2.0 announcement also announced that the 2.0 features (Qt interface etc.) will be released to Open-Source next year. The recent core feature updates (API changes, settings, bug fixes) have already been released to Open-Source, that's why we incremented the version to 1.9. Hope this makes sense to you. Thanks also for pointing out the glitch with searching for msgpack/version_master.h, looks like we're not catching all possible exceptions there. Will fix that too. The setup.py script searches the environment variable PREFIX_PATH for headers and libraries, so if you have stuff in /usr/local, then you could export something like PREFIX_PATH=/usr/local:/usr before running setup.py. Cheers, Thomas > On Oct 20, 2017, at 10:26 PM, mathog <mat...@caltech.edu> wrote: > > On 20-Oct-2017 12:54, Michael Banck wrote: >> Hi, >> On Fri, Oct 20, 2017 at 11:37:56AM -0700, mathog wrote: >>> Pymol 2.0 was recently announced >> That announcement was misleading, while the subject indeed said that, >> what was actually announced was the proprietary Pymol *incentive* 2.0 >> release. >> The open source 2.0 release is apparently pushed back to early next >> year, this was also mentioned in the announcement. > > OK, that solves one part of the puzzle. What about the conflicting version > numbers displayed by the SVN release (1.8.x vs. 1.9.0.0)? Doesn't svn > automatically increment its "revision number", or 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...@caltech.edu > Manager, Sequence 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 tech sites, Slashdot.org! http://sdm.link/slashdot ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] Copy to object on menu forces crashing & compatibility .pse export not working
Hi Rohan, The short answer is: You are using Python 3. The crash issue has been reported last week and we've found the cause, I will push the fix to the SVN repo later today. Regarding session files: This is tricky. PyMOL session files are Python pickle containers, and fundamental type changes between Python 2 and 3 make Python 3 pickles largely incompatible with Python 2. What we can handle so far: - loading old session files into Python 3 builds - limited support for loading Python 3 session files into new builds with Python 2 We can add a warning message if pse_export_version is used with a Python 3 build of PyMOL, because that's currently unsupported (given that all older versions use Python 2). Cheers, Thomas > On Oct 18, 2017, at 5:07 PM, Rohan Eapen <rs...@cam.ac.uk> wrote: > > Dear all, > > I am currently using PyMOL 1.8.7.0 and have noticed a couple of issues, which > I have been unable to solve so far. > > If I highlight over the "copy to object" line on the action bar in PyMOL > viewer it crashes the program. This occurs on both selections and objects. I > have attempted to work my way through the source code, and see nothing > immediately in fault comparing it to codes found on > https://sourceforge.net/p/pymol/code/4177/ > > I am also attempting to export .pse files to be compatible with earlier > versions of PyMOL. I am able to save them (supposedly in their compatible > forms), but no one with any earlier versions of PyMOL are able to open them. > This is the error that is seen when attempting to open the .pse file. > > Detected OpenGL version 2.0 or greater. Shaders available. > Detected GLSL version 1.30. > OpenGL graphics engine: > GL_VENDOR: Intel Open Source Technology Center > GL_RENDERER: Mesa DRI Intel(R) Haswell Mobile > GL_VERSION: 3.0 Mesa 17.0.7 > Adjusting settings to improve performance for Intel cards. > Detected 4 CPU cores. Enabled multithreaded rendering. > > Warning: This session was created with a newer version of PyMOL (1.870). > Warning: Some content may not load completely. > ExectiveSetSession-Error: after settings. > Executive: skipping unrecognized object "" of type 0. > Executive: skipping unrecognized object "" of type 0. > Executive: skipping unrecognized object "" of type 0. > Executive: skipping unrecognized object "" of type 0. > Executive: skipping unrecognized object "" of type 0. > Executive: skipping unrecognized object "" of type 0. > Executive: skipping unrecognized object "" of type 0. > ExectiveSetSession-Error: after names. > ExectiveSetSession-Warning: restore may be incomplete. > > > Any help would be greatly appreciated! > > Many thanks, > Rohan > -- > Rohan Eapen > Itzhaki group - PhD student > Department of Pharmacology > University of Cambridge > Tennis Court Road > CB2 1PD > rs...@cam.ac.uk -- 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! http://sdm.link/slashdot ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] strange issue with graphics with PyMol and Win10
Hi Marko, We have seen this issue with Intel HD graphics, but not with Nvidia. Any chance this is a dual graphics machine and you're actually not using the Nvidia chip? Anyway, for Intel graphics there are several options to resolve it: 1) Upgrade to PyMOL 2.0 (recommended) 2) and/or switch to Nvidia chip in case this is dual graphics setup 3) or downgrade the Intel graphics driver Cheers, Thomas > On Oct 9, 2017, at 1:02 PM, Marko Hyvonen <mh...@cam.ac.uk> wrote: > > Hello, > > any idea what could be wrong when Pymol graphics are too big for the actual > window. See attached. Everything seems zoomed out and part of the menus, > sequence etc are not visible in the window. But mouse responds to correct > position of where the menu items are, ca. half a menu height below what I > see. Can I fix this somehow or should I just reinstall? It happened all of a > sudden and suspect will happen again, so hoping for a fix... Everything else > is ok, including the Pymol Tcl/Tk command window. Looks like PyMol is > thinking my screen resolution is something different from what it is... > This is version 1.8.2 on Win10 with 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://hyvonen.bioc.cam.ac.uk > > -- 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! http://sdm.link/slashdot ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] PyMOL 2.0 released!
Hi again, Bugfix release 2.0.1 is out. It fixes Intel HD graphics support and hardware stereo on Linux and adds some missing libraries on Windows. Find the list of fixes here: https://pymol.org/d/media:new2#pymol_v2.0.1_hotfix_notes_sep_26_2017 Also see the updated list of known issues 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 and sent us their feedback and questions! We've started > collecting questions and known issues here: > > https://pymol.org/2/support.html#faq > https://pymol.org/2/support.html#known-issues > (page may 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 indicates, this release brings some substantial and >> exciting changes: >> >> - A unified, modern user interface brings a single window experience, 4K >> display support, file drag and drop and much more to all platforms >> >> - Open access Incentive PyMOL installers with liberal evaluation policy and >> subscription license control replace the current controlled-access download >> system >> >> - Deployment with Anaconda Cloud lets you install PyMOL side-by-side with >> your favourite Python tools and opens a new dimension for plugin development >> >> Visit https://pymol.org to download PyMOL 2.0 now! >> >> Find the complete release notes at https://pymol.org/d/media:new2 >> >> The new user interface and all core improvements will be pushed to the open >> source SVN repository early next year. >> >> We welcome any feedback 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! http://sdm.link/slashdot ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] PyMOL 2.0 released!
Hi again, 24h post-release feedback summary :) Thanks everyone who already tested the new version and sent us their feedback and questions! We've started collecting questions and known issues here: https://pymol.org/2/support.html#faq https://pymol.org/2/support.html#known-issues (page may 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 indicates, this release brings some substantial and > exciting changes: > > - A unified, modern user interface brings a single window experience, 4K > display support, file drag and drop and much more to all platforms > > - Open access Incentive PyMOL installers with liberal evaluation policy and > subscription license control replace the current controlled-access download > system > > - Deployment with Anaconda Cloud lets you install PyMOL side-by-side with > your favourite Python tools and opens a new dimension for plugin development > > Visit https://pymol.org to download PyMOL 2.0 now! > > Find the complete release notes at https://pymol.org/d/media:new2 > > The new user interface and all core improvements will be pushed to the open > source SVN repository early next year. > > We welcome any feedback 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! http://sdm.link/slashdot ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
[PyMOL] PyMOL 2.0 released!
Dear PyMOL users, We are thrilled to announce the release of Incentive PyMOL 2.0! As the version number indicates, this release brings some substantial and exciting changes: - A unified, modern user interface brings a single window experience, 4K display support, file drag and drop and much more to all platforms - Open access Incentive PyMOL installers with liberal evaluation policy and subscription license control replace the current controlled-access download system - Deployment with Anaconda Cloud lets you install PyMOL side-by-side with your favourite Python tools and opens a new dimension for plugin development Visit https://pymol.org to download PyMOL 2.0 now! Find the complete release notes at https://pymol.org/d/media:new2 The new user interface and all core improvements will be pushed to the open source SVN repository early next year. We welcome any feedback 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! http://sdm.link/slashdot ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] show as cartoon: dashed lines
Hi Raag, Do the two chains have chain identifiers? If not, then PyMOL's atom sorting will mess things up. Try this: set retain_order, 1 Cheers, Thomas > On Sep 13, 2017, at 6:40 PM, Raag Saluja <saluja.r...@gmail.com> wrote: > > Hi! > I predicted the structure of a heterodimer using Swiss Model. Then I > simulated it using GROMACS. When I opened the .gro file in PyMOL, it appeared > normal at first. However, when I chose show as cartoon, I got dashed lines. I > have attached a screenshot of the same. This problem did not occur before the > simulation 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 vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] translation in movies
Hi Gary,
Molecule translation ("independent object motion") is very easy to set up
interactively using the mouse. It can also be scripted with the "mview"
command. Object positions are not stored with scenes, they need to be stored
directly on the movie timeline with key frames.
Scripted example:
https://pymolwiki.org/index.php/Mview#Ligand_binding
Instruction for interactive setup:
- if not already done, extract the molecule to a separate object (select it,
then right click > actions > extract object)
- create frames (with "mset" or "Movie > Append > ...")
- Mouse > 3-Button Motions ("M" button appears in the object menu panel)
- store the initial position of the molecule with "M > store"
- move the movie slider to a different frame
- translate the molecule by dragging it with SHIFT + middle mouse button
Hope that helps.
Cheers,
Thomas
> On Sep 12, 2017, at 10:23 AM, Gary Hunter <gary.hun...@um.edu.mt> wrote:
>
> Is there a way (easy) to make a movie featuring a translation of one molecule?
> So far I have found I can only do it using the mset, mview commands and its
> difficult to put a lot of animations together. translations (positions of
> moleules/objects) do not sem to be recorded using scenes.
> Am I possibly missing a setting whereby I can record positions in a scene?
>
> Gary
>
>
> --
> Prof. Gary J. Hunter,
>
> Laboratory 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/physbiochem
--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.
--
Check out the vibrant tech community on one of the world's most
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Re: [PyMOL] cmd.load_coords does not return
Hi Gregor, I can't reproduce this with a simple program (like calling cmd.load_coords in an endless loop, threaded or non-threaded). Can you give some more details? Which PyMOL version? Which operating system? Do these load_coord calls all target the same object or different objects? Can you use cmd.get_coordset and cmd.load_coordset instead (entire object instead of atom selection) or does the issue persist? Thanks, Thomas > On Aug 29, 2017, at 11:41 AM, Gregor Hagelüken <hagelue...@pc.uni-bonn.de> > wrote: > > Hi, > > I am using the cmd.load_coords function in my script, which does the > following: > > 1-do some calculations with coordinates. I want to use the new coordinates as > input for another program, for which I only have an executable that reads > .pdb files. So my approach is: > 2-Use load_coords to apply the new set of coordinates (numpy array) to a > pymol object > 3-Write this object out as .pdb and use as input for other program > 4-get result > 5-do some other stuff > > In principle, this seems to work - but: > > I am using multiprocessing with 10 processes. Most times that I run the > script, 8 or 9 processes run fine but one or two simply stop doing anything > at step 2. I found that this line is the culprit: > ... > cmd.load_coords(complex, "complex”) > …. > > This also happens about once in 10 runs when I use just 1 process. > > 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. -- Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] select_aminoAcid_by_its_color_value
Hi Karol, Selecting several shades of red is possible with some scripting. The following code modifies the b-factor based on RGB color values, and then selects by b-factor. Change the 0.7 and 0.3 constants if you like to cover a different range. python from pymol import cmd, stored def is_red(color): R, G, B = cmd.get_color_tuple(color) return R > 0.7 and G < 0.3 and B < 0.3 stored.is_red = is_red python end alter all, b = stored.is_red(color) select red_atoms, b > 0.5 Cheers, Thomas > On Aug 29, 2017, at 2:48 PM, Karol K <karolkas...@gmail.com> wrote: > > 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 are colored in red? > > thanks -- 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! http://sdm.link/slashdot ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] select polymer within ribosome cif file ?
