Re: [PyMOL] default water bond lengths in PyMOL
Hi Tom, There is the "connect_cutoff" setting, see https://pymolwiki.org/index.php/connect_cutoff The bonds do not affect residue numbers in PyMOL, those should be unchanged and identical to your original input file. Cheers, Thomas On 03 Jan 2017, at 07:07, Thomas Charles Pochapsky <pocha...@brandeis.edu> wrote: > Hi, I exported a PDB file from PyMOL that includes explicit water from a > dynamics track. However, many of the solvent molecules are either > doubled (same residue number for two different waters) or truncated > (missing a hydrogen, or a hydrogen given a separate residue number). I > am assuming that PyMOL assigns bonds based on distance between atoms, is > there a way to minimize this? The RCSB doesn't like my current PDB file! > > Thanks, Tom Pochapsky -- Thomas Holder 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] aligned and cealign command
Hi Jiri, Try this on the PyMOL command line: # example structures (use your own here) fetch 1ake, s1, async=0 fetch 4ake, s2, async=0 # import the "angle_between_domains" command run https://raw.githubusercontent.com/speleo3/pymol-psico/master/psico/orientation.py # align on chain A align s1 & chain A, s2 & chain A # measure rotation and displacement of chain B angle_between_domains s1 & chain B, s2 & chain B, method=cealign For 1ake and 4ake, this reports: Angle: 21.70 deg, Displacement: 56.08 angstrom See also: https://www.mail-archive.com/pymol-users@lists.sourceforge.net/msg10995.html https://www.mail-archive.com/pymol-users@lists.sourceforge.net/msg13015.html Hope that helps. Cheers, Thomas On 15 Dec 2016, at 07:02, chemocev marker <jirivit...@gmail.com> wrote: > Hi Pymol user > I have a heterodimer protein and I wanted to compare it with homologous > structures. The chain B of both the structures can be align with align > command and in doing so, the chain A is misaligned and which can be only > align by the cealign command. The sequence similarity between chain A is very > low but the both chains have similar fold. I am interested to know, how much > degree the subunits move or rotate when we aligned the chain A with cealign > command. > best > Jiri -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. -- 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] Middle mouse button in Mac Pymol does not work?
Hi Jason, Middle mouse button always worked fine for me with MacPyMOL, using any kind of "normal" mouse (two buttons + wheel as middle button). I haven't tried a magic mouse, but also never received bug reports that those wouldn't work with MacPyMOL. Could it be that any third party tool interferes here (like BetterTouchTool)? A PyMOL script or plugin could also possibly redefine mouse actions (like https://pymolwiki.org/index.php/Mouse_modes ). You can suppress loading of plugins and pymolrc scripts with the -k flag (launch from Terminal as /Applications/MacPyMOL.app/Contents/MacOS/MacPyMOL -k). It's true that a trackpad doesn't fully replace a 3 button mouse. ALT+click mimics the middle click, but it looks like SHIFT+ALT+drag doesn't work. The mouse action codes are not documented anywhere. But you could have a look at the cButMode names, which are a bit more meaningful: https://sf.net/p/pymol/code/HEAD/tree/trunk/pymol/layer1/ButMode.cpp#l501 Cheers, Thomas On 05 Dec 2016, at 18:39, Jason D. Kahn <jdk...@umd.edu> wrote: > Hi -- > > I use Mac Pymol 1.8.4 / Mac OS Sierra, but this issue has been present > forever. I usually cannot get the middle "M" commands to work, either with an > old button mouse, a Magic mouse, or a laptop trackpad. I have tried Better > TouchTool without success. In 3-button editing mode, the middle button is > supposed to Move or MovO, but it just rotates instead. This makes any sort of > docking much more difficult. > > Also, is there a guide to what all the Mouse Mode commands actually do? MvAZ? > MvSZ? PkTB? DrgM? > > -- > Jason D. Kahn > Dept. of Chemistry and Biochemistry > University of Maryland > College Park -- 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] difficulty opening EmrE protein (pdb: 3B5D) in Pymol
Since version 1.8.2, PyMOL auto-detects CA-only models, so no ribbon_trace_atoms or cartoon_trace_atoms needed anymore. A nice tool that can assign secondary structure with CA trace only is SST: http://lcb.infotech.monash.edu.au/sstweb2/ PSICO has an SST wrapper, so you can run it directly in PyMOL: run https://raw.githubusercontent.com/speleo3/pymol-psico/master/psico/editing.py fetch 3b5d, async=0 sst show cartoon Hope that helps. Cheers, Thomas On 02 Dec 2016, at 08:24, Spencer Bliven <spencer.bli...@gmail.com> wrote: > There is a cartoon variant too, although everything will look like a loop > > set cartoon_trace_atoms, on > show cartoon, polymer > > On Wed, Oct 26, 2016 at 12:27 AM, Yuxing Liao > <yuxing.l...@utsouthwestern.edu> wrote: > Hi Mohsen, > > The PDB file of 3B5D only contains CA atoms, so most rendering like cartoon > fails. You could try to visualize it by "set ribbon_trace_atoms, 1" and then > show it as ribbon. > > Yuxing > > -Original Message- > From: pymol-users-requ...@lists.sourceforge.net > [mailto:pymol-users-requ...@lists.sourceforge.net] > Sent: Tuesday, October 25, 2016 4:50 PM > To: pymol-users@lists.sourceforge.net > Subject: PyMOL-users Digest, Vol 125, Issue 14 > > Send PyMOL-users mailing list submissions to > pymol-users@lists.sourceforge.net > > To subscribe or unsubscribe via the World Wide Web, visit > https://lists.sourceforge.net/lists/listinfo/pymol-users > or, via email, send a message with subject or body 'help' to > pymol-users-requ...@lists.sourceforge.net > > You can reach the person managing the list at > pymol-users-ow...@lists.sourceforge.net > > When replying, please edit your Subject line so it is more specific than "Re: > Contents of PyMOL-users digest..." > > -- > > Message: 4 > Date: Tue, 25 Oct 2016 21:34:01 + > From: Mohsen Chitsaz <mohsen.chit...@flinders.edu.au> > Subject: [PyMOL] difficulty opening EmrE protein (pdb: 3B5D) in Pymol > To: "pymol-users@lists.sourceforge.net" > <pymol-users@lists.sourceforge.net> > Message-ID: > > <sg2pr03mb15688f28895fd8bf7a322112d5...@sg2pr03mb1568.apcprd03.prod.outlook.com> > > Content-Type: text/plain; charset="us-ascii" > > Hi everyone, > > Can someone please assist me opening this pdb file? I am trying to open EmrE > protein (pdb: 3B5D) in Pymol a and show it as cartoon representation, but it > opens up as many little cross signs seem to be corresponding to CA atoms. > When I try to preset it pretty or any other preset options, it disappears. > The command "show cartoon" is not doing anything on it. > > Cheers > Mohsen > > > > UT Southwestern > > Medical Center > > The future of medicine, today. -- 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] PDB Format not correct for use in CHARMM
Hi Marko and Rui, The TER records can also be prevented with "set pdb_use_ter_records, off". https://pymolwiki.org/index.php/pdb_use_ter_records Cheers, Thomas On 28 Nov 2016, at 05:03, Rui Sousa <rui.so...@univ-nantes.fr> wrote: > Hi Marko, > > For the order of the atoms, check if "retain_order" is set to 1; if not, > use "set retain_order, 1" before importing your PDB file. For the rest > of your problem, what exactly is being changed from the imported PDB > file and the saved one? Apart from the addition of TER, which is a > fairly trivial problem to solve. > > Best regards, > > Rui > > Le 28/11/2016 10:41, Marko Sever a écrit : >> Hello everybody, >> >> I'm working with a protein-protein complex and am fixing some stuff. >> >> When I save the fixed complex as a pdb the PDB format is not the same as it >> was in the imported pdb files (there it was the same as the CHARMM default >> pdb format). >> >> In the saved pdb it changed the line position of atoms in the pdb file. >> Residues are ok but atoms in a given residue are mixed up. It also added >> addition TER's which I had to manually delete. >> >> So how would I specify the output PDB format to be the same as in the >> original imported pdbs (before manipulation), so same as CHARMM pdb format. >> >> Please help, >> >> Marko -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. -- ___ 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 coloring in ribbon
Hi Yuxing, We have released Incentive PyMOL 1.8.4.1, which fixes the ribbon coloring issue. Cheers, Thomas On 21 Nov 2016, at 15:57, Thomas Holder <thomas.hol...@schrodinger.com> wrote: > Hi Yuxing, > > Thanks for reporting this. Yes it's a bug, luckily with a simple fix. We will > provide a bugfix release soon. > > Cheers, > Thomas > > On 21 Nov 2016, at 15:12, Yuxing Liao <yuxing.l...@utsouthwestern.edu> wrote: > >> Hello All, >> >> I just updated Pymol from 1.8.0 to the latest 1.8.4. But I noticed when the >> structure is rendered in ribbon and you try to color part of it, the >> behavior changed at the boundaries. Instead of beginning and ending at the >> middle of the bonds like before, now the colors start and end at joints >> (actually colors one residue prior to the N-terminal of the selection). Is >> this a bug? >> >> Thanks. >> >> Yuxing >> >> UT Southwestern >> >> Medical Center >> >> The future of medicine, today. -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. -- ___ 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 coloring in ribbon
Hi Yuxing, Thanks for reporting this. Yes it's a bug, luckily with a simple fix. We will provide a bugfix release soon. Cheers, Thomas On 21 Nov 2016, at 15:12, Yuxing Liao <yuxing.l...@utsouthwestern.edu> wrote: > Hello All, > > I just updated Pymol from 1.8.0 to the latest 1.8.4. But I noticed when the > structure is rendered in ribbon and you try to color part of it, the behavior > changed at the boundaries. Instead of beginning and ending at the middle of > the bonds like before, now the colors start and end at joints (actually > colors one residue prior to the N-terminal of the selection). Is this a bug? > > Thanks. > > Yuxing > > UT Southwestern > > Medical Center > > The future of medicine, today. -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. -- ___ 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] Adding a new internal GUI to Pymol for Leap motion support
Hi Johan and Casper, You can create a menu above the mouse mode panel by writing a wizard. There is no API documentation for wizards, so you have to learn from existing wizards as examples. You can create an external menu or panel with Tkinter and/or Pmw. See for example eMovie as an example for a button panel, or BNI Tools for a multi-level menu. Cheers, Thomas On 10 Oct 2016, at 11:47, Schneiders J, Johan <j.schneid...@st.hanze.nl> wrote: > Dear Pymol community, > We are students at the Hanze University of Applied Sciences, the Netherlands. > Together with our teachers, Tsjerk Wassenaar and Jasper Bosman, we are > working on integrating > the leap motion sensor (hand gesture sensor) into Pymol for moving, and > altering the display of, molecules in Pymol. > > We want to create a menu within the GUI of Pymol that will be operated by > hand gestures (the amount of extended fingers) > and display what gestures you can make to manipulate the program. > > Is there a built in way to add/create a menu within Pymol? We have looked on > the Pymol wiki, tried googling > (keywords: 'pymol edit mouse viewing menu', 'Pymol external GUI', 'pymol > adding GUI', 'pymol viewing menu', and so on...), > read some of the source code and searched the Pymol user mailing list archive, > but haven't found a suitable solution. > > In short: > How do we go about adding an internal menu above the 'mouse mode' menu or > adding > an external window that will run alongside Pymol representing a menu, > and adding in our own attributes? > > Thanks in advance, > > Casper Peters and Johan Shcneiders. > > P.S. > Here are our e-mail addresses for contacting us: > Casper Peters: c.c.pet...@st.hanze.nl > Johan Schneiders: j.schneid...@st.hanze.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] Compile error svn 4162
Hi Quyen, This should be fixed in svn rev 4163. Cheers, Thomas On 18 Oct 2016, at 01:05, QT <rdirect...@gmail.com> wrote: > Dear all, > > I'm having a compile error that I've never had before on the current svn > revision 4162. Compile broke on file CifDataValueFormatter.cpp > > g++ -pthread -std=c++0x -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE > -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_FREETYPE -DNO_MMLIBS > -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 > -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/include > -Icontrib/uiuc/plugins/molfile_plugin/src > -I/home/quyen/lib64/python2.7/site-packages/numpy/core/include -I/usr/include > -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python2.7 -c > layer3/CifDataValueFormatter.cpp -o > build/temp.linux-x86_64-2.7/layer3/CifDataValueFormatter.o -Wno-write-strings > -Wno-unused-function -Wno-char-subscripts -ffast-math -funroll-loops -fcommon > -O3 > In file included from layer3/CifDataValueFormatter.cpp:8:0: > layer3/CifDataValueFormatter.h:20:13: error: ISO C++ forbids initialization > of member 'm_i' > layer3/CifDataValueFormatter.h:20:13: error: making 'm_i' static > layer3/CifDataValueFormatter.h:20:13: error: ISO C++ forbids in-class > initialization of non-const static member 'm_i' > > g++ version 4.5.1 > > Do you have any advise on how to get past this blocker? > > Best, > Quyen -- 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 in pthyon get_wizard() problems
cmd.get_wizard() takes no arguments and returns the current active wizard. If
there is no active wizard, it returns None.