Hi Hari, In Incentive PyMOL, the entity id is loaded into the "entity_id" atom property, which is available as p.entity_id in the selection language and in iterate/alter. Since Open-Source PyMOL doesn't support arbitrary atom properties yet, we also populate the "custom" property with the same value. So this should work: # all PyMOL versions select 5S, custom 58 # Incentive PyMOL only select 5S, p.entity_id in 58 See also: https://pymol.org/d/properties#selection_language Cheers, Thomas > On Aug 23, 2017, at 10:38 PM, hari jayaram <hari...@gmail.com> wrote: > > Hi all, > I am trying to select a particular chain ( the 5S RNA) within the E.coli > ribosome cif file ( pdb ID 4V69) > > The sequence info page at rcsb indicates that this chain has the information > given below. I dont know the chain id or segid for this chain 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 Type: polyribonucleotide -- 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! http://sdm.link/slashdot ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] Assembly comparison between cif/pdb and mmtf file format
Hi Gianluca, Interesting observation. As far as I can tell, PyMOL reads the data correct from all files. I'll contact the MMTF folks and suggest to change their assembly ordering. Cheers, Thomas > On Aug 18, 2017, at 6:34 PM, Gianluca Tomasello <giagi...@gmail.com> wrote: > > 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 Developer Schrödinger, Inc. -- Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] Unable to install CAVER plugin
Hi Raag, If you follow these instructions, the caver plugin should work for you: https://pymolwiki.org/index.php/Caver3 Cheers, Thomas > On Aug 14, 2017, at 8:52 AM, Raag Saluja <saluja.r...@gmail.com> wrote: > > Hi! > > I'm using MacPyMOL (PyMOL 1.7.4.5 Edu Incentive 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 PyMOL Principal Developer Schrödinger, Inc. -- Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] Load mmtf data
Hi Gianluca, This is a good find, thanks a lot for the bug report. It took me quite a white to understand what's going wrong here. The solution is: use the "load_raw" function instead of "load". cmd.load_raw(b, "mmtf", "str") Cheers, Thomas > On Jul 25, 2017, at 8:17 AM, Gianluca Tomasello <giagi...@gmail.com> wrote: > > Hi Thomas, something strange happen when I try to load 4v99.mmtf using this > procedure (other PDB files works proprely as far as I know): > > download the file from https://mmtf.rcsb.org/v1.0/full/4V99 > then in script: > > with open(file_path,"rb") as binary: > b = binary.read() > cmd.load(b, "str", 0, cmd.loadable.mmtfstr) > > if i try to load the script with pymol, It gives this result: > > ... > Warning: map key not of type str (type 2). > Warning: map key not of type str (type 2). > Warning: map key not of type str (type 2). > Warning: map key not of type str (type 6). > Warning: map key not of type str (type 2). > Warning: map key not of type str (type 7). > Warning: map key not of type str (type 2). > Error in MMTF_parser_fetch_typed_array: length mismatch 588367 588120 > Warning: map key not of type str (type 2). > Warning: map key not of type str (type 2). > Warning: map key not of type str (type 2). > Warning: map key not of type str (type 2). > MMTF structureId: '4V99', 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 <giagi...@gmail.com>: > Thank you very much! > > 2017-06-22 13:11 GMT+02:00 Thomas Holder <thomas.hol...@schrodinger.com>: > Hi Gianluca, > > Yes this is possible, assuming you're using PyMOL 1.8.6. Use something like > this: > > def read_mmtfstr(contents, oname, state=0): > return cmd.load(contents, oname, state, cmd.loadable.mmtfstr) > > Cheers, > Thomas > > > On Jun 21, 2017, at 12:07 PM, Gianluca Tomasello <giagi...@gmail.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 Developer Schrödinger, Inc. -- Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] Retain order for select segment and write trajectory
Hi Kelly, With retain_order=1, PyMOL will sort by rank, which is the order of time of loading the structure. By setting all rank values to the same value, you'll get segi/chain/resi sorting. So to preserve rank based sorting only for non-solvent, you can do this: set retain_order alter solvent, rank=-1 sort This will sort solvent to the beginning. To put it to the end, pick a number which is beyond the atom count. set retain_order alter solvent, rank= sort The atom ID is never used for sorting. But you could incorporate it in the ranks: set retain_order alter solvent, rank= + ID sort Cheers, Thomas > On Jul 18, 2017, at 2:09 PM, Kelly Tran <k...@georgetown.edu> wrote: > > Hi, > > I'm using PSICO to write a DCD. Is it possible to retain the original order > for one segment (protein) while sorting by atom ID for another segment > (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, Slashdot.org! http://sdm.link/slashdot ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] A structural superimposition and further post-processing
The link wasn't a direct link to the fixed setup.py file. The direct link is: https://raw.githubusercontent.com/speleo3/pymol-psico/master/setup.py MacPyMOL 1.7.4 is recent enough for this exercise. However, your MacPyMOL installation and your Anaconda3 Python are unrelated, so installing PSICO with Anaconda won't make it work with MacPyMOL. The simplest approach to install PSICO with MacPyMOL is to copy the "psico" directory here: /Applications/MacPyMOL.app/Contents/pymol/modules/ Cheers, Thomas > On Jul 18, 2017, at 2:53 PM, James Starlight <jmsstarli...@gmail.com> wrote: > > There were some errors in the executing pymol script with your commands using > @ script.pml > or > run script.pml > > probably because of my MAC Pymol which is v 1.74 mb outdated, no? > > BTW on the same MAC I just have tried to install updated setup.py 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>: >> With super instead of tmalign: >> >> loadall *.pdb >> extra_fit *, reference, method=super, object=aln >> remove not (byres aln) >> >> The PSICO setup.py installation script wasn't Python 3 ready. It's fixed now: >> https://github.com/speleo3/pymol-psico/commit/e92f09374cc5ef7b562e5332292cee4f57f168af >> >> Cheers, >> Thomas >> >>> On Jul 18, 2017, at 1:39 PM, James Starlight <jmsstarli...@gmail.com> wrote: >>> >>> Hi Thomas, >>> >>> could you also send the same script but just with the Super command >>> for the superimposition without PSICO? >>> >>> it's strange I have a problems of PSICO installation on MAC with python 3 >>> >>> Python 3.5.2 |Continuum Analytics, Inc.| (default, Jul 2 2016, 17:52:12) >>> [GCC 4.2.1 Compatible Apple LLVM 4.2 (clang-425.0.28)] on darwin >>> Type "help", "copyright", "credits" or "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 'Warning: could not import version' >>> ^ >>> >>> 2017-07-18 19:37 GMT+02:00 James Starlight <jmsstarli...@gmail.com>: >>>> Hi Thomas, >>>> >>>> could you also send the same script but just with the Super command >>>> for the superimposition without PSICO? >>>> >>>> it's strange I have a problems of PSICO installation on MAC with python 3 >>>> >>>> Python 3.5.2 |Continuum Analytics, Inc.| (default, Jul 2 2016, 17:52:12) >>>> [GCC 4.2.1 Compatible Apple LLVM 4.2 (clang-425.0.28)] on darwin >>>> Type "help", "copyright", "credits" or "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 'Warning: could not import version' >>>> ^ >>>> SyntaxError: Missing parentheses in call to 'print' >>>> >>>> 2017-07-18 19:05 GMT+02:00 Thomas Holder <thomas.hol...@schrodinger.com>: >>>>> Hi Gleb, >>>>> >>>>> If you have PSICO installed (which provides a TMalign wrapper), then this >>>>> script should be sufficient: >>>>> >>>>> loadall *.pdb >>>>> import psico.fitting >>>>> extra_fit *, reference, method=tmalign, object=aln >>>>> remove not (byres aln) >>>>> >>>>> https://pymolwiki.org/index.php/Psico >>>>> >>>>> Cheers, >>>>> Thomas >>>>> >>>>>> On Jul 18, 2017, at 11:35 AM, James Starlight <jmsstarli...@gmail.com> >>>>>> wrote: >>>>>> >>>>>> Dear Pymol Users! >>>>>> >>>>>> In my work dir I have 200 pdb files of GPCRs and one receptor >>>>>> reference.pdb (it consist of only one GPCR monomer - seven >>>>>> transmbembrane scaffold). >>>>>> >>>>>> I need to write a simple script which will do the following things: >>>>>> >>>>>> 1 - allign (in loop) each structure against reference.pdb using >>>>>> "super" or "TMalign" (is better!) >>>>>> >>>>>> 2 - from each of the aligned pdbs, remove not superimposed regions >>>>>> (assuming that each pdb has 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. -- Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] A structural superimposition and further post-processing
With super instead of tmalign: loadall *.pdb extra_fit *, reference, method=super, object=aln remove not (byres aln) The PSICO setup.py installation script wasn't Python 3 ready. It's fixed now: https://github.com/speleo3/pymol-psico/commit/e92f09374cc5ef7b562e5332292cee4f57f168af Cheers, Thomas > On Jul 18, 2017, at 1:39 PM, James Starlight <jmsstarli...@gmail.com> wrote: > > Hi Thomas, > > could you also send the same script but just with the Super command > for the superimposition without PSICO? > > it's strange I have a problems of PSICO installation on MAC with python 3 > > Python 3.5.2 |Continuum Analytics, Inc.| (default, Jul 2 2016, 17:52:12) > [GCC 4.2.1 Compatible Apple LLVM 4.2 (clang-425.0.28)] on darwin > Type "help", "copyright", "credits" or "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 'Warning: could not import version' >^ > > 2017-07-18 19:37 GMT+02:00 James Starlight <jmsstarli...@gmail.com>: >> Hi Thomas, >> >> could you also send the same script but just with the Super command >> for the superimposition without PSICO? >> >> it's strange I have a problems of PSICO installation on MAC with python 3 >> >> Python 3.5.2 |Continuum Analytics, Inc.| (default, Jul 2 2016, 17:52:12) >> [GCC 4.2.1 Compatible Apple LLVM 4.2 (clang-425.0.28)] on darwin >> Type "help", "copyright", "credits" or "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 'Warning: could not import version' >>^ >> SyntaxError: Missing parentheses in call to 'print' >> >> 2017-07-18 19:05 GMT+02:00 Thomas Holder <thomas.hol...@schrodinger.com>: >>> Hi Gleb, >>> >>> If you have PSICO installed (which provides a TMalign wrapper), then this >>> script should be sufficient: >>> >>> loadall *.pdb >>> import psico.fitting >>> extra_fit *, reference, method=tmalign, object=aln >>> remove not (byres aln) >>> >>> https://pymolwiki.org/index.php/Psico >>> >>> Cheers, >>> Thomas >>> >>>> On Jul 18, 2017, at 11:35 AM, James Starlight <jmsstarli...@gmail.com> >>>> wrote: >>>> >>>> Dear Pymol Users! >>>> >>>> In my work dir I have 200 pdb files of GPCRs and one receptor >>>> reference.pdb (it consist of only one GPCR monomer - seven >>>> transmbembrane scaffold). >>>> >>>> I need to write a simple script which will do the following things: >>>> >>>> 1 - allign (in loop) each structure against reference.pdb using >>>> "super" or "TMalign" (is better!) >>>> >>>> 2 - from each of the aligned pdbs, remove not superimposed regions >>>> (assuming that each pdb has 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. -- Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] A structural superimposition and further post-processing
Hi Gleb, If you have PSICO installed (which provides a TMalign wrapper), then this script should be sufficient: loadall *.pdb import psico.fitting extra_fit *, reference, method=tmalign, object=aln remove not (byres aln) https://pymolwiki.org/index.php/Psico Cheers, Thomas > On Jul 18, 2017, at 11:35 AM, James Starlight <jmsstarli...@gmail.com> wrote: > > Dear Pymol Users! > > In my work dir I have 200 pdb files of GPCRs and one receptor > reference.pdb (it consist of only one GPCR monomer - seven > transmbembrane scaffold). > > I need to write a simple script which will do the following things: > > 1 - allign (in loop) each structure against reference.pdb using > "super" or "TMalign" (is better!) > > 2 - from each of the aligned pdbs, remove not superimposed regions > (assuming that each pdb has 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. -- Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] How to identify the pocket of a protein?
Hi Mohammad, If there is already a ligand in the pocket and you just want to know its center x,y,z, you can simply type: centerofmass organic Or if there are multiple organic molecules and you are interested in one with the unique residue name "LIG": centerofmass resn LIG I wound't call that "finding" a pocket though. Cheers, Thomas > On Jul 11, 2017, at 7:42 PM, Mohammad Goodarzi <mohammad.goda...@gmail.com> > wrote: > > Hello, > > I am wondering whether it is possible to find the pocket of a protein in > Pymol? > lets say 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 tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] show nonbonded atoms with stick representation
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 Holder PyMOL Principal Developer Schrödinger, Inc. -- Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] Valence bonding ray trace in batch mode
Hi Gianluca, You get the sphere with stick_ball=on. It's unexpected that batch mode and GUI mode give different results. Could it be that you have the stick_ball setting in a (directory specific) pymolrc file, and/or do you pass -k flag (ignores pymolrc files) in batch mode? Cheers, Thomas > On Jul 2, 2017, at 5:32 PM, Gianluca Tomasello <giagi...@gmail.com> wrote: > > Hi, I am trying to execute a script that sets valence bonding on sticks and > then it gives me back a rendered image. There seems there is a difference > when i try to run the script normally or 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 correctly rendered. -- 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! http://sdm.link/slashdot ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] ray 2400 (NOT ray_trace) each frame of a movie
Hi AC,
In PyMOL 1.8.6 we added width and height arguments to the mpng command. So this
is now possible:
set ray_trace_frames
mpng imageprefix, width=2400
With older PyMOL versions, you have two options:
1) Run PyMOL headless (pymol -c script.pml) so that the display doesn't limit
the viewport size, and put in the script:
viewport 2400, 1800
mpng imageprefix
2) Write your own export loop:
python
for frame in range(1, cmd.count_frames() + 1):
cmd.frame(frame)
cmd.png('imageprefix%04d.png' % frame, width=2400, ray=1)
python end
Cheers,
Thomas
> On Jun 29, 2017, at 8:55 PM, Academic Research <ac.resea...@icloud.com> wrote:
>
> So far there is only info about how to "ray_trace" each frame of a movie
> while exporting to .png images.
>
> My question: How can I "ray 2400" each image (regardless of my computer
> screen 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.
--
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Re: [PyMOL] Load mmtf data
Hi Gianluca, Yes this is possible, assuming you're using PyMOL 1.8.6. Use something like this: def read_mmtfstr(contents, oname, state=0): return cmd.load(contents, oname, state, cmd.loadable.mmtfstr) Cheers, Thomas > On Jun 21, 2017, at 12:07 PM, Gianluca Tomasello <giagi...@gmail.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 Developer Schrödinger, Inc. -- Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] ball stick representation problem
Hi Gianluca, It looks like "stick_ball" setting support never made it into the sticks shader of Open-Source PyMOL. It works with: - Incentive PyMOL (all rendering modes) - Open Source PyMOL in ray tracing and with use_shaders=0 Cheers, Thomas > On Jun 15, 2017, at 11:32 AM, Gianluca Tomasello <giagi...@gmail.com> wrote: > > Hi, I am following the instructuions on > https://pymolwiki.org/index.php/Ball_and_Stick to make a ball and stick > representation. I would like to use only stick representation to accomplish > this task, and I finded the last method in the page is not working properly > on my version of pymol (1.8.4.0) > > show sticks > set valence, on > set stick_ball, on > set stick_ball_ratio, 3 > set stick_radius, 0.12 > > it keeps the bonds but seems to disable completly the spheres. > > I also 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 like this > https://pymolwiki.org/index.php/File:Stick_ball_ratio_1.5.png -- 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! http://sdm.link/slashdot ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] Selection of chains based on PDB header
Hi Julian,
A one-liner to create chain selections looks like this:
for c in cmd.get_chains(): cmd.select("chain_" + c, "chain " + c)
PyMOL doesn't provide access to the PDB header fields. In principle PyMOL
provides a way to access everything inside mmCIF files, see:
https://pymolwiki.org/index.php/Cif_keepinmemory
However, instead of doing this, I recommend to use the PDBe web API which
provides the data in a friendly JSON data structure. I've attached a Python
script which creates molecule (or chain) selections for 5n61 as an example. I
recommend to load PDB structures from mmCIF or MMTF format, which not only have
chain identifiers, but also molecule identifiers ("segi" field in PyMOL).
Hope that helps.
Cheers,
Thomas
> On Jun 12, 2017, at 12:21 PM, Julian Reitz <julianr1...@gmail.com> wrote:
>
> Dear all,
>
> I have a pdb-file with multiple chains (5N61).
>
> Is there an easy way to create selections for all the chains that are defined
> in the pdb-header (A to U) without doing it manually for every chain (select
> A, chain A)?
> Is it also possible to use the MOLECULE information from 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 molecule (if loaded from mmCIF/MMTF) or
every chain (if loaded from PDB), using PDBe REST API.
'''
data = json.load(urllib2.urlopen(
'http://www.ebi.ac.uk/pdbe/api/pdb/entry/molecules/' + code))
# check if we can select by segi (label_asym_id)
has_segi = not cmd.count_atoms('segi ""')
for mol in data.values()[0]:
# only include polymers
if not mol[u'molecule_type'].startswith('poly'):
continue
# entity description (truncated)
desc = mol[u'synonym'][:200]
if has_segi:
# select molecules by label_asym_id (PyMOL 1.7.4+)
for chain in mol[u'in_struct_asyms']:
cmd.select('segi_%s_%s' % (chain, desc), 'segi ' + chain)
else:
# select chains
for chain in mol[u'in_chains']:
cmd.select('chain_%s_%s' % (chain, desc), 'chain ' + chain)
code = '5n61'
cmd.fetch(code)
pdb_chain_selections(code)
--
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Re: [PyMOL] Error aroused when install pymol from source
Hi Yeping, 3 options: 1) Get msgpack 2.x sources from https://github.com/msgpack/msgpack-c and tell the C++ compiler about the headers, e.g. with: export CXXFLAGS="-I/tmp/msgpack-2.1.2/include" 2) If you have installed msgpack 1.x, which is a dynamic library, also install msgpack-devel and build pymol with --use-msgpackc=c 3) Build pymol with --use-msgpackc=no which disables MMTF load support Note that msgpack version 0.x is not supported by PyMOL. Hope that helps. Cheers, Thomas > On Jun 8, 2017, at 4:18 AM, sunyeping via PyMOL-users > <pymol-users@lists.sourceforge.net> wrote: > > Dear pymol users, > > I am trying to intall pymol on my centos 7 system from source using the > mothed discribed at pymolwiki (https://pymolwiki.org/index.php/Linux_Install) > Everything was ok until I run install script: > > #!/bin/bash -e > > prefix=/opt/pymol-svn > modules=$prefix/modules > > # If you want to install as root, then split this line up in "build" > # and "install" and run the "install" with "sudo" > python2.7 setup.py build install \ > --home=$prefix \ > --install-lib=$modules \ > --install-scripts=$prefix > > I got a error message and the installation process was terminated: > > In file included from contrib/mmtf-c/mmtf_parser.cpp:31:0: > contrib/mmtf-c/mmtf_parser_private.h:38:23: fatal error: msgpack.hpp: 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 this problem but cannot find a answer. Could anyone help me here? > > Best regards. > > Yeping Sun -- 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! http://sdm.link/slashdot ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] Problem with 'byring' selection
Hi Vijay,
All "by" operators have a weak priority. This means the following two
expressions are equivalent:
elem S & byring all w. 4 of elem O
elem S & byring (all w. 4 of elem O)
This is a bit unfortunate, I agree that it is not very intuitive. I would
actually expect the highest priority. But we don't want to change the logic of
a program which exists for 17 years now. The solution is to set parenthesis in
the right places. So to get the ring sulfurs which are within 4 Angstroms of
Oxygens, this is the correct expression:
(elem S & byring all) w. 4 of elem O
Which is equivalent to:
((elem S) & (byring all)) w. 4 of (elem O)
It's good to know the priority of operators, but if you are unsure, it never
hurts to place the extra parenthesis to be explicit.
Operator priorities are defined here:
https://sourceforge.net/p/pymol/code/HEAD/tree/trunk/pymol/layer3/Selector.cpp#l323
Hope that helps.
Cheers,
Thomas
> On Jun 3, 2017, at 2:20 PM, Vijay Masand <vijaymas...@gmail.com> wrote:
>
> Dear Tsjerk and Thomas
> For the following small molecule:
> ClC1[OH+]C(Cl)=CN=C1C(=O)N([NH+]1CCC(SC1)F)CCN
> As you advised to use following logic for selecting nitrogen atoms of
> rings exclusively.
> abc=cmd.select('elem N and byring not elem N')
> Likewise, to select Sulphur atoms which are part of rings only and at
> a distance of 4A from Oxygen atom, following should be used:
> abc = cmd.select('elem S and byring not elem S w. 4 of elem O')
> But this selected the Sulphur atoms which is part of a ring but at 4.8
> A from Oxygen atom. In reality, It should not happen.
> When I used the logic, which involves deletion of 'not':
> abc = cmd.select('elem S and byring elem S w. 4 of elem O')
> Sulphur atom present at a distance of 4.8 A from Oxygen atom was not selected.
> I hope I will be benefited with better explanation.
> Cheers
> Vijay
>
> On 6/3/17, Vijay Masand <vijaymas...@gmail.com> wrote:
>> Dear Tsjerk and Thomas
>> Thanks for the information. This important information is not
>> available on this page of PyMOLWiki:
>> https://pymolwiki.org/index.php/Selection_Algebra
>> I hope the page will be modified soon to include this important
>> information.
>> Cheers
>> Vijay
>>
>> On 6/3/17, Tsjerk Wassenaar <tsje...@gmail.com> wrote:
>>> Hi Vijay,
>>>
>>> It is logic. 'byring elem N' selects all nitrogens and then expands the
>>> selection to include the rings in which these participate. 'elem N and
>>> byring elem N' does the same, but then intersects (and) to extract only
>>> nitrogens. But that is the same as 'elem N'. If you want to have the
>>> nitrogens from rings, you can do 'elem N and byring not elem N'. That
>>> selects the non-nitrogen atoms and expands the selection over rings. So
>>> only nitrogens in rings can be added to teh selection. Then intersecting
>>> to
>>> get only nitrogens will yield only those that are members of rings.
>>>
>>> Hope it helps,
>>>
>>> Tsjerk
>>>
>>> On Jun 3, 2017 5:45 AM, "Vijay Masand" <vijaymas...@gmail.com> wrote:
>>>
>>>> Dear PyMOL Users,
>>>> I am using PyMOL 1.8.6 on Windows 10 (64 bit) with Python 2.7.12. I
>>>> was working with small molecule
>>>> (ClC1[OH+]C(Cl)=CN=C1C(=O)N([NH+]1CCC(SC1)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
>>>> atoms of the ring also.
>>>> But, following command worked perfectly:
>>>> abc=cmd.select('elem N & byring elem N')
>>>> Is it a bug or something else?
>>>> Cheers
>>>> Vijay
>
>
> --
> Assistant Professor
> Department of Chemistry,
> Vidya Bharati College, Amravati, 444 602
> Maharashtra, India.
> Phone number- +91-9403312628
> https://sites.google.com/site/vijaymasand/
--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.
--
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Re: [PyMOL] [External] Unable to initialize plugin annocryst
Hi Jon, As far as I see, you're running Open-Souce PyMOL on some unix system. I suggest you install "idle" on the system, e.g. if this is Ubuntu, install https://packages.ubuntu.com/xenial/idle-python2.7 Cheers, Thomas > On Jun 2, 2017, at 7:30 PM, Luo, Jonathan Z. <jzl...@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 <thomas.hol...@schrodinger.com> > Sent: Friday, June 2, 2017 5:52 AM > To: Luo, Jonathan Z. > Cc: pymol-users@lists.sourceforge.net > Subject: [External] Re: [PyMOL] Unable to initialize plugin annocryst > > Hi Jon, > > try this: In file "annocryst.py" on line 22, replace: > > from modules.idlelib.TreeWidget import TreeItem, TreeNode > > with: > > from idlelib.TreeWidget import TreeItem, TreeNode > > Hope that works for you. > > Cheers, > Thomas > > >> On Jun 1, 2017, at 7:03 PM, Luo, Jonathan Z. <jzl...@geisinger.edu> wrote: >> >> Hello, >> I've just installed pymol and am running into this error at startup: >>No module named modules.idlelib.TreeWidget >>Unable to initialize plugin 'annocryst' (pmg_tk.startup.annocryst) >> >> When I try to import: >> PyMOL>import pmg_tk.startup.annocryst >> Traceback (most recent call last): >> File "/opt/pymol/modules/pymol/parser.py", line 262, in parse >>exec(layer.com2+"\n",self.pymol_names,self.pymol_names) >> File "", line 1, in >> File "/opt/pymol/Pymol-script-repo/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/TreeWidget.py >> What should I do? >> >> Thank you! >> Jon -- 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! http://sdm.link/slashdot ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] Unable to initialize plugin annocryst
Hi Jon, try this: In file "annocryst.py" on line 22, replace: from modules.idlelib.TreeWidget import TreeItem, TreeNode with: from idlelib.TreeWidget import TreeItem, TreeNode Hope that works for you. Cheers, Thomas > On Jun 1, 2017, at 7:03 PM, Luo, Jonathan Z. <jzl...@geisinger.edu> wrote: > > Hello, > I've just installed pymol and am running into this error at startup: > No module named modules.idlelib.TreeWidget > Unable to initialize plugin 'annocryst' (pmg_tk.startup.annocryst) > > When I try to import: > PyMOL>import pmg_tk.startup.annocryst > Traceback (most recent call last): > File "/opt/pymol/modules/pymol/parser.py", line 262, in parse > exec(layer.com2+"\n",self.pymol_names,self.pymol_names) > File "", line 1, in > File "/opt/pymol/Pymol-script-repo/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/TreeWidget.py > What should I do? > > Thank you! > Jon -- 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! http://sdm.link/slashdot ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] Is there a way to "count" hydrogen bond interactions?