PyMOL> print cmd.get_wizard()
None
PyMOL> cmd.wizard("mutagenesis")
PyMOL> print cmd.get_wizard()
There is no wizard architecture documentation other than code, I'm sorry.
Here is an example script that adds a new wizard:
https://github.com/speleo3/pymol-psico/blob/master/psico/wizards.py
Cheers,
Thomas
On 11 Oct 2016, at 15:09, Timothy Craig <utimcr...@gmail.com> wrote:
> Yes I totally agree, the question I have is "What needs to go there?". I
> tried using things like:
>
> pymol.cmd.get_wizard("mutagenesis").set_dep("dep")
>
> since in the previous line I called:
>
>
> pymol.cmd.wizard("mutagenesis")
>
> but then I get this error:
>
> ---
>
> Traceback (most recent call last):
>
> File "pngCSVmutate.py", line 141, in
>
> pymol.cmd.get_wizard("Mutagenesis").set_dep("dep")
>
> File
> "/Users/craigt2/anaconda/pymol/lib/python2.7/site-packages/pymol/wizarding.py",
> line 166, in get_wizard
>
> _self.unlock(r,_self)
>
>
> AttributeError: 'str' object has no attribute 'unlock'
>
> -
>
> Which makes it look like it's not looking for a string to tell it which
> wizard I'm wanting to use. Very confusing.
>
> Thanks,
>
> -Tim
>
>
> On Tue, Oct 11, 2016 at 12:03 PM, Sampson, Jared M.
> <jms2...@cumc.columbia.edu> wrote:
> Hi Tim - It seems to me that cmd.get_wizard() needs some argument to be
> passed to it, because right now that function is returning `None`. This
> explains the error, which states you're trying to call .set_dep() of a `None`
> object.
>
> Hope that helps.
>
> Cheers,
> Jared
>
>> On Oct 11, 2016, at 2:48 PM, Timothy Craig <utimcr...@gmail.com> wrote:
>>
>> Hello,
>> I'm trying to adapt this script in python to do a variety of different
>> mutations from a csv file using this previous message as a template.
>>
>> https://sourceforge.net/p/pymol/mailman/message/11671708/
>>
>> I'm a python novice so please excuse me if this is something simple. Here is
>> a line that I have in my script that is giving me an error, which is now
>> quite long so I don't want to post it all here now:
>> ---
>> pymol.cmd.get_wizard().set_dep("dep")
>>
>> error:
>>
>> Error: unable to get setting type.
>>
>> Traceback (most recent call last):
>>
>> File "pngCSVmutate.py", line 141, in
>>
>> pymol.cmd.get_wizard().set_dep("dep")
>>
>> AttributeError: 'NoneType' object has no attribute 'set_dep'
--
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] problem of optirun in Pymol
Hi Albert, Which Linux OS and version (e.g. Ubuntu 12.04 64bit) is this? Does PyMOL work without optirun? Does it work in headless mode (pymol -c)? Thanks, Thomas On 10 Oct 2016, at 14:29, Albert <mailmd2...@gmail.com> wrote: > Hello: > > I've got 2 graphic card in my laptop: > > Intel® HD Graphics 4600+ Nvidia M1100M > > I have installed Bumblee optirun in my Linux OS. Currently, command line > > optirun pymol > > works fine for Pymol-1.8.2.3. However, I found that it doesn't work for > Pymol-1.8.4. When I type > > optirun pymol > > Pymol doesn't start and I didn't get any error messages from terminal > either. > > I am just wondering how can we solve the problem? > > Thx a lot > > Albert -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. -- 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 of internal_gui
Hi Albert, "internal_gui" is now a blacklisted setting not be stored or restored from session files. You can launch PyMOL without internal gui like this from a Terminal: pymol -i session.pse When inserting in AxPyMOL, please check the option [x] PyMOL Show (Hide controls) For older versions of AxPyMOL (before 1.7 I think) the session needs to be saved as a "PyMOL Show file" (with .psw Extension) to be loaded without controls into AxPyMOL. Hope that helps. Cheers, Thomas On 06 Oct 2016, at 15:39, Albert <mailmd2...@gmail.com> wrote: > Hello: > > I used commad line: > > set internal_gui, off > > to hide the internal gui. Then I save my pymol session as a .pse file. > > However, when I reopen this .pse file, the internal_gui is still there. > When I insert .pse file to a PPT file, the internal_gui is also there. > > I am just wondering how to solve this problem? I am using PyMOL-1.8.2.3. > > I also tested in the latest 1.8.4, it has the same issue. > > Thank you very much. > > Albert -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. -- 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 1.8.4 released
Greetings, We are happy to announce the release of PyMOL v1.8.4. PyMOL sponsors can download ready-to-use installers from http://pymol.org/download . The open-source code has been pushed to sourceforge svn (revision 4162). New features include: File formats: - experimental MMTF load support (http://mmtf.rcsb.org) - map export in CCP4 format - SDF V3000 import/export support - PLY geometry import - MAE export (Incentive PyMOL only) - SDF export with properties (Incentive PyMOL only) New "unset_deep" command clears settings on all levels: https://pymolwiki.org/index.php/unset_deep Setting "stick_h_scale" refactored: This was a somehow hidden setting in previous versions. It scales the stick radius of bonds to hydrogen atoms. See: https://pymolwiki.org/index.php/stick_h_scale Symmetric +/- isomesh and isosurface (e.g. for difference density) can now be controlled from the menu. See: https://pymolwiki.org/index.php/mesh_negative_visible Legacy session export with "pse_export_version" now supports scenes before version 1.7.6. Incentive PyMOL only features: - Atom right click > edit label - Atom right click > inspect properties - display_scale_factor: Internal GUI scaling for 4K and Retina displays Find the complete release notes at: http://pymol.org/d/media:new184 We welcome any feedback and bug reports. Cheers, - The PyMOL Team at Schrödinger -- Thomas Holder PyMOL 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] regarding pymol plugin windows
Hi Priyan, Did you consider to open the Plugin Manager and uncheck "Load on startup" for plugins that you don't use often? Cheers, Thomas On 14 Sep 2016, at 13:30, ccp4 pymol <ccp4.py...@gmail.com> wrote: > Hello everyone > > The number of plugins has become long and hence can not see the one listed > at the end. Is there a way to reorganise the list of plugins in the plugin > window of pymol or have a scroll bar to browse downwards. > > Thank you > > Best Regards > Priyan -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. -- ___ 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] Error whle running pymol
Hi Vijaykumar, On CentOS, libXss.so.1 is provided by the LibXScrnSaver package (as root: yum install LibXScrnSaver). Your symlinking/copying solution might also work, if you put the file into "pymol folder"/ext/lib. Hope that helps. Cheers, Thomas On 29 Sep 2016, at 01:51, Vijaykumar Pillalamarri <vijaypkuma...@hotmail.com> wrote: > Dear Community, > > I am getting an error while running pymol on my computer. When I run pymol in > terminal, it is giving the following error. > > "error while loading shared libraries: libXss.so.1: cannot open shared object > file: No such file or directory" > > I am using CentOS 7 running work station. I have tried sym linking and tried > copying the libXss.so.1 file to the pymol folder. > Please help me in solving the problem. > > Thanks in advance. > Vijaykumar -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. -- ___ 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 hide dashed artificial cartoon?