Hi Chi,
The file needs a .py extension to be recognized as a Python script. Microsoft
Windows can be tricky when it comes to changing a file extension. I recommend
to follow these steps when downloading a Python file from the PyMOLWiki:
1) Visit https://pymolwiki.org/index.php/Get_raw_distances
2) Box on the right side, right click on "Download get_raw_distances.py"
3) "Save Link As..." or "Save target as..." (depends on browser)
File name: get_raw_distances.py
Save as type: PY File
Hope that helps.
Cheers,
Thomas
> On May 19, 2017, at 9:41 PM, Chi Celestine <chi.celest...@phys.chem.ethz.ch>
> wrote:
>
> Dear Thomas,
> Many thanks! I copied and saved the script as a dot txt but can not run it
> from file> run on pymol. Do I need yo save the file in a special folder? I
> am actually really new with pymol and not vey good in scripting
>
> Thanks for your understanding
>
> Sincerely
> Chi
> -
> Celestine Chi, PhD
> ETH Zürich
> Laboratory for Physical Chemistry
> Vladimir-Prelog-Weg 2 HCI F 222
> CH-8093 Zürich
> 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? You can do that by:
>>
>> run
>> https://raw.githubusercontent.com/Pymol-Scripts/Pymol-script-repo/master/get_raw_distances.py
>>
>> Or better: Download it to your computer and run it from there ("run" command
>> or "File > Run Script..." from the menu).
>>
>> After running the script, you can use the "get_raw_distances" command.
>>
>> Cheers,
>> Thomas
>>
>>> On May 19, 2017, at 2:26 PM, Chi Celestine
>>> <chi.celest...@phys.chem.ethz.ch> wrote:
>>>
>>> Hi Thomas,
>>> I am also interesting in getting bond distances between two pairs of
>>> molecule. I tried running the commands to suggested but I get an error
>>> message e.g
>>> When I tried the following (see below) the fist command was well executed
>>> but the second gave an error message “ SyntaxError: invalid syntax”
>>>
>>> I got a similar error message when I tried to execute this command D =
>>> get_raw_distances("distname”) as well
>>>
>>>
>>> Sincerely,
>>> Celestine
>>>
>>> Example
>>> fetch 2xwu, async=0
>>>
>>>
>>>
>>> # interface polar contacts
>>> 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
>>> CH-8093 Zürich
>>> Email: chi.celest...@phys.chem.ethz.ch
>>> tele: 004144 63 37510
>>>
>>>> On May 19, 2017, at 1:16 PM, Thomas Holder <thomas.hol...@schrodinger.com>
>>>> wrote:
>>>>
>>>> Hi Ahmad,
>>>>
>>>> Unfortunately there is no proper API for this. But I can think of two
>>>> approaches. Note that the results can differ because the two method do
>>>> slightly different h-bond detection!
>>>>
>>>> 1) Use "cmd.find_pairs" with mode=1 on "donors" and "acceptors" selection.
>>>> Example:
>>>>
>>>> sele1 = "chain A & (donors | acceptors)"
>>>> sele2 = "chain B & (donors | acceptors)"
>>>> radius = 3.5
>>>> D = cmd.find_pairs(sele1, sele2, mode=1, cutoff=radius)
>>>> print("number of h-bonds:", len(D))
>>>>
>>>> 1) Use "cmd.distance" and the "get_raw_distances" script. Example:
>>>>
>>>> run
>>>> https://raw.githubusercontent.com/Pymol-Scripts/Pymol-script-repo/master/get_raw_distances.py
>>>>
>>>> sele1 = "chain A"
>>>> sele2 = "chain B"
>>>> radius = 3.5
>>>> cmd.distance("distname", sele1, sele2, mode=2, cutoff=radius)
>>>> D = get_raw_distances("distname")
>>>> print("number of h-bonds:", len(D))
>>>>
>>>> See also:
>>>> https://pymolwiki.org/index.php/Get_raw_distances
>>>> https://pymolwiki.org/index.php/Distance
>>>> https://pymolwiki.org/index.php/Find_pairs
>>>>
>>>> Hope that helps.
>>>>
>>>> Cheers,
>>>> Thomas
>>>>
>>>>> On May 5, 2017, at 5:08 AM, Ahmad Abdelzaher <underoath...@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?
>>>>>
>>>>> Regards.
--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.
--
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Re: [PyMOL] Is there a way to "count" hydrogen bond interactions?
Hi Celestine,
Did you run the "get_raw_distances.py" script first? You can do that by:
run
https://raw.githubusercontent.com/Pymol-Scripts/Pymol-script-repo/master/get_raw_distances.py
Or better: Download it to your computer and run it from there ("run" command or
"File > Run Script..." from the menu).
After running the script, you can use the "get_raw_distances" command.
Cheers,
Thomas
> On May 19, 2017, at 2:26 PM, Chi Celestine <chi.celest...@phys.chem.ethz.ch>
> wrote:
>
> Hi Thomas,
> I am also interesting in getting bond distances between two pairs of
> molecule. I tried running the commands to suggested but I get an error
> message e.g
> When I tried the following (see below) the fist command was well executed but
> the second gave an error message “ SyntaxError: invalid syntax”
>
> I got a similar error message when I tried to execute this command D =
> get_raw_distances("distname”) as well
>
>
> Sincerely,
> Celestine
>
> Example
> fetch 2xwu, async=0
>
>
>
> # interface polar contacts
> 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
> CH-8093 Zürich
> Email: chi.celest...@phys.chem.ethz.ch
> tele: 004144 63 37510
>
>> On May 19, 2017, at 1:16 PM, Thomas Holder <thomas.hol...@schrodinger.com>
>> wrote:
>>
>> Hi Ahmad,
>>
>> Unfortunately there is no proper API for this. But I can think of two
>> approaches. Note that the results can differ because the two method do
>> slightly different h-bond detection!
>>
>> 1) Use "cmd.find_pairs" with mode=1 on "donors" and "acceptors" selection.
>> Example:
>>
>> sele1 = "chain A & (donors | acceptors)"
>> sele2 = "chain B & (donors | acceptors)"
>> radius = 3.5
>> D = cmd.find_pairs(sele1, sele2, mode=1, cutoff=radius)
>> print("number of h-bonds:", len(D))
>>
>> 1) Use "cmd.distance" and the "get_raw_distances" script. Example:
>>
>> run
>> https://raw.githubusercontent.com/Pymol-Scripts/Pymol-script-repo/master/get_raw_distances.py
>>
>> sele1 = "chain A"
>> sele2 = "chain B"
>> radius = 3.5
>> cmd.distance("distname", sele1, sele2, mode=2, cutoff=radius)
>> D = get_raw_distances("distname")
>> print("number of h-bonds:", len(D))
>>
>> See also:
>> https://pymolwiki.org/index.php/Get_raw_distances
>> https://pymolwiki.org/index.php/Distance
>> https://pymolwiki.org/index.php/Find_pairs
>>
>> Hope that helps.
>>
>> Cheers,
>> Thomas
>>
>>> On May 5, 2017, at 5:08 AM, Ahmad Abdelzaher <underoath...@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?
>>>
>>> Regards.
--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.
--
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Re: [PyMOL] reproduce special vrml-output
Hi Anke,
surface_type 0 will produce faces (solid triangles).
There are no triangle faces in surface_type 2, only edges.
Thomas
> On May 19, 2017, at 12:43 PM, Anke Schultz <anke.schu...@tu-braunschweig.de>
> wrote:
>
> Hi Thomas,
>
> thanks for the explanation on adjusting view, it works fine. This leaves me
> with one question: How do I get a .wrl-file containing only faces? Using
> "show surface" and setting surface_type to 2 (triangles) gives me sticks and
> spheres in the .wrl-file (sticks as edges, spheres at the ends of every 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 has
>> faces (could be surface or cartoon).
>>
>> The other difference is the viewport z position (zoom distance), which is
>> 0.0 in the second sample. This can be set as follows before exporting the
>> file (note that the molecule might not be visible anymore, it could be
>> behind the camera):
>>
>> view = list(cmd.get_view())
>> view[11] = 0.0
>> cmd.set_view(view)
>>
>> Hope that helps.
>>
>> Cheers,
>> Thomas
>>
>>> On May 17, 2017, at 4:27 PM, Anke Schultz <anke.schu...@tu-braunschweig.de>
>>> wrote:
>>>
>>> Hi all,
>>>
>>> I've been experimenting with exporting surface meshes as .wrl-files. I
>>> played with the geometry_export_mode setting and the set_view() options,
>>> since I wanted to get the surface's coordinates corresponding to the atom's
>>> coordinates of the sd-file I imported to pymol initially. I realized that
>>> by exporting .wrl-format I got the camera-view instead of the "real"
>>> coordinates as long as I left everything else on default. This resulted in
>>> a shift between atom- and surface-coordinates.
>>>
>>> While playing around to align camera and reality, I somehow managed to
>>> change the way my .wrl-file looked in the end and it seems to be exactly
>>> what I was looking for. I have tried for two days now, but unfortunately I
>>> can't reproduce my steps leading to this special .wrl-file.
>>>
>>> This is (part of) a .wrl-file without changing default settings:
>>> ###
>>> #VRML V2.0 utf8
>>>
>>> Viewpoint {
>>> position 0 0 20.39730644
>>> orientation 1 0 0 0
>>> description "Z view"
>>> fieldOfView 0.465421
>>> }
>>> DirectionalLight {
>>> direction -0.348155 -0.348155 -0.870
>>> }
>>> NavigationInfo {
>>> headlight TRUE
>>> type "EXAMINE"
>>> }
>>> Transform {
>>> translation -1.820169 2.166291 -3.211221
>>> rotation -0.199343 0.00 0.979930 2.401556
>>> children [
>>> Shape {
>>>geometry Cylinder {
>>> radius 0.024352
>>> height 0.139351
>>> bottom FALSE
>>> topFALSE
>>>}
>>>appearance Appearance {
>>>material Material { diffuseColor 0.9000 0.9000 0.9000
>>>specularColor 0.8 0.8 0.8
>>>shininess 0.8 }
>>>}
>>> }
>>> Transform {
>>>translation 0.0 0.069676 0.0
>>>children Shape {
>>> geometry Sphere { radius 0.024352 }
>>> appearance Appearance {
>>>material Material { diffuseColor 0.9000 0.9000 0.9000
>>>specularColor 0.8 0.8 0.8
>>>shininess 0.8 }
>>> }
>>>}
>>> }
>>> Transform {
>>>translation 0.0 -0.069676 0.0
>>>children Shape {
>>> geometry Sphere { radius 0.024352 }
>>> appearance Appearance {
>>>material Material { diffuseColor 0.9000 0.9000 0.9000
>>>specularColor 0.8 0.8 0.8
>>>shininess 0.8 }
>>> }
>>>}
>>> }
>>> ]
>>> }
>>> Transform {
>>> translation -1.906664 2.148911 -3.187284
>>> rotation 0.635566 0.00 0.772046 0.994256
>>> [...]
>>> ###
>>>
>>> And this is (part of) the special
Re: [PyMOL] Is there a way to "count" hydrogen bond interactions?
Hi Ahmad,
Unfortunately there is no proper API for this. But I can think of two
approaches. Note that the results can differ because the two method do slightly
different h-bond detection!
1) Use "cmd.find_pairs" with mode=1 on "donors" and "acceptors" selection.
Example:
sele1 = "chain A & (donors | acceptors)"
sele2 = "chain B & (donors | acceptors)"
radius = 3.5
D = cmd.find_pairs(sele1, sele2, mode=1, cutoff=radius)
print("number of h-bonds:", len(D))
1) Use "cmd.distance" and the "get_raw_distances" script. Example:
run
https://raw.githubusercontent.com/Pymol-Scripts/Pymol-script-repo/master/get_raw_distances.py
sele1 = "chain A"
sele2 = "chain B"
radius = 3.5
cmd.distance("distname", sele1, sele2, mode=2, cutoff=radius)
D = get_raw_distances("distname")
print("number of h-bonds:", len(D))
See also:
https://pymolwiki.org/index.php/Get_raw_distances
https://pymolwiki.org/index.php/Distance
https://pymolwiki.org/index.php/Find_pairs
Hope that helps.
Cheers,
Thomas
> On May 5, 2017, at 5:08 AM, Ahmad Abdelzaher <underoath...@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?
>
> Regards.
--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.