Hi Albert, The dashed loop should only appear if you have changed the "cartoon_gap_cutoff" setting: http://pymolwiki.org/index.php/cartoon_gap_cutoff Cheers, Thomas On 09 Sep 2016, at 04:26, Albert <mailmd2...@gmail.com> wrote: > Hello: > > I noticed that if I show my structure as cartoon, there would be a > "dashed loop" cartoon filling in the missing part of my structure. I am > just wondering how can we disable PyMol show the missing part automatically? > > Thank you very much > > Albert -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. -- ___ 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 Command window not displaying
Hi Srikanth, Is your custom Python installation properly set up with the custom Tcl/Tk installation? Does the following work and open a Tk window? shell> /app/python/intel/2.7.12/bin/python # path guessed python> import Tkinter python> Tkinter.Tk() If not, then I think you need to set TCL_LIBRARY and/or TK_LIBRARY environment variables first. Hope that helps. Cheers, Thomas On 31 Aug 2016, at 00:46, Srikanth Gumma <sri4mail...@gmail.com> wrote: > Hi, > > I recently installed pymol from source using python-2.7.12 in my cluster. I > have to install python, tcl in a non standard location as this is a cluster. > > After successful installation of pymol, I'm facing an issue while opening > pymol. I'm not able to see pymol command window, and receiving the below > error on the console. > > PyMOL(TM) Molecular Graphics System, Version 1.8.2.0. > 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 prior to 2.0. Shaders and volumes unavailable. > OpenGL graphics engine: > GL_VENDOR: Intel > GL_RENDERER: Intel(R) HD Graphics 4600 > GL_VERSION: 1.4 (4.0.0 - Build 9.18.10.3272) > Traceback (most recent call last): > File "/app/python/intel/pymol/lib/python/pmg_tk/__init__.py", line 35, in > run > PMGApp(pymol_instance,skin).run(poll) > File "/app/python/intel/pymol/lib/python/pmg_tk/PMGApp.py", line 323, in > __init__ > self.root = Tk() # creates the root window for the application > File "/app/python/intel/2.7.12/lib/python2.7/lib-tk/Tkinter.py", line 1815, > in __init__ > self.tk = _tkinter.create(screenName, baseName, className, interactive, > wantobjects, useTk, sync, use) > TclError: invalid command name "tcl_findLibrary" > Detected 24 CPU cores. Enabled multithreaded rendering. > > > Appreciate any help to resolve the issue. > > -srikanth -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. -- ___ 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 alignment help
Hi Clarisa, Please rephrase your question and describe what your goal is. Please give some details about what you already tried, and at what step you got stuck or need help. "Download an aligment" is not common terminology, so it's likely that nobody on the list understood your question. You might be looking for this: http://pymolwiki.org/index.php/Align Cheers, Thomas On 24 Aug 2016, at 09:10, Clarisa Alvarez <clarisae.alva...@gmail.com> wrote: > Hello! > could someone help me to download a pymol alignment? and know with which > score it makes the alignment. > Thanks in advance. > > Clarisa. -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. -- ___ 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] Plugin menu options and measuring protein cavity volumes in PyMol
Hi Tom, To get the Plugin menu with MacPyMOL, see the "X11 Hybrid" section on the PyMOLWiki: http://pymolwiki.org/index.php/MAC_Install#X11_Hybrid Cheers, Thomas On 25 Aug 2016, at 13:52, Thomas Pochapsky <pocha...@brandeis.edu> wrote: > I am trying to load a plugin (CAVER) onto my MacPyMOL v 1.7, and > according to the Wiki, any version later than 1.5 should have a menu > option to manage plugins, but I do not see this anywhere. Was something > incorrectly set at installation? Can I correct this? > Alternatively (or additionally), if anybody has any info on how to > measure cavity volumes in a protein structure by PyMOL with standard > commands, I would appreciate it. > Thanks, > Tom Pochapsky -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. -- ___ 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] dump_binary and PyMOL 1.8 PSE files
I'll continue this off-list with Bob. Anyone who's interested in following along please drop me an email :) On 08 Aug 2016, at 17:38, Robert Hanson <hans...@stolaf.edu> wrote: > Almost have it. Having trouble fitting all that into 120 bytes, though. I'm > good through bytes 96-99, visrep. Somehow, though I count 124 bytes total, > not 120 (which is clearly the case in the PSE file). What is > sizeof(AtomInfo_1_8_1) ? I calculate: > > ... > 100-105 (six booleans) > 106-111 (six characters) > 112-116 (5 char for ElemName) > 117-118 (2 char for SSType) > 119-120 (2 char for Chain) > 121 stereo > 123 chemFlag > 123 protekted > > I need this to end at 119, not 123, to be consistent with the pickle data. -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. -- What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic patterns at an interface-level. Reveals which users, apps, and protocols are consuming the most bandwidth. Provides multi-vendor support for NetFlow, J-Flow, sFlow and other flows. Make informed decisions using capacity planning reports. http://sdm.link/zohodev2dev ___ 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] dump_binary and PyMOL 1.8 PSE files
On 08 Aug 2016, at 16:01, Robert Hanson <hans...@stolaf.edu> wrote:
> I see this in 1.8.2.1:
>
> #define _PyMOL_VERSION "1.8.2.1"
>
> and in AtomInfo.h:
>
> #if _PyMOL_VERSION_int < 1770
> #define AtomInfoVERSION 176
> #define BondInfoVERSION 176
> #elif _PyMOL_VERSION_int < 1810
> #define AtomInfoVERSION 177
> #define BondInfoVERSION 177
> #else
> #define AtomInfoVERSION 181
> #define BondInfoVERSION 181
> #endif
>
> So that must be where that 181 version indicator is coming from in a PSE file
> saved by 1.8.2.3, right?
Correct.
> But when you look at AtomInfoType in that same file, we see:
>
> typedef struct AtomInfoType {
> union {
> float * anisou; // only allocate with get_anisou
> int64_t dummyanisou;
> };
>
> lexidx_t segi;
> lexidx_t chain;
> lexidx_t resn;
> lexidx_t name;
> lexidx_t textType;
> lexidx_t custom;
> lexidx_t label;
> ...
>
> What am I missing?
You're looking at the wrong struct. When doing the binary dump, structs from
layer2/AtomInfoHistory.h are used. See
https://sourceforge.net/p/pymol/code/HEAD/tree/trunk/pymol/layer2/AtomInfoHistory.h#l187
Cheers,
Thomas
--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.
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Re: [PyMOL] dump_binary and PyMOL 1.8 PSE files
look here: https://sourceforge.net/p/pymol/code/HEAD/tree/trunk/pymol/layer2/AtomInfoHistory.h The AtomInfoType_1_8_1 version (used in 1.8.2) stores ANISOU as shorts (PDB precision). The AtomInfoType_1_7_7 version (used in 1.8.0) doesn't support ANISOU (will indeed write an unused NULL pointer), at the time it was work in progress for a specific use case which didn't require ANISOU. Cheers, Thomas On 08 Aug 2016, at 11:32, Robert Hanson <hans...@stolaf.edu> wrote: > I do like the compactness of that and the quicker loading, but I do see how > this could be a nightmare. I'm looking at a file that lists the dump version > as 1.8.1, but I don't even see how that would ever work, since in that > AtomInfo structure the ANISOU data is just a 64-bit pointer. That would end > up just a useless reference, wouldn't it? > > On Mon, Aug 8, 2016 at 10:05 AM, Thomas Holder > <thomas.hol...@schrodinger.com> wrote: > Hi Bob, > > I assume those are PSE files with setting "pse_binary_dump=on". This is not > the default. You can load such files into PyMOL, set pse_binary_dump=off and > save it as a regular serialized PSE. I definitely recommend the conversion > step over reimplementing the "pse_binary_dump" decoding. Right now there are > 3 binary atom layouts (for 1.7.6, 1.8.0 and 1.8.2). Grep the PyMOL code for > "AtomInfoTypeConverter" if you're interested in the details. > > The default (in 1.8.2) is to save PyMOL 1.7.6 compatible PSE files, and with > the "pse_export_version" setting you can also export for older PyMOL versions. > > Cheers, > Thomas > > On 08 Aug 2016, at 07:57, Robert Hanson <hans...@stolaf.edu> wrote: > > > Thomas, > > > > In reading PyMOL PSE files into Jmol I have recently run into the problem > > with some of these files (version 1.8.2.3). Jmol has no problem reading the > > standard Pickle format, but there seems to be an option in PyMOL to > > serialize binary data structures as BINSTRING or SHORT_BINSTRING format > > along with other standard strings. This sounds like a great idea; I have no > > doubt that this will lead to considerably smaller PSE files and also faster > > loading. However, I'm struggling with atom information deserialization. > > > > Q: Is this the default format now for saving PyMOL PSE files? > > > > Q: Is there a way to turn that off? > > > > Q: In order to do this properly, how many versions of the atom info data > > structure do I need to be able to process? > > > > Bob > > -- > Robert M. Hanson > Larson-Anderson Professor of Chemistry > St. Olaf College > Northfield, MN > http://www.stolaf.edu/people/hansonr > > > If nature does not answer first what we want, > it is better to take what answer we get. > > -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. -- What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic patterns at an interface-level. Reveals which users, apps, and protocols are consuming the most bandwidth. Provides multi-vendor support for NetFlow, J-Flow, sFlow and other flows. Make informed decisions using capacity planning reports. http://sdm.link/zohodev2dev ___ 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] dump_binary and PyMOL 1.8 PSE files
Hi Bob, I assume those are PSE files with setting "pse_binary_dump=on". This is not the default. You can load such files into PyMOL, set pse_binary_dump=off and save it as a regular serialized PSE. I definitely recommend the conversion step over reimplementing the "pse_binary_dump" decoding. Right now there are 3 binary atom layouts (for 1.7.6, 1.8.0 and 1.8.2). Grep the PyMOL code for "AtomInfoTypeConverter" if you're interested in the details. The default (in 1.8.2) is to save PyMOL 1.7.6 compatible PSE files, and with the "pse_export_version" setting you can also export for older PyMOL versions. Cheers, Thomas On 08 Aug 2016, at 07:57, Robert Hanson <hans...@stolaf.edu> wrote: > Thomas, > > In reading PyMOL PSE files into Jmol I have recently run into the problem > with some of these files (version 1.8.2.3). Jmol has no problem reading the > standard Pickle format, but there seems to be an option in PyMOL to serialize > binary data structures as BINSTRING or SHORT_BINSTRING format along with > other standard strings. This sounds like a great idea; I have no doubt that > this will lead to considerably smaller PSE files and also faster loading. > However, I'm struggling with atom information deserialization. > > Q: Is this the default format now for saving PyMOL PSE files? > > Q: Is there a way to turn that off? > > Q: In order to do this properly, how many versions of the atom info data > structure do I need to be able to process? > > Bob > > -- > Robert M. Hanson > Larson-Anderson Professor of Chemistry > St. Olaf College > Northfield, MN > http://www.stolaf.edu/people/hansonr > > > If nature does not answer first what we want, > it is better to take what answer we get. > > -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. -- ___ PyMOL-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 residue in cartoon mode
Hi Maria and Adam, I think it's not that complicated. You need "cartoon_ring_mode" for the residue selection. Example: fetch 1rna, async=0 as cartoon select firstres, chain A & resi 1 set cartoon_ring_finder, 2 set cartoon_ring_mode, 2, firstres color blue color red, firstres extend 1 Hope that helps. Cheers, Thomas On 02 Aug 2016, at 12:42, harold steinberg <h.adam.steinb...@gmail.com> wrote: > I believe that you can only apply the cartoon setting to an entire obj > (object). And so you are correct in trying to duplicate the nucleotide so you > can apply one setting to it, while allowing the other setting to display the > rest of them. But that doesn’t work either since the program will only allow > one display type at a time. There may be a complex way to override it but I > do not know it. > > The way I have gotten around this in the past is to set up the entire object > the way you want it, then render it once with each setting. > > Then open both of the resulting images in photoshop or similar program. Put > them both into one file as layers. > > Then delete most of one of the files (say the top one) so only the single > nucleotide is left in the cartoon setting that you want in that layer. The > rest of the image will appear from the bottom layer. > > Then you can flatten the image and save it. It’s fast and works great. > > >> On Aug 2, 2016, at 9:41 AM, COSTA Maria <maria.co...@i2bc.paris-saclay.fr> >> wrote: >> >> Dear pymol-users, >> >> I’m still learning how to use pymol to do basic things. >> At present, I’m working with a nucleic acid molecule that is colored by >> sequence domains (each domain is a different objet). All the domains are >> displayed in the cartoon mode, with backbone as dumbbell and >> cartoon_ring_finder,0 (no nucleobases or riboses displayed). Now, I would >> like to display only the first residue of one of the domains as >> cartoon_ring_finder,2 (ring only for nucleobases) and then color it >> entirely (dumbbell + ribose stick + base ring) with a different color from >> the rest of the domain sequence. The problem is that it does not work ! >> >> I tried to copy that nucleotide into a new objet to manipulate it >> independently but all the arguments I write in the command line do not apply >> to it, nothing is changing on the screen. The only thing that works is the >> menu on the right, use the objet line corresponding to this residue, display >> it entirely as sticks and then change the color of the sticks. But that’s >> not what I need! >> >> Do you have any ideas how to display the desired nucleotide? >> >> Many thanks in advance, >> >> Maria > > H. Adam Steinberg > 7904 Bowman Rd > Lodi, WI 53555 > 608/592-2366 -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. -- ___ 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 1.8.2.3 bugfix release
Greetings, PyMOL 1.8.2.3 fixes an annoying picking bug, where picking atoms with the mouse can select the wrong atoms. If you use Incentive PyMOL 1.8.x, we recommend to upgrade. Builds are available as usual from http://pymol.org/download Cheers, - The PyMOL Team at Schrödinger -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. -- What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic patterns at an interface-level. Reveals which users, apps, and protocols are consuming the most bandwidth. Provides multi-vendor support for NetFlow, J-Flow, sFlow and other flows. Make informed decisions using capacity planning reports.http://sdm.link/zohodev2dev ___ 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] Grammar for PyMOL selection algebra
Hi Lukas, All operators: https://sourceforge.net/p/pymol/code/4159/tree/trunk/pymol/layer3/Selector.cpp#l455 Operator types (e.g. number of arguments) and priority (order of operation): https://sourceforge.net/p/pymol/code/4159/tree/trunk/pymol/layer3/Selector.cpp#l365 Hope that helps. Cheers, Thomas On 19 Jul 2016, at 05:52, Lukáš Pravda <xpra...@ncbr.muni.cz> wrote: > Dear PyMOL users, > > I am trying to add support for pymol-like selection algebra into one of your > software tools. Therefore, I was wondering, if there is any formal > description of the language available in for example as context-free grammar. > I was trying to find something in the source code rather unsuccessfully. > > All the best > > Lukas Pravda > > CEITEC | Central European Institute of Technology > http://webchem.ncbr.muni.cz/ -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. -- What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic patterns at an interface-level. Reveals which users, apps, and protocols are consuming the most bandwidth. Provides multi-vendor support for NetFlow, J-Flow, sFlow and other flows. Make informed decisions using capacity planning reports.http://sdm.link/zohodev2dev ___ 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] Structural matching of Side-chain selection
Hi James, The "super" method requires CA atoms in the selection because it aligns based on the backbone trace. You should use "rms" or "rms_cur" to get a side chain RMSD. Cheers, Thomas On 12 Jul 2016, at 10:10, James Starlight <jmsstarli...@gmail.com> wrote: > Dear pymol users! > > I need to estimate how the side-chains dynamics are differs in MD > compared to X-ray structure. > > Assuming that I have 2 structures one from md and another from X-ray > and I select Sidechains from the both as obj1 and obj02 > select xray &! n. n+ca+c+o > select md &! n. n+ca+c+o > > now trying to align both objects with any method I obtain error like > > PyMOL>super obj01, obj02 > ExecutiveAlign: invalid selections for alignment. > > How I can fix it? > > James -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. -- What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic patterns at an interface-level. Reveals which users, apps, and protocols are consuming the most bandwidth. Provides multi-vendor support for NetFlow, J-Flow, sFlow and other flows. Make informed decisions using capacity planning reports.http://sdm.link/zohodev2dev ___ 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] Corrupted/too large MacPymol Files
Hi Angelica, Which version of MacPyMOL do you use? If the files are really corrupt, I might be able to help if you send them to me. Cheers, Thomas On 28 Jun 2016, at 18:54, Angelica Parente <angelicaparent...@gmail.com> wrote: > Hey pymol community, > > I’ve had significant issues with saving MacPymol session files, once I get > too many objects in a file it will crash and I won’t be able to open the file > again on any computer no matter how much RAM it has (I’ve only tried Windows > machines though since thats all I have access to besides my macbook air). I > work on a large 400kDa+ protein-DNA complex, and have tried removing atoms to > reduce file size. It still happens 70% of the time I’m using pymol and I > usually have to start from scratch. Any help in trying to rescue the pymol > files I have would be greatly appreciated. > > > Thanks, > > Angelica -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. -- Attend Shape: An AT Tech Expo July 15-16. Meet us at AT Park in San Francisco, CA to explore cutting-edge tech and listen to tech luminaries present their vision of the future. This family event has something for everyone, including kids. Get more information and register today. http://sdm.link/attshape ___ 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] Selective valency on bond
Hi Patrick and Andreas, "valence" is actually a bond-level setting, so you don't need to create individual objects. This should work: set_bond valence, 1, organic Cheers, Thomas On 14 Jun 2016, at 10:01, Andreas Warnecke <4ndreas.warne...@gmail.com> wrote: > The easiest way to deal with this is setting the valence or valence_mode > individually for the object. > > set valence, 0, object1 > set valence, 1, object2 > > Cheers, > > Andreas > > On Mon, Jun 13, 2016 at 11:56 AM, McIntyre, Patrick <pm...@leicester.ac.uk> > wrote: > Dear PyMol users, > > I have a crystal structure of my protein with an unnatural amino acid > present. This amino acid has a double bond within it, which I would like to > display as such. However I would like the surrounding protein side chains to > not show double bond character. Is this possible at all? > > So far, I can either keep valence mode set to '0' and see no double bonds > across the whole protein, or set to '1' and see all of the double bonds, > which I don't want. > > My question is, is it possible to selectively 'set valency' onto a single > bond, or is it a global command which is not capable of this fine-tuning? I > am using MacPyMol if this makes a difference at all? > > Thanks for your help, > Patrick -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. -- What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic patterns at an interface-level. Reveals which users, apps, and protocols are consuming the most bandwidth. Provides multi-vendor support for NetFlow, J-Flow, sFlow and other flows. Make informed decisions using capacity planning reports. https://ad.doubleclick.net/ddm/clk/305295220;132659582;e ___ 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] Details of the morph interpolation?
Hi Emilia, On 03 Jun 2016, at 18:39, Emilia C. Arturo (Emily) <ec...@drexel.edu> wrote: > Thank you for the reply, Thomas. I have a few items in reply: > > 1) I have not yet tried to change the refinement settings, but (for > educational purposes, if nothing else) I would like to know what it is that > this particular command that you typed, does: PyMOL> refine(5, "mout", > sculpt_field_mask=(0xFFF & ~0x60)). I haven't found any online documentation > for sculpt_field_mask. "sculpt_field_mask" is a bit mask, every bit enables a term. Look at the link to Sculpt.h that I sent in the previous email. 0x60 is the "or" combination of cSculptVDW and cSculptVDW14, and the tilde (~) inverts all bits, so effectively enabling all terms except VDW and VDW14. > 2) Thank you for showing me how to fix atoms by typing > > PyMOL> flag fix, (selection), set > > before I call the morph command. Now how does one UNfix the atoms in the > selection? Navigating Build>Scultping>Clear memory does not do it. Do I > really need to exit the session to accomplish the reset (which is what worked > for me)? "unfix" atoms: PyMOL> flag fix, (selection), clear > 3) I encountered a warning message about the match command when I type: > > PyMOL> morph mout, sele1, sele2, refinement=0 > > (where sele1 and sele2 both have 4 iron ions each, each labeled 'FE') > > The result is several lines that say 'Match-Warning: unknown residue type > 'FE' (using X).' No Fe ions are used/observed in the interpolation. If, > however, I type: > > PyMOL> morph mout, sele1, sele2, match=in, refinement=0 > > then the Fe ions do appear as part of the interpolation. Why does the 'align' > argument (which is default for 'match') ignore the Fe? This is indeed not obvious. The "align" command uses a BLOSUM62 substitution matrix to score the alignment. Since "FE" is not an amino acid, it gets assigned "X" as the single letter code. With the BLOSUM62 matrix, X matched to X has a score of -1 (penalty). In theory you could modify the file /Applications/MacPyMOL.app/Contents/pymol/data/pymol/matrices/BLOSUM62 and change the X/X score to 1, then PyMOL will align the FE atoms. > Thank you for your time, Thomas. > > Regards, > > Emily. Cheers, Thomas > On Tue, May 31, 2016 at 4:44 PM, Thomas Holder > <thomas.hol...@schrodinger.com> wrote: > Hi Emily, > > PyMOL's morphing performs two steps: (1) RigiMOL, and (2) refinement of > non-backbone atoms by sculpting. The second part can be skipped with > "refinement=0". > > Unfortunately, there is no RigiMOL publication or method documentation. > > The sculpting refinement tries to avoid clashes and maintain the local > sidechain geometry, based on start and end conformation as references. You > are right that sculpting doesn't consider the Ramachandran plot or a real > energy force field. But it does consider clashes (it has a VDW term). Check > "Build > Sculpting > ...", the bottom part of that submenu lists some of the > available terms. The corresponding numerical values can be found here: > https://sourceforge.net/p/pymol/code/HEAD/tree/trunk/pymol/layer2/Sculpt.h > > The "morph" command refinement uses all sculpting terms. You could customize > that, e.g. exclude VDW repulsion, like this: > > PyMOL> morph mout, sele1, sele2, refinement=0 > PyMOL> from epymol.rigimol import refine > PyMOL> refine(5, "mout", sculpt_field_mask=(0xFFF & ~0x60)) > > You can also "fix" atoms, e.g. all non-polymer atoms, like free ions, which > tend to bounce around as a result of the refinement: > > PyMOL> morph mout, sele1, sele2, refinement=0 > PyMOL> from epymol.rigimol import refine > PyMOL> flag fix, (not polymer), set > PyMOL> refine(5, "mout") > > Hope that helps. > > Cheers, > Thomas > > On 30 May 2016, at 12:43, Emilia C. Arturo (Emily) <ec...@drexel.edu> wrote: > > > Hello. > > > > I would like to know more about the type of interpolation that is done when > > morph is called, and what calculations are done at each refinement cycle. > > Is there a literature reference or previous forum discussion to which you > > can point me? > > > > From my sifting through the internet, I settled on the likelihood that > > refinement is done using the "molecular sculpting" algorithm that has been > > employed since at least this discussion took place in 2002: > > http://www.mail-archive.com/pymol-users@lists.sourceforge.net/msg00359.html > > In other words, refinement is not done on th
Re: [PyMOL] Details of the morph interpolation?