--
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Re: [PyMOL] B-factor
Hi Kingsley, The b-factor is a result of the X-ray crystallography experiment. If you have X-ray data, I suggest to consult the CCP4BB mailing list (http://www.ccp4.ac.uk/ccp4bb.php). If you don’t have such data, then you can’t calculate a b-factor. There are computational methods which analyze a structure for potential flexibility, for example Normal Mode Analysis (NMA). These methods can approximate real b-factors. If you have an ensemble of structures (e.g. from an MD simulation) you could also calculate the root mean square fluctuation per atom (RMSF), which is related to the b-factor in the sense that it describes a distribution around a center position. See for example “rmsf2b” in the PSICO library: https://github.com/speleo3/pymol-psico/blob/master/psico/editing.py#L69 Cheers, Thomas > On May 8, 2017, at 2:42 PM, Kingsley Theras Primus Dass . > <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 Principal Developer Schrödinger, Inc. -- Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] Difference between action -> align -> to molecule and using align via command line
Hi Dolev, The difference is that the menu action only aligns on C-alpha atoms. Since PyMOL 1.8 the menu label says “align > to molecule (*/CA)” to make this more obvious. The exact command which is executed by the menu action is: align 4A11 & name CA & polymer, 3W15 & name CA & polymer, object=aln_4A11_to_3W15 The “polymer” selection makes sure that calcium atoms are not included, which also have name CA. See also: https://pymolwiki.org/index.php/Align Cheers, Thomas > On May 18, 2017, at 12:41 PM, do r <dolevra...@gmail.com> wrote: > > Hello > > I have noted that using action -> align -> to molecule via the GUI gives > (sometimes radically) different result then running align on the same > structures via command line. > > For examples, for PDB structures 4A11 and 3W15, the command > align 4A11,3W15, aligns 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 in advance > Dolev Rahat -- 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! http://sdm.link/slashdot ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] reproduce special vrml-output
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 has faces
(could be surface or cartoon).
The other difference is the viewport z position (zoom distance), which is 0.0
in the second sample. This can be set as follows before exporting the file
(note that the molecule might not be visible anymore, it could be behind the
camera):
view = list(cmd.get_view())
view[11] = 0.0
cmd.set_view(view)
Hope that helps.
Cheers,
Thomas
> On May 17, 2017, at 4:27 PM, Anke Schultz <anke.schu...@tu-braunschweig.de>
> wrote:
>
> Hi all,
>
> I've been experimenting with exporting surface meshes as .wrl-files. I played
> with the geometry_export_mode setting and the set_view() options, since I
> wanted to get the surface's coordinates corresponding to the atom's
> coordinates of the sd-file I imported to pymol initially. I realized that by
> exporting .wrl-format I got the camera-view instead of the "real" coordinates
> as long as I left everything else on default. This resulted in a shift
> between atom- and surface-coordinates.
>
> While playing around to align camera and reality, I somehow managed to change
> the way my .wrl-file looked in the end and it seems to be exactly what I was
> looking for. I have tried for two days now, but unfortunately I can't
> reproduce my steps leading to this special .wrl-file.
>
> This is (part of) a .wrl-file without changing default settings:
> ###
> #VRML V2.0 utf8
>
> Viewpoint {
> position 0 0 20.39730644
> orientation 1 0 0 0
> description "Z view"
> fieldOfView 0.465421
> }
> DirectionalLight {
> direction -0.348155 -0.348155 -0.870
> }
> NavigationInfo {
> headlight TRUE
> type "EXAMINE"
> }
> Transform {
> translation -1.820169 2.166291 -3.211221
> rotation -0.199343 0.00 0.979930 2.401556
> children [
> Shape {
>geometry Cylinder {
> radius 0.024352
> height 0.139351
> bottom FALSE
> topFALSE
>}
>appearance Appearance {
>material Material { diffuseColor 0.9000 0.9000 0.9000
>specularColor 0.8 0.8 0.8
>shininess 0.8 }
>}
> }
> Transform {
>translation 0.0 0.069676 0.0
>children Shape {
> geometry Sphere { radius 0.024352 }
> appearance Appearance {
>material Material { diffuseColor 0.9000 0.9000 0.9000
>specularColor 0.8 0.8 0.8
>shininess 0.8 }
> }
>}
> }
> Transform {
>translation 0.0 -0.069676 0.0
>children Shape {
> geometry Sphere { radius 0.024352 }
> appearance Appearance {
>material Material { diffuseColor 0.9000 0.9000 0.9000
>specularColor 0.8 0.8 0.8
>shininess 0.8 }
> }
>}
> }
> ]
> }
> Transform {
> translation -1.906664 2.148911 -3.187284
> rotation 0.635566 0.00 0.772046 0.994256
> [...]
> ###
>
> And this is (part of) the special .wrl-file I mysteriously created:
>
> ###
> #VRML V2.0 utf8
>
> Viewpoint {
> position 0 0 -0.
> orientation 1 0 0 0
> description "Z view"
> fieldOfView 0.465421
> }
> DirectionalLight {
> direction -0.348155 -0.348155 -0.870
> }
> NavigationInfo {
> headlight TRUE
> type "EXAMINE"
> }
> Shape {
> appearance Appearance {
> material Material { diffuseColor 1.0 1.0 1.0 }
> }
> geometry IndexedFaceSet {
> coord Coordinate {
>point [
> 1.121935 1.360173 -0.410155,
> 1.840800 1.307029 -0.904629,
> 1.445710 1.051540 -1.083943,
> 1.301289 0.550209 -1.380068,
> 1.445710 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,
> [...]
> ###
>
> If anyone knows the way to this .wrl-format, I would really appreciate your
> help.
> I'm using Pymol Version 1.8.6.0 on Ubuntu.
>
> Thanks in advance,
> Anke
--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.
--
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Re: [PyMOL] Residue selection along coordinates on z-axis
Hi Marko, Have you tried this? select zplane, z > 6.377 and z < 7.139 This works since PyMOL 1.6 (I think). Cheers, Thomas > On May 19, 2017, at 9:49 AM, Marko Sever <marko.se...@ki.si> wrote: > > Hello everyone! Could someone help me figure out, how I could do a residue > 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 Principal Developer Schrödinger, Inc. -- Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] how to alter the "reps"
Hi Junjun, Yes, representations need to be refreshed. This should do it: PyMOL> rebuild Note that "reps" is only available in alter since PyMOL 1.7.4 Of course, to hide all representations, you can also do: PyMOL> hide everything, resi 84 and name CE1 Cheers, Thomas > On May 15, 2017, at 11:33 AM, liu junjun <ljjl...@gmail.com> wrote: > > Hi all, > > I have a question about alter command on "reps" variable. I find reps is zero > when object being set with "hide everything". I try to modify one atom's reps > to be 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? > > Thanks in advance! > > Junjun -- 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! http://sdm.link/slashdot ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] Replace main/side chain with a H atom in a script
Hi Qianyi, The command to replace an atom is "replace". It replaces the currently picked atom, the command for picking is "edit". Example: edit first (resn ALA & name CB) replace H, 1, 1 See also: https://pymolwiki.org/index.php/Replace Cheers, Thomas > On May 2, 2017, at 5:49 PM, Qianyi Cheng <milochen...@gmail.com> wrote: > > I want to run QM calculation on reaction center of a large protein. So I need > to chop off many parts of the protein. I want to replace some side/main > chains with H atoms (for example replace the CB atom 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. -- Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] Text Font size
Hi Mykola, Incentive PyMOL 1.8.4 introduced the “display_scale_factor” setting which allows scaling of the internal GUI, prompt, fonts etc. by a factor of 2. In MacPyMOL this is also linked to the “Display > Retina Resolution” menu option and the “--retina” launch argument. Hope that helps. Cheers, Thomas > On May 1, 2017, at 7:00 PM, Mykola Dimura <mykola.dim...@gmail.com> wrote: > > It's a pity, that internal_gui font size does not scale with > internal_gui_control_size. This is the only thing missing for pymol to > be usable on high-dpi displays. Is it possible 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_gui_control_size, 40 -- 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! http://sdm.link/slashdot ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] Sausage representation
Hi Daniel,
Apparently, no b-factors were assigned, or the CA positions in all states are
identical.
Here is a similar script, maybe that works better for you (uses “rmsf2b” from
PSICO):
run
https://raw.githubusercontent.com/speleo3/pymol-psico/master/psico/editing.py
fetch 1nmr, async=0
rmsf2b 1nmr
spheroid 1nmr
as cartoon
cartoon putty
spectrum b, blue_white_red, 1nmr & guide
Hope that helps.
Cheers,
Thomas
> On Apr 27, 2017, at 4:11 PM, Daniel Munoz Escudero <dmun...@unal.edu.co>
> wrote:
>
> Hello,
>
> I found in this repository http://muralab.org/~cmura/PyMOL/ an script
> (average3d.py) to perform the sausage representation in PyMOL. Although it
> works perfectly good with the pdbs given in the examples, I couldn't get the
> same results for my molecule. After performing all the RMSD calculations (I
> have 51 states in my molecule), 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
> could help me out?
>
> Thank you very much,
>
> Daniel.
--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.
--
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Re: [PyMOL] plugin manager
Hi Raag, You need to run MacPyMOL with the "X11 Hybrid" interface, see: https://pymolwiki.org/index.php/MAC_Install#X11_Hybrid Cheers, Thomas On 12 Apr 2017, at 08:02, Raag Saluja <saluja.r...@gmail.com> wrote: > Hi! > > I needed to install PyTMs but am unable 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 Holder PyMOL Principal Developer Schrödinger, Inc. -- Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] Segmentation fault
Hi João, Before diving into the hassle of installing additional compilers (which probably won't make a difference) I recommend to get familiar with a debugger like gdb and obtain a stack trace of the crash. To compile PyMOL with debug symbols, do export DEBUG=1 before running setup.py. Then run PyMOL (actually: python) with gdb. There is a bit of a learning curve to get familiar with gdb, but considering that you already spend time on this problem and are willing to spend more, I think it's worthwhile. Cheers, Thomas On 11 Apr 2017, at 19:08, João M. Damas <jmda...@itqb.unl.pt> wrote: > Thanks for the feedback, Folmer! > > I am using CentOS. I already used --use-msgpackc=no and it did not improve. > gcc --version gives me 4.8.5 (I cannot update more). Do you think it would be > worth it to install gcc 4.9? On the install page there was said that a > regression to 4.4 could work, but I don’t know. > > Anyone else using CentOS having problems with pymol installation? > > Thanks, > João > > > On Wed, Mar 29, 2017 at 10:35 AM, Folmer Fredslund <folm...@gmail.com> wrote: > Hi João, > > On Ubuntu 16.04 (you didn't mention what you were running) with gcc-4.9 and > "--use-msgpackc=no" I get a working pymol with revision 4170. > > Have you tried creating a new user and test pymol from that account? That > should help you identify if it is solely a problem with your own account. > > HTH, > Folmer > > > On 2017-03-28 03:15, João M. Damas wrote: >> Nobody experiencing the same issues? Any tips on what I may be doing wrong >> on the installation? >> >> João >> >> On Fri, Mar 17, 2017 at 4:08 PM, João M. Damas <jmda...@itqb.unl.pt> wrote: >> Dear all, >> >> I started experiencing segmentation fault on a pymol that I had installed >> through the omnia channel on conda. >> >> Then, I decided to install from scratch using this recipe: >> https://pymolwiki.org/index.php/Linux_Install#Get_latest_source_from_SVN >> >> Still getting the segmentation fault, so maybe something changed in my >> system and it's conflicting with? >> >> The segmentation fault is not on launching PyMOL, but rather when I do >> stuff: loading a PDB file, building a fragment. Like this: >> >> ``` >> ./pymol: line 3: 28505 Segmentation fault "/usr/bin/python2.7" >> "/data/joao/maindisk/software/pymol-svn/modules/pymol/__init__.py" "$@" >> ``` >> >> Curiously, when I load a 1.740 session (.pse file I had saved), it works (no >> segmentation fault), I can even perform commands like select and stuff, and >> they work. If I load a more recent 1.803 session, it also seg faults: >> >> ``` >> Executive: Loading version 1.803 session... >> ./pymol: line 3: 29221 Segmentation fault "/usr/bin/python2.7" >> "/data/joao/maindisk/software/pymol-svn/modules/pymol/__init__.py" "$@" >> ``` >> >> Any clues? Am I doing something wrong? >> >> Thanks, >> João >> >> -- >> João M. Damas >> PhD Student >> Protein Modelling Group >> ITQB-UNL, Oeiras, Portugal >> Tel:+351-214469613 -- 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! http://sdm.link/slashdot ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] Calculating center of mass for the entire protein