Hi Emily, PyMOL's morphing performs two steps: (1) RigiMOL, and (2) refinement of non-backbone atoms by sculpting. The second part can be skipped with "refinement=0". Unfortunately, there is no RigiMOL publication or method documentation. The sculpting refinement tries to avoid clashes and maintain the local sidechain geometry, based on start and end conformation as references. You are right that sculpting doesn't consider the Ramachandran plot or a real energy force field. But it does consider clashes (it has a VDW term). Check "Build > Sculpting > ...", the bottom part of that submenu lists some of the available terms. The corresponding numerical values can be found here: https://sourceforge.net/p/pymol/code/HEAD/tree/trunk/pymol/layer2/Sculpt.h The "morph" command refinement uses all sculpting terms. You could customize that, e.g. exclude VDW repulsion, like this: PyMOL> morph mout, sele1, sele2, refinement=0 PyMOL> from epymol.rigimol import refine PyMOL> refine(5, "mout", sculpt_field_mask=(0xFFF & ~0x60)) You can also "fix" atoms, e.g. all non-polymer atoms, like free ions, which tend to bounce around as a result of the refinement: PyMOL> morph mout, sele1, sele2, refinement=0 PyMOL> from epymol.rigimol import refine PyMOL> flag fix, (not polymer), set PyMOL> refine(5, "mout") Hope that helps. Cheers, Thomas On 30 May 2016, at 12:43, Emilia C. Arturo (Emily) <ec...@drexel.edu> wrote: > Hello. > > I would like to know more about the type of interpolation that is done when > morph is called, and what calculations are done at each refinement cycle. Is > there a literature reference or previous forum discussion to which you can > point me? > > From my sifting through the internet, I settled on the likelihood that > refinement is done using the "molecular sculpting" algorithm that has been > employed since at least this discussion took place in 2002: > http://www.mail-archive.com/pymol-users@lists.sourceforge.net/msg00359.html > In other words, refinement is not done on the basis of energy differences, > Ramachandran plot, interatomic clashes, or other problems with geometry that > could arise at each interpolation step. > > Is that correct? If so, is there a way to customize the refinement that's > done? > > I am using MacPyMOL version 1.7.6.2. > > Regards, > > Emily. -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. -- What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic patterns at an interface-level. Reveals which users, apps, and protocols are consuming the most bandwidth. Provides multi-vendor support for NetFlow, J-Flow, sFlow and other flows. Make informed decisions using capacity planning reports. https://ad.doubleclick.net/ddm/clk/305295220;132659582;e ___ 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] Numpy in incentive pymol
Hi Filip, Incentive PyMOL includes numpy and scipy. However, the 1.8.0.0 release on Windows was missing some dlls, that's why "import numpy" fails. The 1.8.0.7 update fixes that. Cheers, Thomas On 30 May 2016, at 06:44, Filip Leonarski <leonar...@unistra.fr> wrote: > Hi, > >I have a question - is it possible to have numpy and scipy available in > pymol 1.8 incentive version. I have some plugins that worked perfectly well > with pymol 1.7, however after upgrade to 1.8 they fail on "import numpy" step. > > Thanks, > Filip > > -- > Filip Leonarski, PhD > IBMC/CNRS > 15 rue René Descartes > 67084 Strasbourg Cedex -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. -- What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic patterns at an interface-level. Reveals which users, apps, and protocols are consuming the most bandwidth. Provides multi-vendor support for NetFlow, J-Flow, sFlow and other flows. Make informed decisions using capacity planning reports. https://ad.doubleclick.net/ddm/clk/305295220;132659582;e ___ 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] post-processing of pdb ensemble
or simply:
alter bound_combined, chain = chr(ord(chain) - 1)
Cheers,
Thomas
On 25 May 2016, at 11:06, Tsjerk Wassenaar <tsje...@gmail.com> wrote:
> Hi James,
>
> This should do:
>
> for i in range(65:78): cmd.alter("bound_combined and chain
> %s"%chr(i+1),'chain="%s"'%chr(i))
>
> Cheers,
>
> Tsjerk
>
>
> On Wed, May 25, 2016 at 5:00 PM, James Starlight <jmsstarli...@gmail.com>
> wrote:
> More precisely I would like to know how to script in pymol the
> following alteration fo the chains for the multi-chain pdb
>
>
> PyMOL>alter (bound_combined and chain B), chain="A"
> Alter: modified 5157 atoms.
> PyMOL>alter (bound_combined and chain C), chain="B"
> Alter: modified 2285 atoms.
> PyMOL>alter (bound_combined and chain D), chain="C"
> Alter: modified 2778 atoms.
> PyMOL>alter (bound_combined and chain E), chain="D"
> Alter: modified 1560 atoms.
> PyMOL>alter (bound_combined and chain F), chain="E"
> Alter: modified 1114 atoms.
> PyMOL>alter (bound_combined and chain G), chain="F"
> Alter: modified 950 atoms.
> PyMOL>alter (bound_combined and chain H), chain="G"
> Alter: modified 895 atoms.
> PyMOL>alter (bound_combined and chain I), chain="H"
> Alter: modified 843 atoms.
> PyMOL>alter (bound_combined and chain J), chain="I"
> Alter: modified 806 atoms.
> PyMOL>alter (bound_combined and chain K), chain="J"
> Alter: modified 574 atoms.
> PyMOL>alter (bound_combined and chain L), chain="K"
> Alter: modified 501 atoms.
> PyMOL>alter (bound_combined and chain M), chain="L"
> Alter: modified 511 atoms.
> PyMOL>alter (bound_combined and chain N), chain="M"
> Alter: modified 433 atoms.
>
>
> So each step we rename chain i to the i-1 name within given model :)
>
> Thanks!
>
> J.
>
> 2016-05-23 19:11 GMT+02:00 James Starlight <jmsstarli...@gmail.com>:
> > Dear Pymol users!
> >
> > After some post-processing of MD simulation I have extracted from the
> > traejctory several snapshots as individual pdbs which I need to
> > 1- to re-assign information regarding chain letters (which was lost
> > after some operations on pdbs) for all of those structures assuming
> > that within each of these pdbs residues are ordered correctly e.g from
> > (1-104 which
> > should be chain A) than from 1-100 (it should be chain B), than 1-70
> > (in should be chain C) etc.
> >
> > 2- superimpose and combine all of the pdbs within one model in nmr-like
> > format.
> >
> > Thanks for help!
> >
> > James
>
> --
> Tsjerk A. Wassenaar, Ph.D.
--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.
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Re: [PyMOL] pymol plugins Problem
Hi Rituraj, To get a meaningful stack trace, import a plugin's module, e.g.: PyMOL> import pmg_tk.startup.align_all Not all plugins will add an entry to the "Plugin" menu, some just register new commands. Hope that helps. Cheers, Thomas On 19 May 2016, at 02:28, Rituraj Purohit <riturajpurohi...@gmail.com> wrote: > Hello, > > I am using pymol (1.6.x) in ubuntu 14.04, I install few plugins (Autodock, > tconcoord and align_all) but none of them are displaying in plugin list. I am > getting following error in pymol command screen. Please help me to rectify > this error. > > . > > . > > convert given font files to the PIL raster font format. > > This version of pilfont supports X BDF and PCF fonts. > > Unable to initialize plugin 'pilfont' (pmg_tk.startup.pilfont). > > Unable to initialize plugin 'tconcoord' (pmg_tk.startup.tconcoord). > > Unable to initialize plugin 'align_all' (pmg_tk.startup.align_all). > > Regards > > RP -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. -- Mobile security can be enabling, not merely restricting. Employees who bring their own devices (BYOD) to work are irked by the imposition of MDM restrictions. Mobile Device Manager Plus allows you to control only the apps on BYO-devices by containerizing them, leaving personal data untouched! https://ad.doubleclick.net/ddm/clk/304595813;131938128;j ___ 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] High Resolution Ray Tracing
Hi Stephen, This is not an artificial Open Source PyMOL limitation. PyMOL's ray tracing code was written at a time when probably nobody had a computer with 64GB of RAM, or at least didn't attempt to ray trace images that size. The code is pretty hard to read and understand, and currently there is nobody who's familiar with it and could easily fix such a limitation. I assume the code makes an assumption which is only true up to a certain memory address range. Cheers, Thomas On 12 May 2016, at 10:20, Stephen Kerry <stephen.kerr...@outlook.com> wrote: > So the images are back from the printers and I can easily tell the difference > between 180 and 300 dpi. You have to look closely to tell the difference > between 300 and 600 dpi. I am unable to distinguish between 600 and 1200 dpi. > > My image size is still limited to 7500 x 6000, which at 600 dpi gives a 12.5 > x 10 inch image. Is this an artificial Open Source PyMOL software limitation > or a genuine bug/memory leak? The segmentation faults also seems to happen > even with 128 GB and 256 GB of RAM! > > On my system with 32 GB of RAM, I see PyMOL reserves more virtual RAM than > the amount of physical RAM, which might be why it crashes when trying to > write the PNG at the end of ray tracing? It does not appear to use this > virtual RAM or even compress any RAM, according to activity monitor on OSX > 10.10. Disabling memory compression and/or swap makes no difference. > > Is there anything else I can try to successfully output such a large image? > > ____ > From: Thomas Holder <thomas.hol...@schrodinger.com> > Sent: 10 May 2016 20:34:44 > To: harold steinberg > Cc: Stephen Kerry; pymol-users@lists.sourceforge.net > Subject: Re: [PyMOL] High Resolution Ray Tracing > > Hi Adam et al., > > This is a super interesting and helpful discussion! > > Just wanted to throw in the following shortcut for creating the 6" test > images: > > png image1.png, 6in, ray=1, dpi=180 > png image2.png, 6in, ray=1, dpi=300 > png image3.png, 6in, ray=1, dpi=600 > png image4.png, 6in, ray=1, dpi=1200 > > Cheers, > Thomas > > On 10 May 2016, at 14:27, harold steinberg <h.adam.steinb...@gmail.com> wrote: > >> The 9600 x 4800 is a very common poster printer spec. Most print shops use >> 180 dpi images on their poster printers (for best print speed) and customers >> cannot tell the difference between that and a higher resolution. >> >> As a test, render a small image (say 6” x 6”) in PyMOL at four different >> dpi, 180 dpi (ray 1080), 300 dpi (ray 1800), 600 dpi (ray 3600) and 1200 dpi >> (ray 7200). Then use Photoshop or GIMP to make them all 6” x 6”. >> >> Put them together side-by-side in a layout program and print them on one >> sheet to compare. I bet you will have an extremely difficult time telling >> them apart. >> >>> On May 10, 2016, at 12:40 PM, Stephen Kerry <stephen.kerr...@outlook.com> >>> wrote: >>> >>> Harold, I agree 2400 dpi might be wasted, but the professional printer >>> supports up to 9600 horizontal dpi x 4800 vertical dpi, so a source image >>> with 1200 dpi would be a nice step up from 600 dpi. The lpi is 1200 as the >>> four passes from each CMYK component apparently increases the vertical dpi >>> by four. >> >> H. Adam Steinberg >> 7904 Bowman Rd >> Lodi, WI 53555 >> 608/592-2366 -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. -- Mobile security can be enabling, not merely restricting. Employees who bring their own devices (BYOD) to work are irked by the imposition of MDM restrictions. Mobile Device Manager Plus allows you to control only the apps on BYO-devices by containerizing them, leaving personal data untouched! https://ad.doubleclick.net/ddm/clk/304595813;131938128;j ___ 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] High Resolution Ray Tracing