deroath...@gmail.com>> wrote: > > Well I'm assuming the selection goes in the > argument of cmd.centerofmass(), however, does it > have to be an atom? How should I calculate the > center of mass for an entire protein? > > On Thu, Apr 6, 2017 at 4:48 AM, David Hall > <li...@cowsandmilk.net > <mailto:li...@cowsandmilk.net>> wrote: > > It returns the x, y, and z coordinates of > the center of mass as a list of 3 floats, > presumably in that order? > > Is there another question? The page > describes the arguments and their defaults > so I am unsure what is lacking. > > -David > > On Apr 5, 2017, at 10:29 PM, Ahmad > Abdelzaher <underoath...@gmail.com > <mailto:underoath...@gmail.com>> wrote: > > I find the documentation about the python > api here to be a bit lacking. > > https://pymolwiki.org/index.php/Centerofmass > <https://pymolwiki.org/index.php/Centerofmass> > > I would appreciate more info on how to use > this: cmd.centerofmass() returns a list of > 3 floats. > > -- > Tsjerk A. Wassenaar, Ph.D. > > > -- > João M. Damas > PhD Student > Protein Modelling Group > ITQB-UNL, Oeiras, Portugal > Tel:+351-214469613 -- 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! http://sdm.link/slashdot ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] selection of residues
Hi Abhinav, - Object name is the "model" variable. Check this page: https://pymolwiki.org/index.php/Iterate#Exposed_Variables - Limit selection to enabled objects: "enabled" selection keyword - Limit selection to one atom per residue: "byca" will do the trick for proteins iterate byca (rep sticks & enabled), print(model,chain,resi,resn) Cheers, Thomas > iterate rep sticks, print(cmd.get_names(enabled_only=1),chain,resi,resn) On 22 Mar 2017, at 16:43, Kumar, Abhinav <aku...@intrexon.com> wrote: > Hi Thomas, > Thanks very much. It works well. > However, can you please help me refine the print out? > I want to include the object name and print only once the residue info for > each residue. Currently it prints for all atoms of residues. > I tried the following: > iterate rep sticks, print(cmd.get_names(enabled_only=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] selection of residues > > Hi Abhinav, > > You can select by representation, e.g.: > > iterate rep sticks, print(chain, resi) > > or directly add labels on CA atoms: > > label byca rep sticks, resi > > Hope that helps. > > Cheers, > Thomas > > On 22 Mar 2017, at 15:43, Kumar, Abhinav <aku...@intrexon.com> wrote: > >> Hi, >> Is there a way of extracting residue information from a session file in >> which a few residues are shown in sticks representation? >> I am interested in changing representation/adding labels to only those >> residues with stick representation. >> >> Thanks, >> Abhinav >> >> Abhinav 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. -- Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] selection of residues
Hi Abhinav, You can select by representation, e.g.: iterate rep sticks, print(chain, resi) or directly add labels on CA atoms: label byca rep sticks, resi Hope that helps. Cheers, Thomas On 22 Mar 2017, at 15:43, Kumar, Abhinav <aku...@intrexon.com> wrote: > Hi, > Is there a way of extracting residue information from a session file in which > a few residues are shown in sticks representation? > I am interested in changing representation/adding labels to only those > residues with stick representation. > > Thanks, > Abhinav > > Abhinav 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. -- Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
[PyMOL] PyMOL 1.8.6 released
Greetings, We are happy to announce the release of PyMOL v1.8.6. PyMOL sponsors can download ready-to-use installers from http://pymol.org/download . The open-source code has been pushed to sourceforge svn (revision 4170). Exciting new features include: - Fast MMTF load support. MMTF is a new binary format for PDB structures which allows for very small file sizes while being self contained with explicit bond orders and formal charges. MMTF files now load into PyMOL about 5x as fast as mmCIF files. Learn more about MMTF at http://mmtf.rcsb.org/ - Ray tracing support for chromadepth (Incentive feature) - Edge smoothing for partial surfaces (Incentive feature) - A convenient CTRL-L shortcut to zoom on organic molecules Find the complete release notes at: http://pymol.org/d/media:new186 We've also added several new pages to the PyMOLWiki documenting old and new stuff: https://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. -- Announcing the Oxford Dictionaries API! The API offers world-renowned dictionary content that is easy and intuitive to access. Sign up for an account today to start using our lexical data to power your apps and projects. Get started today and enter our developer competition. http://sdm.link/oxford ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] Disable ray tracing in script for volumes
Hi Tom, As you have analyzed very correctly, volume is only available with on-screen rendering. I've added a section to the PyMOLWiki which describes the options and limitations: https://pymolwiki.org/index.php/Volume#Ray_Tracing Hope that helps. Cheers, Thomas On 23 Feb 2017, at 13:19, Thomas Grant <tomer...@gmail.com> wrote: > Dear all, > > I've written a .pml script to render volumes and save png files. The script > works fine when running it from the GUI, but for some reason when I run in > command line mode with pymol -cqr myscript.pml the image saved is blank. > > It appears that when running from the command line it automatically ray > traces the image, even when I set ray = 0 in the png command, and since > volumes don't work well with ray tracing, the images end up blank. > > I tried setting ray_volume=1, but that still doesn't fix the problem. > > My script is below, as is the output from the command line and from the GUI. > Notice that when running from the command line there is a "Ray: render time:" > line that doesn't appear when running from the GUI. > > Thanks for any insight. > > Tom > > myscript.pml: > $>cat myscript.pml: > bg white > fetch 1oky, type=2fofc, async=0 > volume 1okyVol, 1oky_2fofc > set ray_volume, 1 > png volume.png, ray=0 > > command line output (doesn't work): > $>pymol -cqr myscript.pml: > PyMOL>bg white > PyMOL>fetch 1oky, type=2fofc, async=0 > ObjectMapLoadBRIXFile: Loading from './1oky_2fofc.omap'. > BRIXStrToMap: Map Size 102 x 99 x 92 > BRIXStrToMap: Range = -0.906629 to 2.095844 > BRIXStrToMap: Calculated Mean = -0.006, Sigma =0.251 > BRIXStrToMap: Normalizing... > Crystal: Unit Cell 124.162 124.162 47.300 > Crystal: Alpha Beta Gamma90.000 90.000 120.000 > Crystal: RealToFrac Matrix > Crystal:0.00810.0046 -0. > Crystal:0.0.0093 -0. > Crystal:0.0.0.0211 > Crystal: FracToReal Matrix > Crystal: 124.1625 -62.08120. > Crystal:0. 107.52790. > Crystal:0.0. 47.3000 > Crystal: Unit Cell Volume 631499. > CmdLoad: "./1oky_2fofc.omap" loaded as "1oky_2fofc". > PyMOL>volume 1okyVol, 1oky_2fofc > Executive: object "1okyVol" created. > Volume: created "1okyVol" > PyMOL>set ray_volume, 1 > Setting: ray_volume set to on. > PyMOL>png volume.png, ray=0 > Ray: render time: 0.01 sec. = 242165.4 frames/hour (0.01 sec. accum.). > ScenePNG: wrote 640x480 pixel image to file "volume.png". > > GUI output (works): > $>pymol -qr myscript.pml: > Detected OpenGL version 2.0 or greater. Shaders available. > Detected GLSL version 1.20. > PyMOL>bg white > PyMOL>fetch 1oky, type=2fofc, async=0 > ObjectMapLoadBRIXFile: Loading from './1oky_2fofc.omap'. > BRIXStrToMap: Map Size 102 x 99 x 92 > BRIXStrToMap: Range = -0.906629 to 2.095844 > BRIXStrToMap: Calculated Mean = -0.006, Sigma =0.251 > BRIXStrToMap: Normalizing... > Crystal: Unit Cell 124.162 124.162 47.300 > Crystal: Alpha Beta Gamma90.000 90.000 120.000 > Crystal: RealToFrac Matrix > Crystal:0.00810.0046 -0. > Crystal:0.0.0093 -0. > Crystal:0.0.0.0211 > Crystal: FracToReal Matrix > Crystal: 124.1625 -62.08120. > Crystal:0. 107.52790. > Crystal:0.0. 47.3000 > Crystal: Unit Cell Volume 631499. > CmdLoad: "./1oky_2fofc.omap" loaded as "1oky_2fofc". > PyMOL>volume 1okyVol, 1oky_2fofc > Executive: 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". > > > > > -- > Thomas D. Grant, Ph.D. > Staff Scientist > BioXFEL Science and Technology Center > Hauptman-Woodward Medical Research Institute > 700 Ellicott St. > Buffalo, NY 14203 -- 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! http://sdm.link/slashdot ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] problem with alter chain Id
clearing the "rank" property also works for me, then the script should not
depend on retain_order anymore:
currentName = "%s_%s" % (solutionPymolString, currentChain)
cmd.alter(currentName, "chain='%s';rank=-1" % currentChain)
However, I think there is also a problem with your script, you're creating
copies of copies, every iteration will pick up the previously created chains
and create another copy of the whole thing. Creating the copies in a new object
will fix this:
newPymolString = 'newobj'
cmd.create(newPymolString, "none")
angle = 360.0/monomers
chains = ["A", "B", "C", "D", "E", "F", "G", "H", "I", "J", "K", "L", "M", "N",
"O", "P", "Q", "R", "S", "T", "U", "V", "W", "X", "Y", "Z"]
for i in range(1, monomers):
currentChain = chains[i]
currentName = "%s_%s" % (solutionPymolString, currentChain)
cmd.create(currentName, solutionPymolString, 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,
Thomas
On 01 Mar 2017, at 14:10, Thomas Holder <thomas.hol...@schrodinger.com> wrote:
> Hi Gregor,
>
> Looks like retain_order is on for her. This should fix it:
>
> PyMOL> set retain_order, off
>
> https://pymolwiki.org/index.php/Retain_order
>
> Cheers,
> Thomas
>
> On 01 Mar 2017, at 10:28, Gregor Hagelüken <hagelue...@pc.uni-bonn.de> wrote:
>
>> Hi,
>>
>> I use a python script to copy an object, rotate it, alter its chain ID and
>> then merge it with the original object.
>> Here is the relevant part of my script:
>>
>> angle = 360.0/monomers
>> chains = ["A", "B", "C", "D", "E", "F", "G", "H", "I",
>> "J", "K", "L", "M", "N", "O", "P", "Q", "R", "S", "T", "U", "V", "W", "X",
>> "Y", "Z"]
>> for i in range(1, monomers):
>> currentChain = chains[i]
>> cmd.create("%s_%s" %(solutionPymolString,
>> currentChain), solutionPymolString, 1, 1)
>> cmd.rotate([1, 0, 0], i * angle, "%s_%s"
>> %(solutionPymolString, currentChain), 1, 0, None, [0, 0, 0])
>> cmd.alter("%s_%s" %(solutionPymolString,
>> currentChain), "chain='%s'" %currentChain)
>> cmd.create("%s" %(solutionPymolString), "%s or
>> %s_%s" %(solutionPymolString, solutionPymolString, currentChain), 1, 1)
>> cmd.delete("%s_%s" %(solutionPymolString,
>> currentChain))
>>
>> This works fine with PyMOL 1.8.3 and 1.8.5 on my computer (macOS Sierra).
>>
>> I have given the script to another person and for her it produces a very
>> strange result.
>> The resulting structure is only visible in lines or sticks mode. And it
>> looks like this in the sequence viewer:
>>
>>
>> She used the same input structure as I did but she has PyMOL 1.8.4 and uses
>> Windows. Could this be a PyMOL bug?
>>
>> Cheers,
>> Gregor
>
> --
> Thomas Holder
> PyMOL Principal Developer
> Schrödinger, Inc.
--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.