Hi Adam et al., This is a super interesting and helpful discussion! Just wanted to throw in the following shortcut for creating the 6" test images: png image1.png, 6in, ray=1, dpi=180 png image2.png, 6in, ray=1, dpi=300 png image3.png, 6in, ray=1, dpi=600 png image4.png, 6in, ray=1, dpi=1200 Cheers, Thomas On 10 May 2016, at 14:27, harold steinberg <h.adam.steinb...@gmail.com> wrote: > The 9600 x 4800 is a very common poster printer spec. Most print shops use > 180 dpi images on their poster printers (for best print speed) and customers > cannot tell the difference between that and a higher resolution. > > As a test, render a small image (say 6” x 6”) in PyMOL at four different dpi, > 180 dpi (ray 1080), 300 dpi (ray 1800), 600 dpi (ray 3600) and 1200 dpi (ray > 7200). Then use Photoshop or GIMP to make them all 6” x 6”. > > Put them together side-by-side in a layout program and print them on one > sheet to compare. I bet you will have an extremely difficult time telling > them apart. > >> On May 10, 2016, at 12:40 PM, Stephen Kerry <stephen.kerr...@outlook.com> >> wrote: >> >> Harold, I agree 2400 dpi might be wasted, but the professional printer >> supports up to 9600 horizontal dpi x 4800 vertical dpi, so a source image >> with 1200 dpi would be a nice step up from 600 dpi. The lpi is 1200 as the >> four passes from each CMYK component apparently increases the vertical dpi >> by four. > > H. Adam Steinberg > 7904 Bowman Rd > Lodi, WI 53555 > 608/592-2366 -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. -- Mobile security can be enabling, not merely restricting. Employees who bring their own devices (BYOD) to work are irked by the imposition of MDM restrictions. Mobile Device Manager Plus allows you to control only the apps on BYO-devices by containerizing them, leaving personal data untouched! https://ad.doubleclick.net/ddm/clk/304595813;131938128;j ___ 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 attach the command area to the viewing area in pymol for windows
Hi Ashika, This is not yet possible. We are working on a single window version for Windows and Linux, which will become available later this year. But with the current version, the two windows can't be attached. Cheers, Thomas On 04 May 2016, at 10:38, ashika torikora <ashika.torik...@gmail.com> wrote: > Hi, > > I am trying to attach the command area to the molecule viewing area in pymol > instead of having them in seperate windows. > > I have noticed that in the mac version, this is the case by default. > > How can I do this for my windows version. > > Please see images below for reference. > > In windows 7 > http://s32.postimg.org/mrhxqcox1/pymol_PNG_in_windows7.png > > In mac > http://s32.postimg.org/cbczjm1wl/pymol_macosx.png > > > Thanks for your help. -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. -- Find and fix application performance issues faster with Applications Manager Applications Manager provides deep performance insights into multiple tiers of your business applications. It resolves application problems quickly and reduces your MTTR. Get your free trial! https://ad.doubleclick.net/ddm/clk/302982198;130105516;z ___ 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] query
Hi Ankita, set depth_cue, 0 http://pymolwiki.org/index.php/Depth_cue Cheers, Thomas On 27 Apr 2016, at 11:06, H. Adam Steinberg <h.adam.steinb...@gmail.com> wrote: > Scrolling the mouse will not move the molecule, it will reduce the fog that > pymol puts in the image, making it less gray. > > Sent from my iPhone > > On Apr 27, 2016, at 6:45 AM, ankita mehta <mehtaroad...@gmail.com> wrote: > >> No, I can not do this becos i have to show the complex that is protein in a >> fix orientation. >> Suggest some alternative.. >> Thanks! >> >> On Wed, Apr 27, 2016 at 4:01 PM, Dheeraj Prakaash <dhee...@gmail.com> wrote: >> Try pointing your (mouse) cursor in the Pymol Viewer and scrolling up and >> down! >> Usually (if you have not changed any settings), SCROLLING UP should solve >> your problem. >> >> Cheers. >> >> On Wed, Apr 27, 2016 at 6:15 PM, ankita mehta <mehtaroad...@gmail.com> wrote: >> Hii, >> I want to save the image in pymol >> I am using white background but it gives me dull colouring of the protein >> which is at the background than the protein part at foreground. >> I want a unified sceme for all protein . >> pls suggest. >> thanks! -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. -- Find and fix application performance issues faster with Applications Manager Applications Manager provides deep performance insights into multiple tiers of your business applications. It resolves application problems quickly and reduces your MTTR. Get your free trial! https://ad.doubleclick.net/ddm/clk/302982198;130105516;z ___ 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 mouse button problem since version 1.8 with PyMOL for Linux
Hi Christoph, This sounds like a serious picking bug, possibly related to your graphics driver. Please send further details directly to me (I'll send an update to the list once we've figured it out). Thanks, Thomas On 27 Apr 2016, at 05:24, Christoph Parthier <cparth...@googlemail.com> wrote: > Hi, > > I have a strange issue with (incentive) PyMOL version >= 1.8 for Linux > running under Scientic Linux 6.x (64-bit, current OPENGL driver for > NVIDIA Quadro graphics cards). > > Independent of the mouse mode in PyMOL (2-Button/3-Button) selecting > (left mouse button), ID-ing (right mouse button) or centering (middle > mouse button) residues, from time to time the wrong residues are > selected/IDd/centered which are not even in close proximity to the > intended residue (or just hidden by too narrow slab settings). > Furthermore this doesn't happen consistently, about 2-3 out of 10 mouse > clicks (still annoying...), possibly with minimal mouse movement > inbetween but still pointing at the same residue. Interestingly, the > same 'wrong' residues keep popping up, when getting selected erroneously > (but I can't get figure out any 'systematic' behind it yet). The > behaviour appears with any molecule loaded (also the '1tii' built-into > the cartoon demo of PyMOL). > > Interesting also, I do not observe this behaviour with PyMOL 1.7.4.3. > and also not when running PyMOL 1.8.x via remote login > (X-windows-powered SSH), which might indicate a local graphics/mouse > driver problem? > > Any comments are welcome! > > Thanks, > Christoph -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. -- Find and fix application performance issues faster with Applications Manager Applications Manager provides deep performance insights into multiple tiers of your business applications. It resolves application problems quickly and reduces your MTTR. Get your free trial! https://ad.doubleclick.net/ddm/clk/302982198;130105516;z ___ 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] morph issues
r PhD >>>>> Department >>>>> of Biochemistry >>>>> Zürich University >>>>> Winterthurerstrasse 190 >>>>> CH-8057 Zürich >>>>> Switzerland >>>>> >>>>> e-Mail: honeg...@bioc.uzh.ch >>>>> >>>>> websites >>>>> http://www.bioc.uzh.ch/plueckthun >>>>> http://www.bioc.uzh.ch/plueckthun/antibody >>>>> http://www.bioc.uzh.ch/plueckthun/nanowelt >>>>> >>>>> >>>>> >>>>> >>>>> >>>>>> >>>>>> >>>>>> Message: 6 >>>>>> Date: Mon, 25 Apr 2016 20:54:01 -0500 >>>>>> From: harold steinberg <h.adam.steinb...@gmail.com> >>>>>> Subject: [PyMOL] morph issues >>>>>> To: pymol-users <pymol-users@lists.sourceforge.net> >>>>>> Message-ID: <0e82e310-1d03-40cd-838d-50616a246...@gmail.com> >>>>>> Content-Type: text/plain; charset="utf-8" >>>>>> >>>>>> Hi all, >>>>>> >>>>>> I need to generate a morph from 3J5R to 3J5Q. When I load both files and >>>>>> generate the morph, it?s all messed up. When I generate a morph of other >>>>>> structures it works just fine. >>>>>> >>>>>> In the structures that do not morph correctly a sample selection is: >>>>>> /3j5r/A/B/ILE`573/CD1 >>>>>> /3j5q/C/E/ILE`573/CD1 >>>>>> >>>>>> Notice that these files have an extra letter (?A? and ?C? before the >>>>>> chain identifier). >>>>>> >>>>>> In files that the morph does work this letter is missing (it?s a blank >>>>>> space): >>>>>> /3lut//D/GLY`338/CA >>>>>> >>>>>> Is that what is messing up the morph? >>>> >>>> H. Adam Steinberg >>>> 7904 Bowman Rd >>>> Lodi, WI 53555 >>>> 608/592-2366 >>>> -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. -- Find and fix application performance issues faster with Applications Manager Applications Manager provides deep performance insights into multiple tiers of your business applications. It resolves application problems quickly and reduces your MTTR. Get your free trial! https://ad.doubleclick.net/ddm/clk/302982198;130105516;z ___ 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] Autosave session Pymol
Hi Matic,
As a proof of concept, the following snippet would save a session file every 30
seconds. You can put this in your pymolrc file.
python
import os
import threading
import time
from pymol import cmd
def _auto_save():
filename = os.path.expanduser(time.strftime('~/pymol-auto-save-%s.pse'))
while True:
time.sleep(30) # interval in seconds
cmd.save(filename, quiet=0)
_auto_save = threading.Thread(target=_auto_save)
_auto_save.setDaemon(1)
_auto_save.start()
python end
Saving session files is not very fast, so with larger molecules, the
interruption will be very noticeable. There is a new experimental setting in
PyMOL 1.8.2 which can improve this: pse_binary_dump
Cheers,
Thomas
On 22 Apr 2016, at 02:31, Matic Kisovec <matic.kiso...@ki.si> wrote:
> Dear PyMOL users,
>
> I would just like to bump this question again.
> I would be glad to see some replies either from users or developers.
>
> Best regards,
> Matic
>
>
> On 31. 03. 2016 08:02, Matic Kisovec wrote:
>> Dear Pymol users,
>>
>> a quick google search returned empty regarding the ability of Pymol to
>> autosave the session at a specified time interval.
>> The feature is available in different programs from text to vector
>> editors etc.
>> I would find it useful to have the ability to automatically save a
>> couple of recent checkpoints while I am using Pymol.
>>
>> My question is if this would be interesting/useful for anybody and a
>> question to the developers if this can be implemented?
>>
>> Best regards,
>> Matic
--
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PyMOL Principal Developer
Schrödinger, Inc.
--
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Re: [PyMOL] Dynamic reloading of plugin
Hi Martin, how about: set_key F1, run script.py; function_from_script() Reduces step 3) and 4) to hitting "F1" on the keyboard. Cheers, Thomas On 24 Apr 2016, at 06:36, Martin Hediger <ma@bluewin.ch> wrote: > Hi all > > When working on a PyMOL extension script, my workflow is currently something > like this: > > 1) Start PyMOL > 2) Work on script > 3) PyMOL> run script.py > 4) PyMOL> function_from_script() > 5) See if function works, go back to 2) > > Is it possible to have PyMOL automatically re-run the script everytime i save > it? > > Thanks and best regards > Martin > > -- > Martin R. Hediger, PhD > Mittlere Strasse 65 > 4056 Basel -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. -- Find and fix application performance issues faster with Applications Manager Applications Manager provides deep performance insights into multiple tiers of your business applications. It resolves application problems quickly and reduces your MTTR. Get your free trial! https://ad.doubleclick.net/ddm/clk/302982198;130105516;z ___ 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] ccmutate
Hi Martin,
short answer: Your PyMOL version is too old, this script works with PyMOL 1.8.
PyMOL 1.8 can download fragments from PDBeChem with type=cc, e.g.:
PyMOL> fetch ALA, type=cc
I assume you found the ccmutate script on my user page. It's an experimental
script to provide a mutation command with all the fragments which are available
from PDBeChem.
Cheers,
Thomas
On 23 Apr 2016, at 18:15, Martin Hediger <ma@bluewin.ch> wrote:
> I found the ccmutate script on the pymol wiki
>
> I tried it but I receive a weird error:
>
> PyMOL>ccmutate "ALA", resi 112
> Traceback (most recent call last):
> File
> "/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/pymol/parser.py",
> line 254, in parse
> self.result=apply(layer.kw[0],layer.args,layer.kw_args)
> File "021_scripts/ccmutate.py", line 47, in ccmutate
> cmd.fetch(code, tmp_frag, type='cc', zoom=0)
> File
> "/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/pymol/importing.py",
> line 1417, in fetch
> r = _multifetch(*args)
> File
> "/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/pymol/importing.py",
> line 1352, in _multifetch
> discrete, multiplex, zoom, type, path, file, quiet, _self)
> File
> "/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/pymol/importing.py",
> line 1263, in _fetch
> raise ValueError('type')
> ValueError: type
>
>
> What could be going on? The PyMOL mutagenesis wizard in any case works when I
> do the mutation by hand.
>
> Thanks for hints
> Martin
>
> --
> Martin R. Hediger, PhD
> Mittlere Strasse 65
> 4056 Basel
--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.
--
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[PyMOL] PyMOL 1.8.2 released
Greetings, We are happy to announce the release of PyMOL v1.8.2! Official PyMOL sponsors can download ready-to-use installers from http://pymol.org/download . The open-source code has been pushed to sourceforge svn (revision 4156). Highlights in this release: - new "cartoon_gap_cutoff" setting lets you display dashed loop segments with incomplete models (like missing loops) - new "auto_show_classified" setting automatically shows cartoon, with ligand sticks and inorganic spheres, when loading a structure (Setting > Auto Show... > ... by Classification) - new “Distances between rings” measurement mode in Measurements Wizard To take advantage of the new settings by default, you can put this into your pymolrc: set auto_show_classified, 1 set cartoon_gap_cutoff, 20 Find the complete release notes at: http://pymol.org/d/media:new182 We welcome any feedback and bug reports. Cheers, - The PyMOL Team at Schrödinger -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. -- Find and fix application performance issues faster with Applications Manager Applications Manager provides deep performance insights into multiple tiers of your business applications. It resolves application problems quickly and reduces your MTTR. Get your free trial! https://ad.doubleclick.net/ddm/clk/302982198;130105516;z ___ 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] selecting faces and vertices in CGOs
Hi Albert, This is currently not possible and adding this would be a very major project. Cheers, Thomas On 30 Mar 2016, at 10:40, Albert Solernou <a.soler...@leeds.ac.uk> wrote: > Dear All, > I was wondering if there is a way to select faces, vertices and/or edges > from a CGO either using the mouse or the command line. How difficult > would be to add this, and how would you do that? > > It would be very useful for us if we could get that working. > > Thanks, > Albert > > -- > - > Dr Albert Solernou > EPSRC Research Fellow, > Department of Physics and Astronomy, > University of Leeds > Tel: +44 (0)1133 431451 -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. -- Find and fix application performance issues faster with Applications Manager Applications Manager provides deep performance insights into multiple tiers of your business applications. It resolves application problems quickly and reduces your MTTR. Get your free trial! http://pubads.g.doubleclick.net/ gampad/clk?id=1444514301=/ca-pub-7940484522588532 ___ 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] Cryo Maps - gaussian isosurface
Hi Adam, As I understand, you want to do some low-pass smoothing on the map, correct? I'm not aware that this functionality would be available in PyMOL. However, PyMOL can downsample the map, which averages 8 voxels into 1 and thus also provides some level of smoothing. Try this: fetch emd_6413, map, async=0 map_halve map map_halve map isomesh mesh, map Hope that helps. Cheers, Thomas On 05 Apr 2016, at 15:24, harold steinberg <h.adam.steinb...@gmail.com> wrote: > Hi All, > > I’m trying to make an isomesh of EMD-6413 (a cryo map) in Pymol. It’s a large > map with a lot of extra, not very clean. In Chimera I can just gaussian the > map with a new map to the level I want with a slider and it looks good, but > I’d much rather work in PyMOL! > > PyMOL can gaussian maps, I do it all the time, but on maps that I create in > PyMOL. How do I get an isomesh on EMD-6413 that I can gaussian? > > Normally I would use: > alter all, q=1 > set gaussian_resolution, 5 > map_new mapA, gaussian, 1, pdb code, 6 > isosurface surfA, mapA > > But in in this case I don’t want to use a pdb, just the cryo map. > > I can isosurface the cryo map with the following: > isosurface mapname, EMD-6413, 4 (any number between 1-6) > > but that doesn’t allow me to apply the gaussian to the map… > > How do I create an isosurface with a gaussian? > > Thanks for any help, > > H. Adam Steinberg > 7904 Bowman Rd > Lodi, WI 53555 > 608/592-2366 -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. -- Find and fix application performance issues faster with Applications Manager Applications Manager provides deep performance insights into multiple tiers of your business applications. It resolves application problems quickly and reduces your MTTR. Get your free trial! http://pubads.g.doubleclick.net/ gampad/clk?id=1444514301=/ca-pub-7940484522588532 ___ 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 add multiline labels
Hi Amin,
Multi-line labels are supported in Incentive PyMOL 1.7.0 and later. Simply use
a linefeed character ("\n") to break a line.
Examples:
label all, "Hello\nWorld"
label guide, resn + "\n" + resi
See also the related label_multiline_* settings:
http://pymol.org/d/setting:label
Cheers,
Thomas
On 07 Apr 2016, at 01:12, a...@imtech.res.in wrote:
> Hi everyone. I am having what seems like a trivial problem. I am not able to
> figure out how to add mutiline lables i.e. how do I specify the point at
> which I would like the text to go to the next line? Any suggestions would be
> highly appreciated.
>
> Regards,
>
> Amin.
--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.
--
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Re: [PyMOL] Text Font size
Hi Abhinav, 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 The default preset rendering is available in our latest beta version (currently 1.8.1.1). Download it from http://pymol.org/download/1811 To enable it, put this into your pymolrc: set auto_show_classified To launch with a different window size, put a "viewport" call in your pymolrc: viewport 1200, 900 Or launch PyMOL with arguments: pymol -W 1200 -H 900 Hope that helps. Cheers, Thomas On 07 Apr 2016, at 14:00, Kumar, Abhinav <aku...@intrexon.com> wrote: > Thanks Thomas. > This is great. > Is there something similar for the font in the graphics window (object names > etc) as well? > > Also, can I configure my pymolrc file to always start with a given window > size (viewport) and always draw the pretty rendering (cartoon, ligands, ..) > > > Thanks, > Abhinav > > Abhinav Kumar, PhD > Senior Scientist, Bioinformatics > Intrexon, Inc. > 329 Oyster Point Blvd., South San Francisco, CA 94080 > (650) 597-4072 | aku...@intrexon.com > > From: Thomas Holder [thomas.hol...@schrodinger.com] > Sent: Thursday, April 07, 2016 9:59 AM > To: Kumar, Abhinav > Cc: pymol-users@lists.sourceforge.net > Subject: Re: [PyMOL] Text Font size > > Hi Abhinav, > > The attached plugin will set a larger font when PyMOL starts. Install it with > the plugin manager. Requires PyMOL 1.8. > > Cheers, > Thomas > > > On 07 Apr 2016, at 11:41, Kumar, Abhinav <aku...@intrexon.com> wrote: > > > Thanks Matic. > > > > This is a temporary solution; the fonts return to their original size after > > you quit the current session. > > > > I am looking for a permanent solution. > > > > Thanks, > > Abhinav > > > > Abhinav Kumar, PhD > > Senior Scientist, Bioinformatics > > Intrexon, Inc. > > 329 Oyster Point Blvd., South San Francisco, CA 94080 > > (650) 597-4072 | aku...@intrexon.com > > > > From: Matic Kisovec [matic.kiso...@ki.si] > > Sent: Wednesday, April 06, 2016 10:26 PM > > To: pymol-users@lists.sourceforge.net > > Subject: Re: [PyMOL] Text Font size > > > > Dear Abhinav, > > > > in Pymol version 1.8.0 under Settings>GUI Font Size you can set the GUI > > Font Size. > > Unfortunately this does not affect the fonts in the graphics window as far > > as I know. > > > > Kind regards, > > Matic > > > > > > On 06. 04. 2016 18:01, Kumar, Abhinav wrote: > >> Hi, > >> > >> Is there some way to change the font size of menu items and dropdown > >> options? > >> Also for object names and options in the main graphics window (on the > >> right side)? > >> > >> > >> Thanks, > >> Abhinav > >> > >> Abhinav Kumar, PhD > >> Senior Scientist, Bioinformatics > >> Intrexon, Inc. > >> 329 Oyster Point Blvd., South San Francisco, CA 94080 > >> (650) 597-4072 | aku...@intrexon.com > > -- > Thomas Holder > PyMOL Principal Developer > Schrödinger, Inc. > > > > CONFIDENTIAL TRANSMISSION - This message, including any attachments, is > confidential and may be privileged. If you are not the intended recipient, > please delete it without further distribution and reply to the sender that > you have received the message in error. -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. -- ___ 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 Abhinav, The attached plugin will set a larger font when PyMOL starts. Install it with the plugin manager. Requires PyMOL 1.8. Cheers, Thomas ''' PyMOL plugin. Sets bigger fonts for the external GUI ''' def __init_plugin__(self): self.skin.inc_fontsize(5) On 07 Apr 2016, at 11:41, Kumar, Abhinav <aku...@intrexon.com> wrote: > Thanks Matic. > > This is a temporary solution; the fonts return to their original size after > you quit the current session. > > I am looking for a permanent solution. > > Thanks, > Abhinav > > Abhinav Kumar, PhD > Senior Scientist, Bioinformatics > Intrexon, Inc. > 329 Oyster Point Blvd., South San Francisco, CA 94080 > (650) 597-4072 | aku...@intrexon.com > > From: Matic Kisovec [matic.kiso...@ki.si] > Sent: Wednesday, April 06, 2016 10:26 PM > To: pymol-users@lists.sourceforge.net > Subject: Re: [PyMOL] Text Font size > > Dear Abhinav, > > in Pymol version 1.8.0 under Settings>GUI Font Size you can set the GUI Font > Size. > Unfortunately this does not affect the fonts in the graphics window as far as > I know. > > Kind regards, > Matic > > > On 06. 04. 2016 18:01, Kumar, Abhinav wrote: >> Hi, >> >> Is there some way to change the font size of menu items and dropdown options? >> Also for object names and options in the main graphics window (on the right >> side)? >> >> >> Thanks, >> Abhinav >> >> Abhinav Kumar, PhD >> Senior Scientist, Bioinformatics >> Intrexon, Inc. >> 329 Oyster Point Blvd., South San Francisco, CA 94080 >> (650) 597-4072 | aku...@intrexon.com -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. -- ___ 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 ribbon
Hi Mark, Thanks for the bug report. Confirming that this is a picking bug with ribbon_as_cylinders=1, affecting 1.8.0.0 and later. Picking works correct for me with ribbon_as_cylinders=0 (default). Thomas On 05 Apr 2016, at 10:47, Mark A Saper <sa...@umich.edu> wrote: > Hi All & Thomas > > There appears to be a problem with ribbon representations. I am testing > MacPyMOL on v 1.8.1.1 but the same behavior is seen with 1.8.0.4. Create a > ribbon of a test protein, for example, > > show ribbon, test and (resi 10:20 or resi 25:35) > > Double click on the endpoints (to see the residue number) > > The one that should be 25, displays residue 20. > > Labels do show the correct residue numbers. > > Mark -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. -- ___ 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 isomesh without map
Hi Filip, This is a bug, we'll fix that (probably by next week, looks like an easy fix). Cheers, Thomas On 01 Apr 2016, at 16:16, Filip Leonarski <f.leonar...@ibmc-cnrs.unistra.fr> wrote: > Hi, > >I'm struggling with making compact PSE files with Pymol state for ribosome > structures with electron density maps. In general these maps are huge in > 200-500 MB range. In previous versions of PyMol (1.7.x) a following trick > worked: > a) make isomesh > b) delete map > c) save pse > PSE was of a decent size. Currently PyMol crashes when trying to do that. > > Is it possible to fix this one? > > Best, > Filip > > > -- > Filip Leonarski, PhD > IBMC/CNRS > 15 rue René Descartes > 67084 Strasbourg Cedex -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. -- Transform Data into Opportunity. Accelerate data analysis in your applications with Intel Data Analytics Acceleration Library. Click to learn more. http://pubads.g.doubleclick.net/gampad/clk?id=278785471=/4140 ___ 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] The Wiki appears outdated or in error