--
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Re: [PyMOL] PyMOL for iPad issues
Hi João, 1QFU has a three-fold symmetry, and only one copy of each molecule is contained in the asymmetric unit. PyMOL (on the desktop) can load the biological assembly like this: PyMOL> set assembly, 1 PyMOL> fetch 1qfu Hope that helps. Cheers, Thomas On 28 Feb 2017, at 16:16, João Oliveira Jr. <joaodej...@gmail.com> wrote: > Thank you all for your time. > > Someone could please explain me why some structures aren't fully displayed? > > For example, in 1QFU, I just get 01 HA attached to 01 Fab antibody arm, > instead of 03 HA + 03 Fabs... > > 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" scene is to > load a PyMOL session file (.pse) which already has the setting enabled. > > Cheers, > Thomas > > On 28 Feb 2017, at 11:57, João Oliveira Jr. <joaodej...@gmail.com> wrote: > > > Dear Andreas > > > > Where do I find this typing command option? > > > > Em ter, 28 de fev de 2017 às 13:53, Andreas Forster <docandr...@gmail.com> > > escreveu: > > Dear João, > > > > type > > > > set grid_mode, on > > > > to see your models side by side. You might have to align them first. Use > > the command > > > > super model1, model2 > > > > for that. > > > > All best. > > > > > > Andreas > > > > > > On Tue, Feb 28, 2017 at 5:27 PM, João Oliveira Jr. <joaodej...@gmail.com> > > wrote: > > Hi > > > > Please, when using PyMOL app for iPad is that possible to set up multiple > > structures from diffent PDB codes at the same time? > > > > I'm a Immunology teacher and I'd like a slide with 04 antibodies (PDB > > codes: 1IGY, 1IGT, 1HZH, and 5DK3) aligned side by side 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. -- Check out the vibrant tech community on one of the world's most engaging tech sites, SlashDot.org! http://sdm.link/slashdot ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] change in VRML format output
Hi Paul, Interesting observation. This change was not intentional, it's a side effect of a very low level change in the geometry generation. We should be able to optimize this for the next PyMOL release. Cheers, Thomas On 24 Feb 2017, at 12:02, Paul Paukstelis <shocksofmig...@gmail.com> wrote: > There seem to have been some changes in how the VRML2 output is done > between 1.7.X and 1.8.X, though I can't find it documented in change logs. > > In 1.7.X, vrml2 output would convert sticks to cylinders that was > dependent on color. If a bond were split into two colors, it would > output as two cylinders, but if the bond were one color it would just be > one longer cylinder. There was also the annoying property that no matter > what settings you included, vrml2 would always put extra spheres at the > ends of cylinders to make them smooth (even though they were inside atoms) > > In 1.8.X bond cylinders are always exported as two separate cylinders, > even when everything is colored the same, but the annoying spheres at > the end of bonds are gone (yay!). > > Unfortunately, it turns out that when working with blender 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. > > Thanks. -- 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! http://sdm.link/slashdot ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] PyMOL for iPad issues
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" scene is to load a PyMOL session file (.pse) which already has the setting enabled. Cheers, Thomas On 28 Feb 2017, at 11:57, João Oliveira Jr. <joaodej...@gmail.com> wrote: > Dear Andreas > > Where do I find this typing command option? > > Em ter, 28 de fev de 2017 às 13:53, Andreas Forster <docandr...@gmail.com> > escreveu: > Dear João, > > type > > set grid_mode, on > > to see your models side by side. You might have to align them first. Use > the command > > super model1, model2 > > for that. > > All best. > > > Andreas > > > On Tue, Feb 28, 2017 at 5:27 PM, João Oliveira Jr. <joaodej...@gmail.com> > wrote: > Hi > > Please, when using PyMOL app for iPad is that possible to set up multiple > structures from diffent PDB codes at the same time? > > I'm a Immunology teacher and I'd like a slide with 04 antibodies (PDB codes: > 1IGY, 1IGT, 1HZH, and 5DK3) aligned side by side 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. -- Check out the vibrant tech community on one of the world's most engaging tech sites, SlashDot.org! http://sdm.link/slashdot ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] Execution time of color command
Hi Leonhard,
Very interesting analysis. I'm wondering if this slowdown actually scales with
number of objects or rather total number of atoms.
If your color scheme lookup by (object, resi) key is fast in Python (let's say
you have it all in a dictionary), then you can use cmd.alter() with a single
pass, which probably will be faster than cmd.color() in multiple passes.
Example:
colors = {
'obj1': {
1: 0xFF,
2: 0x00,
3: 0x66,
},
'obj2': {
1: 0x001234,
2: 0x121212,
3: 0x009900,
},
}
cmd.alter('all', 'color = 0x4000 | colors[model][resv]', space={'colors':
colors})
cmd.recolor()
The magic number 04000 is the cColor_TRGB_Bits mask which tells PyMOL that
this is not a color index, but an RGB color.
Instead of a dictionary lookup, you may also use a callback function.
Check out these examples for alter with space argument:
https://pymolwiki.org/index.php/Iterate#.22space.22_argument
Cheers,
Thomas
On 28 Feb 2017, at 09:34, Leonhard Heizinger <leonhard.heizin...@ur.de> wrote:
> Hi,
> coloring a certain residue in an object takes about 4 ms when only one
> object is loaded in PyMol:
>
> %time cmd.color("blue", "obj1of1 and resi 1")
> CPU times: user 3.33 ms, sys: 0 ns, total: 3.33 ms
> Wall time: 4.13 ms
>
> Performing the same operation when a lot of other objects (~300) are
> loaded results in a highly increased execution time:
>
> %time cmd.color("blue", "obj1of300 and resi 1")
> CPU times: user 243 ms, sys: 0 ns, total: 243 ms
> Wall time: 234 ms
>
> This is 60-fold increment compared to a PyMol Session with only one
> object loaded. All structures in this example have ~240 residues.
>
> Consequently, coloring each residue of 300 objects in an individual
> color would take more then 4.5 hours on my machine. Of course this use
> case is pretty unlikely.
>
> In my case I only have limited number of colors (255 colors gradient)
> which each residue could obtain. So I'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 this in a reasonable amount of time?
> Thanks!
>
> Best,
>
> Leonhard
--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.
--
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Re: [PyMOL] Convert multiple .mae to .pdb files
Hi Kar Weng,
This is possible with a Python script. Save the following to a file (e.g.
"mae2pdb.py") and run it with PyMOL ("File > Run Script..." or use the "run"
command). This will convert all .mae files from the current directory to .pdb
files.
from pymol import cmd
import glob
for filename in glob.glob('*.mae'):
cmd.load(filename)
cmd.save(filename[:-4] + '.pdb')
cmd.delete('*')
Hope that helps.
Cheers,
Thomas
On 20 Feb 2017, at 01:58, Kar Weng Ng <karweng.t...@gmail.com> wrote:
> Dear Sir/Madam,
>
> I am final year School of Pharmacy student, currently working on a homology
> modelling project. I am relatively new to using PyMOL. I would like to
> convert .mae ligand structures that were produced by glide_dock into .pdb
> files. I understand that I could use the: load ligand_1.mae, then go to 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 Lakeside Campus, Malaysia
--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.
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Re: [PyMOL] Side chain conformations percentages
Hi Timofey, These are frequencies from the 2002 Dunbrack rotamer library (files "bbdep02.May.lib" and "bbind02.May.lib"). Cheers, Thomas On 10 Feb 2017, at 05:20, Timofey Tyugashev <tyugas...@niboch.nsc.ru> wrote: > What is the source for these numbers (the 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.org! http://sdm.link/slashdot ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] Connectivity
Hi Laurie, The list of bonds is accessible with cmd.get_model(), see https://pymolwiki.org/index.php/Get_Model PyMOL> m = cmd.get_model() PyMOL> print m.bond[0].index [0, 1] PyMOL> print m.bond[0].order 1 Cheers, Thomas On 26 Jan 2017, at 13:50, Laurence Williams <williams...@cardiff.ac.uk> wrote: > Dear pymol users, > > I understand that pymol does not explicitly need connectivity data to > visualise molecules as bonds are drawn when two atoms are within in a given > distance. However, once those bonds are drawn for the molecule, is > connectivity 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. -- Check out the vibrant tech community on one of the world's most engaging tech sites, SlashDot.org! http://sdm.link/slashdot ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] how to convert .pse to html?
Hi Albert, For batch processing (no GUI), run PyMOL with -c. See also https://pymolwiki.org/index.php/Command_Line_Options I fixed the script, it was written for an old PyMOL version. Cheers, Thomas On 25 Jan 2017, at 17:01, Albert <mailmd2...@gmail.com> wrote: > BTW, I try to run the example command line, but it always failed with > messages: > > > PyMOL>pymol2glmol 1tqn > Traceback (most recent call last): > File "/usr/lib64/python2.7/site-packages/pymol/parser.py", line 256, in parse >self.result=apply(layer.kw[0],layer.args,layer.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? > > THX again. > > > On 01/25/2017 10:46 PM, Thomas Holder wrote: >> Hi Albert, >> >> What kind of HTML content do you expect? A page with a PNG image? Or an >> interactive 3D model? Check out >> this:https://pymolwiki.org/index.php/Pymol2glmol >> >> Cheers, >> Thomas -- 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! http://sdm.link/slashdot ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] unable to initialize pymol plugin
Hi Hena, You're probably missing additional module requirements for these plugins. To get a meaningful stacktrace, import the plugin modules on the PyMOL command line. E.g.: import pmg_tk.startup.mtsslDockGui For 3D stereo: Have you tried "Display > Stereo" from the menu? Cheers, Thomas On 21 Jan 2017, at 18:09, Hena Dutta <hdutt...@gmail.com> wrote: > Dear Users, > Could someone help to solve the following initializing problem? I am using a > Toshiba Qosmio laptop. Also how can I see 3d here? > Thank you in advance. > Hena > > PyMOL(TM) Molecular Graphics System, Version 1.7.2.1. > Copyright (c) Schrodinger, LLC. > All Rights Reserved. > > Created by Warren L. DeLano, Ph.D. > > PyMOL is user-supported open-source software. Although some versions > are freely available, PyMOL is not in the public domain. > > If PyMOL is helpful in your work or study, then please volunteer > support for our ongoing efforts to create open and affordable scientific > software by purchasing a PyMOL Maintenance and/or Support subscription. > > More information can be found at "http://www.pymol.org;. > > Enter "help" for a list of commands. > Enter "help " for information on a specific command. > > Hit ESC anytime to toggle between text and graphics. > > Detected OpenGL version 2.0 or greater. Shaders available. > Detected GLSL version 4.50. > OpenGL graphics engine: > GL_VENDOR: NVIDIA Corporation > GL_RENDERER: GeForce GTX 670M/PCIe/SSE2 > GL_VERSION: 4.5.0 NVIDIA 369.09 > Detected 8 CPU cores. Enabled multithreaded rendering. > OpenGL quad-buffer stereo 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.mtsslPlotter). > Unable to initialize plugin 'mtsslTrilaterate' > (pmg_tk.startup.mtsslTrilaterate). -- 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! http://sdm.link/slashdot ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] how to convert .pse to html?
Hi Albert, What kind of HTML content do you expect? A page with a PNG image? Or an interactive 3D model? Check out this: https://pymolwiki.org/index.php/Pymol2glmol Cheers, Thomas On 23 Jan 2017, at 16:11, Albert <mailmd2...@gmail.com> wrote: > Hello, > > I've got a pymol .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 Principal Developer Schrödinger, Inc. -- Check out the vibrant tech community on one of the world's most engaging tech sites, SlashDot.org! http://sdm.link/slashdot ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] How to convert .mae files to .PDB
Hi Himesh, On the PyMOL command line, this should do the trick: # load desmond trajectory load sample-out.cms, mytraj load_traj sample_trj/clickme.dtr, mytraj # save multi-model PDB file save multi.pdb, mytraj, state=0 See also: https://pymolwiki.org/index.php/Load_Traj#Examples https://pymolwiki.org/index.php/Save Cheers, Thomas On 25 Jan 2017, at 03:46, Himesh Makala <him...@sastra.ac.in> wrote: > Hello, > > I would like to convert the simulation output [which was performed by using > Desmond (maestro)] into .PDB format. It will be very helpful if anyone help > me out with the same. > > Thanks a lot, > > Himesh > > -- > > Thanks & Regards, > > Himesh Makala -- 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! http://sdm.link/slashdot ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] PyMol & PDBe
Hi Filip, This is already done. The update was in PyMOL 1.8.4.2 and in Open-Source PyMOL rev 4165. The object names are still the same, so it's backwards compatible. The only difference is the file format, previously we downloaded omap format, now it's ccp4 map format (larger files but higher data precision). Cheers, Thomas On 24 Jan 2017, at 12:42, Filip Leonarski <leonar...@unistra.fr> wrote: > Hi, > > I'm writing in regards of downloading electron density maps in Pymol. As you > know EDS is soon to be decomissioned and PDBe (PDB in Europe) is a new source > of electron density maps for crystal structures. Is it possible with next > update of Pymol to change "fetch , type=2fofc" command to get maps from > PDBe instead of EDS. Is it also possible to leave old names "_2fofc" and > "_fofc" (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 tech community on one of the world's most engaging tech sites, SlashDot.org! http://sdm.link/slashdot ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] New plugin: PyMOLProbity
Great work Jared! Cheers, Thomas On 17 Jan 2017, at 20:02, Albert <mailmd2...@gmail.com> wrote: > fantastic job!! > > Thanks a lot. > > Albert > On 01/16/2017 10:16 PM, Sampson, Jared M. wrote: >> Dear PyMOL Users, >> >> I am pleased to introduce a new plugin called PyMOLProbity which allows a >> PyMOL user to visualize MolProbity-style structural validation data directly >> in a PyMOL session. The programs Reduce, Flipkin, and Probe from the >> well-known MolProbity software package allow generation of data in >> "kinemage" (kinetic image) format to illustrate atom-atom contacts (dots) >> and clashes (spikes), and the new plugin now makes it possible to utilize >> the same programs to produce similar results in PyMOL scenes. >> >> I have put together a page on the PyMOL Wiki with a brief summary of its >> features and basic how-to information. (Please note that the MolProbity >> executables are only available for Linux/MacOS, so PyMOLProbity isn't yet >> useful on Windows.) >> >> My work on this plugin was supported by the Warren L. DeLano Memorial PyMOL >> Open-Source Fellowship. I would like once again to thank Schrödinger for >> the opportunity to work on this project, and in particular would like to >> thank the PyMOL developers for their support and feedback along the way. >> >> I hope 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 Holder PyMOL Principal Developer Schrödinger, Inc. -- Check out the vibrant tech community on one of the world's most engaging tech sites, SlashDot.org! http://sdm.link/slashdot ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] Line transparency
Hi Praz, There is no line transparency setting. But since the ray tracer anyway renders lines as thin sticks, you can show sticks instead of lines and use stick_transparency. show sticks hide lines set stick_radius, 0.1 set stick_transparency, 0.5 ray Hope that helps. Cheers, Thomas On 14 Jan 2017, at 16:48, Praz Nina <praz...@gmail.com> wrote: > Dear all, > > I am wondering if it's possible to vary the transparency of the line > representation in PyMol. > > Currently I display the protein as a cartoon, then duplicate the object and > display it as a line (preset: technical, to be specific), but I want the line > representation to be less visible. Of course I could render out 2 separate > files and blend them in photoshop, but I'm wondering if it's possible in > PyMol. > > The set_transparency command is for surfaces and 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. -- Developer Access Program for Intel Xeon Phi Processors Access to Intel Xeon Phi processor-based developer platforms. With one year of Intel Parallel Studio XE. Training and support from Colfax. Order your platform today. http://sdm.link/xeonphi ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] Save command output to a file in pymol
Spencer's example was in PyMOL command syntax (.pml script). To use it in a
Python script, it would look like this:
from pymol import cmd, stored
stored.f = open("ss.txt", "w")
cmd.iterate("n. CA", "stored.f.write(resi + ':' + ss+'\n')")
stored.f.close()
Cheers,
Thomas
On 13 Jan 2017, at 18:44, Academic Research <ac.resea...@icloud.com> wrote:
> Thank you for your replay.
>
> Running the command from a python code is much better for me. But can you
> elaborate more about the code? it still gives me a syntax error:
>
> file.py
> import pymol
> f=open("ss.txt","w")
> iterate n. CA, f.write(resi + ':' + ss+"\n")
> f.close()
>
> Result:
> File "1.py", line 3
> iterate n. CA, print ss #f.write(resi + ':' + ss+"\n")
> ^
> SyntaxError: invalid syntax
>
>
> How can I fix it?
> Where do I call the .pdb file?
>
> On Jan 13, 2017, at 02:59 pm, Spencer Bliven <spencer.bli...@gmail.com> wrote:
>
>> This can be done using normal python file i/o:
>>
>> f=open("ss.txt","w")
>> iterate n. CA, f.write(resi + ':' + ss+"\n")
>> f.close()
>>
>> On Fri, Jan 13, 2017 at 10:38 AM, Academic Research <ac.resea...@icloud.com>
>> wrote:
>> That would be good as well, How?
>>
>> keep in mind, my protein is synthetic, it is not from the PDB database, and
>> the .pdb file only contains ATOMS, no header or anything else.
>>
>> On Jan 13, 2017, at 12:37 pm, Albert <mailmd2...@gmail.com> wrote:
>>
>>> I think you can obtain it from your Linux terminal
>>>
>>>
>>>
>>> On 01/13/2017 10:34 AM, Academic Research wrote:
>>>> Pymol Professionals I need your help,
>>>>
>>>> I have the following command:
>>>>
>>>> iterate n. CA, print resi + ':'
>>>> + ss
>>>>
>>>> I use this command in pymol to print out each residue number and its
>>>> corresponding secondary structure. The command prints out the result in
>>>> pymol itself.
>>>>
>>>> My question is: How can I save the output from this command into a file?
>>>>
>>>> AC Research
--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.
--
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Re: [PyMOL] isosurface stays gray after using "surface_color" command and "rebuild"
Hi Samuel,
Thanks for the data range output, it looks fine.
I checked the version history and found a bug which was fixed in 1.7.6. Color
ramps didn't take the transformation matrix on the map into account, but cube
files typically have such a matrix. Any chance you can upgrade to PyMOL 1.7.6
or newer?
Cheers,
Thomas
On 12 Jan 2017, at 08:18, Fux Samuel (ID SIS) <samuel@id.ethz.ch> wrote:
> Hi Thomas,
>
> thank you for your reply. Please find below the data range of densf:
>
> PyMOL>print(cmd.get_volume_histogram("densf", 0))
> [-149.1259765625, 17.788000106811523, -1.1102406978607178, 29.603145599365234]
> Best regards
>
> Samuel
>
> --
> ETH Zurich, Dr. sc. ETH Samuel Fux
> High Performance Computing, Scientific IT Services
> WEC D 13, Weinbergstrasse 11, 8092 Zurich, Switzerland
> Phone +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: [PyMOL] isosurface stays gray after using "surface_color"
> command and "rebuild"
>
> Hi Samuel,
>
> What's the data range of the "densf" map?
> You can query the [min, max, mean, stdev] with:
> print(cmd.get_volume_histogram("densf", 0))
>
> Does the color show up with "ray"? (That is independent of OpenGL
> capabilities)
>
> Thanks,
> Thomas
>
> On 11 Jan 2017, at 16:11, Fux Samuel (ID SIS) <samuel@id.ethz.ch> wrote:
>
> > Hi all,
> >
> > I am using PyMOL 1.7.4 on a HPC cluster (with X11-forwarding). The graphics
> > card (ATI) of my workstation supports OpenGL 1.4.
> >
> > I am trying to color an isosurface with a color ramp from a cube file. I
> > use the following commands:
> >
> > load PhCH2-2Py2H.xyz
> > hide everything
> > show sticks
> > show spheres
> > set stick_radius, .06
> > set sphere_scale, .18
> > set sphere_scale, .10, elem H
> > set bg_rgb=[1, 1, 1]
> > set stick_quality, 50
> > set sphere_quality, 4
> > color gray50, elem C
> > color red, elem O
> > color slate, elem N
> > color gray98, elem H
> > set stick_color, black
> > set ray_trace_mode, 1
> > set ray_texture, 2
> > set antialias, 3
> > set ambient, 0.5
> > set spec_count, 5
> > set shininess, 50
> > set specular, 1
> > set reflect, .1
> > set dash_gap, 0
> > set dash_color, black
> > set dash_gap, .15
> > set dash_length, .05
> > set dash_round_ends, 0
> > set dash_radius, .05
> > set fog, off
> > ray
> >
> > load PhCH2-2Py2H_inter_py-dens.cube, densf
> > load PhCH2-2Py2H_inter_py-grad.cube, gradf
> >
> > preset.ball_and_stick(selection='all')
> > isosurface gradpos, gradf, 0.50
> > ramp_new ramp1, densf, [-5.0,0.0,5.0], [red,green,blue]
> > set surface_color, ramp1, gradpos
> > set two_sided_lighting, value=1
> > set transparency, 0.30
> > set surface_quality, 1
> >
> > rebuild
> >
> > turn z,45
> > turn y,-3
> > turn z,-2
> >
> > png PhCH2-2Py2H_inter_b.png, width=400, height=300, dpi=100, ray=1
> >
> > turn z,-45
> > turn y,3
> > turn z,2
> > turn z,40.0
> > turn x,25
> > turn y,30
> >
> > png PhCH2-2Py2H_inter_a.png, width=400, height=300, dpi=100, ray=1
> > 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 under CentOS 6.8, on my workstation I am running
> > Ubuntu 16.04.
> >
> > If there is any additional information that I can provide, then please let
> > me know.
> >
> > Best regards and thank you
> >
> > Samuel
--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.
--
Developer Access Program for Intel Xeon Phi Processors
Access to Intel Xeon Phi processor-based developer platforms.
With one year of Intel Parallel Studio XE.
Training and support from Colfax.
Order your platform today. http://sdm.link/xeonphi
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Re: [PyMOL] isosurface stays gray after using "surface_color" command and "rebuild"
Hi Samuel,
What's the data range of the "densf" map?
You can query the [min, max, mean, stdev] with:
print(cmd.get_volume_histogram("densf", 0))
Does the color show up with "ray"? (That is independent of OpenGL capabilities)
Thanks,
Thomas
On 11 Jan 2017, at 16:11, Fux Samuel (ID SIS) <samuel@id.ethz.ch> wrote:
> Hi all,
>
> I am using PyMOL 1.7.4 on a HPC cluster (with X11-forwarding). The graphics
> card (ATI) of my workstation supports OpenGL 1.4.
>
> I am trying to color an isosurface with a color ramp from a cube file. I use
> the following commands:
>
> load PhCH2-2Py2H.xyz
> hide everything
> show sticks
> show spheres
> set stick_radius, .06
> set sphere_scale, .18
> set sphere_scale, .10, elem H
> set bg_rgb=[1, 1, 1]
> set stick_quality, 50
> set sphere_quality, 4
> color gray50, elem C
> color red, elem O
> color slate, elem N
> color gray98, elem H
> set stick_color, black
> set ray_trace_mode, 1
> set ray_texture, 2
> set antialias, 3
> set ambient, 0.5
> set spec_count, 5
> set shininess, 50
> set specular, 1
> set reflect, .1
> set dash_gap, 0
> set dash_color, black
> set dash_gap, .15
> set dash_length, .05
> set dash_round_ends, 0
> set dash_radius, .05
> set fog, off
> ray
>
> load PhCH2-2Py2H_inter_py-dens.cube, densf
> load PhCH2-2Py2H_inter_py-grad.cube, gradf
>
> preset.ball_and_stick(selection='all')
> isosurface gradpos, gradf, 0.50
> ramp_new ramp1, densf, [-5.0,0.0,5.0], [red,green,blue]
> set surface_color, ramp1, gradpos
> set two_sided_lighting, value=1
> set transparency, 0.30
> set surface_quality, 1
>
> rebuild
>
> turn z,45
> turn y,-3
> turn z,-2
>
> png PhCH2-2Py2H_inter_b.png, width=400, height=300, dpi=100, ray=1
>
> turn z,-45
> turn y,3
> turn z,2
> turn z,40.0
> turn x,25
> turn y,30
>
> png PhCH2-2Py2H_inter_a.png, width=400, height=300, dpi=100, ray=1
> 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 under CentOS 6.8, on my workstation I am running
> Ubuntu 16.04.
>
> If there is any additional information that I can provide, then please let me
> know.
>
> Best regards and thank you
>
> Samuel
--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.
--
Developer Access Program for Intel Xeon Phi Processors
Access to Intel Xeon Phi processor-based developer platforms.
With one year of Intel Parallel Studio XE.
Training and support from Colfax.
Order your platform today. http://sdm.link/xeonphi
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Re: [PyMOL] electrostatic potential as cartoon?
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 since version 1.8 can color ribbon by ramp, if that helps. > > However, electrostatic potential locally probed along the backbone will not > be very meaningful. Typically you would look at electrostatics beyond the > solvent excluded surface, which you'll get in PyMOL either with > surface_solvent=1 or with surface_ramp_above_mode=1, > seehttps://pymolwiki.org/index.php/surface_ramp_above_mode > > To visualize the distribution of charged or polar residues with cartoon, your > "flimsy" color scheme by residue type seems quite valid. > > Cheers, > Thomas > > On 04 Jan 2017, at 11:05, vincent Chaptal <vincent.chap...@ibcp.fr> wrote: > >> Hi everyone, >> >> is there a way to color by electrostatic potential but display the structure >> as cartoon? >> >> a workaround could be : >> color white, molecule >> color red, resn asp+glu+thr+ser etc.. >> color blue, resn arg+lys >> >> ... but this seems rather flimsy. >> >> Thank you and best wishes for the new year. >> Vincent >> >> >> -- >> Vincent Chaptal, PhD >> Institut de Biologie et Chimie 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. -- Check out the vibrant tech community on one of the world's most engaging tech sites, SlashDot.org! http://sdm.link/slashdot ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] electrostatic potential as cartoon?
Hi Vincent, Coloring the cartoon with a color ramp is not possible unfortunately. Incentive PyMOL since version 1.8 can color ribbon by ramp, if that helps. However, electrostatic potential locally probed along the backbone will not be very meaningful. Typically you would look at electrostatics beyond the solvent excluded surface, which you'll get in PyMOL either with surface_solvent=1 or with surface_ramp_above_mode=1, see https://pymolwiki.org/index.php/surface_ramp_above_mode To visualize the distribution of charged or polar residues with cartoon, your "flimsy" color scheme by residue type seems quite valid. Cheers, Thomas On 04 Jan 2017, at 11:05, vincent Chaptal <vincent.chap...@ibcp.fr> wrote: > Hi everyone, > > is there a way to color by electrostatic potential but display the structure > as cartoon? > > a workaround could be : > color white, molecule > color red, resn asp+glu+thr+ser etc.. > color blue, resn arg+lys > > ... but this seems rather flimsy. > > Thank you and best wishes for the new year. > Vincent > > > -- > Vincent Chaptal, PhD > Institut de Biologie et Chimie 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. -- Check out the vibrant tech community on one of the world's most engaging tech sites, SlashDot.org! http://sdm.link/slashdot ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