Hi Jim, There is a beta version of Incentive PyMOL available for download from http://pymol.org/download/1811/ (version 1.8.1.1 BETA). Cheers, Thomas On 29 Mar 2016, at 23:30, James Kress <jimkress...@kressworks.org> wrote: > Does that mean it is in the pay version now? If yes, how do I get it, > through the normal download link? > > Jim > > James Kress Ph.D., President > The KressWorks® Foundation > An IRS Approved 501 (c)(3) Charitable, Nonprofit Organization > “ENGINEERING THE CURE” © > (248) 605-8770 > > Learn More and Donate At: > Website: http://www.kressworks.org > Facebook: https://www.facebook.com/KressWorks.Foundation/ > Twitter: @KressWorksFnd > > Confidentiality Notice | This e-mail message, including any attachments, is > for the sole use of the intended recipient(s) and may contain confidential > or proprietary information. Any unauthorized review, use, disclosure or > distribution is prohibited. If you are not the intended recipient, > immediately contact the sender by reply e-mail and destroy all copies of the > original message. > > -Original Message- > From: Thomas Holder [mailto:thomas.hol...@schrodinger.com] > Sent: Sunday, March 27, 2016 4:10 PM > To: pymol-users <pymol-users@lists.sourceforge.net> > Subject: Re: [PyMOL] The Wiki appears outdated or in error > > Hi Jared, > > Thanks a lot for the patch. Applied to SVN rev 4154. > > Cheers, > Thomas > > On 25 Mar 2016, at 20:03, Sampson, Jared M. <jms2...@cumc.columbia.edu> > wrote: > >> Hi Jim - >> >> Here's a patch for Open Source PyMOL (rev4153) that adds the > "collada_background_box" setting (default=0). If you're using Open Source > PyMOL and are up to applying it and rebuilding, feel free to use it. > Otherwise, I already sent it to Thomas, so hopefully it will be incorporated > into SVN and Incentive PyMOL soon. >> >> Cheers, >> Jared >> >> -- >> Jared Sampson >> Columbia University >> >>> On Mar 24, 2016, at 2:26 PM, Sampson, Jared M. > <jms2...@cumc.columbia.edu> wrote: >>> >>> Hi Jim - >>> >>>> When I >>>> >>>> set geometry_export_mode, 1 >>>> >>>> in PyMOL, then save myfile.dae, then import into MeshLab, MeshLab hangs. >>> >>> I can confirm that this happens for me, too. I guess maybe Meshlab > requires the camera? >>> >>> As a workaround, you can go back to the previous version with > collada_geometry_mode=1 and simply delete the box. You can do this within > Meshlab by using the "Select Connected Components in a region" tool to > select a corner the box, then clicking the "Delete the current set of > selected faces and all the vertices surrounded by that faces" button (see > attached screenshot). Then, if you zoom in (the box is 100x larger than the > largest dimension of the scene), your scene will be there. >>> >>> I'm working on a patch right now to exclude the bounding background box > from default COLLADA output and make it optional via a new > `collada_background_box` setting. >>> >>> Sorry for the confusion, hope this clears it up. >>> >>> Cheers, >>> Jared >>> >>> -- >>> Jared Sampson >>> Columbia University >>> >> >> > - -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. -- Transform Data into Opportunity. Accelerate data analysis in your applications with Intel Data Analytics Acceleration Library. Click to learn more. http://pubads.g.doubleclick.net/gampad/clk?id=278785471=/4140 ___ 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] The Wiki appears outdated or in error
Hi Jared, Thanks a lot for the patch. Applied to SVN rev 4154. Cheers, Thomas On 25 Mar 2016, at 20:03, Sampson, Jared M. <jms2...@cumc.columbia.edu> wrote: > Hi Jim - > > Here's a patch for Open Source PyMOL (rev4153) that adds the > "collada_background_box" setting (default=0). If you're using Open Source > PyMOL and are up to applying it and rebuilding, feel free to use it. > Otherwise, I already sent it to Thomas, so hopefully it will be incorporated > into SVN and Incentive PyMOL soon. > > Cheers, > Jared > > -- > Jared Sampson > Columbia University > >> On Mar 24, 2016, at 2:26 PM, Sampson, Jared M. <jms2...@cumc.columbia.edu> >> wrote: >> >> Hi Jim - >> >>> When I >>> >>> set geometry_export_mode, 1 >>> >>> in PyMOL, then save myfile.dae, then import into MeshLab, MeshLab hangs. >> >> I can confirm that this happens for me, too. I guess maybe Meshlab requires >> the camera? >> >> As a workaround, you can go back to the previous version with >> collada_geometry_mode=1 and simply delete the box. You can do this within >> Meshlab by using the "Select Connected Components in a region" tool to >> select a corner the box, then clicking the "Delete the current set of >> selected faces and all the vertices surrounded by that faces" button (see >> attached screenshot). Then, if you zoom in (the box is 100x larger than the >> largest dimension of the scene), your scene will be there. >> >> I'm working on a patch right now to exclude the bounding background box from >> default COLLADA output and make it optional via a new >> `collada_background_box` setting. >> >> Sorry for the confusion, hope this clears it up. >> >> Cheers, >> Jared >> >> -- >> Jared Sampson >> Columbia University >> > > - -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. -- Transform Data into Opportunity. Accelerate data analysis in your applications with Intel Data Analytics Acceleration Library. Click to learn more. http://pubads.g.doubleclick.net/gampad/clk?id=278785351=/4140 ___ 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] Morph DNA?
Hi Adam, PyMOL should be able to morph DNA. Feel free to send me your input files if you think something is wrong. Cheers, Thomas On 14 Mar 2016, at 13:27, H. Adam Steinberg <h.adam.steinb...@gmail.com> wrote: > Hi All, > > I’m doing a number of morphs for a project and have one example that includes > DNA. > > I generated a second piece of straight DNA from scratch, and would like to > show it morph into the protein bound DNA. > > PyMol 1.8 doesn’t seem to want to morph DNA. It goes through the exercise but > nothing is generated. Does it only work with proteins? Both nucleotides > strings are ATOM (no HETEROATOM) and both are in the AGCT format, no DA DG DC > DT format. > > Does anyone know a program or web site that will morph DNA? > > Thanks, > > Adam -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. -- Transform Data into Opportunity. Accelerate data analysis in your applications with Intel Data Analytics Acceleration Library. Click to learn more. http://pubads.g.doubleclick.net/gampad/clk?id=278785231=/4140 ___ 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 feedback push
Hi Spencer,
Yes this is a bug in the feedback stack. As a workaround, you can enable "cmd"
and "parser" feedback manually before popping:
_ feedback enable, cmd parser, warnings errors results
_ feedback pop
Hope that helps.
Cheers,
Thomas
On 11 Mar 2016, at 04:48, Spencer Bliven <spencer.bli...@gmail.com> wrote:
> Here's a minimal .pymolrc to demonstrate the issue:
>
> #prints response, as expected
> get cartoon_power
>
> _ feedback push
> _ feedback disable,all,everything
>
> # Nothing prints here, as expected
> get cartoon_power_b
>
> _ feedback pop
>
> # Still nothing prints!
> get cartoon_use_shader
>
>
> P.S. The feedback docs don't mention the push/pop commands. I likely got them
> from MacOSX-specific_.pymolrc_file
>
>
> On Fri, Mar 11, 2016 at 10:41 AM, Spencer Bliven <spencer.bli...@gmail.com>
> wrote:
> Since time immemorial my .pymolrc file has been wrapped by the construct
> _ feedback push
> _ feedback disable,all,everything
>
> ...
>
> _ feedback pop
>
> However, I've noticed that my `get` command doesn't print anything unless I
> specifically re-enable all feedback after starting pymol (or use the unwieldy
> `print cmd.get("var")`). Removing the feedback manipulation from my pymolrc
> restores the expected output from get. Is this a bug with the feedback stack?
>
> -Spencer
--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.
--
Transform Data into Opportunity.
Accelerate data analysis in your applications with
Intel Data Analytics Acceleration Library.
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Re: [PyMOL] How to store matrix settings for individual scenes?
Hi Carsten, What's your use case? Since movie frames can store object matrices, would creating an actual movie solve your problem? Example of an animated superposition: # get sample data fetch 1hbb, async=0 split_chains delete 1hbb # set up movie frames mset 1x100 # make "align" modify the motion matrix (but without # instant storing to current frame) set matrix_mode, 1 set movie_auto_store, 0 # store object matrices to frame 1 mview store, 1, object=* # superpose structures and store matrices to frame 100 extra_fit mview store, 100, object=* # optional: add scenes color blue scene blue, store color red scene red, store mview store, 1, scene=blue mview store, 100, scene=red If this doesn't fit your use case, I'd go with Jared's solution of an enhanced scene function. Cheers, Thomas On 07 Mar 2016, at 12:35, Schubert, Carsten [JRDUS] <cschu...@its.jnj.com> wrote: > Yeah, but not my preferred choice. Tried to do this the elegant way, but > bumping up against Pymol’s limits unless Thomas has a workaround. > > From: Sampson, Jared M. [mailto:jms2...@cumc.columbia.edu] > Sent: Monday, March 07, 2016 12:15 PM > To: Schubert, Carsten [JRDUS] > Cc: pymol-users@lists.sourceforge.net > Subject: Re: [PyMOL] How to store matrix settings for individual scenes? > > Hi Carsten - > > I'd probably create new objects and use those for superimposition, rather > than moving the originals. That would leave your scenes intact. > > Cheers, > Jared > > -- > Jared Sampson > Columbia University > > On Mar 7, 2016, at 12:10 PM, Schubert, Carsten [JRDUS] <cschu...@its.jnj.com> > wrote: > > Hi, > > I am trying to create a session file of a multimeric protein, in which each > monomer is displayed first using the original matrix settings broken out > into individual scenes. After that all monomers are overlayed on top of each > other and the superposition matrices are copied and applied to the ligands, > etc. So far so good, however once the matrices are applied this also affects > the matrices for the scenes created previous to the overlay and matrix_copy. > Any way I can store the matrices in each scene instead of having them applied > globally once? > > Cheers, > > Carsten -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. -- Transform Data into Opportunity. Accelerate data analysis in your applications with Intel Data Analytics Acceleration Library. Click to learn more. http://makebettercode.com/inteldaal-eval ___ 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] Immediately crashing
Hi Joachim, Are the graphics drivers (both Intel and AMD) up-to-date? Such crashes are almost always graphics driver related. Note that only one of the two graphics cards will be active for PyMOL, depending on your setup (performance vs. power-saving). Cheers, Thomas On 07 Mar 2016, at 11:05, Reichelt, Joachim <joachim.reich...@helmholtz-hzi.de> wrote: > Dear all, > > I just got a used DELL LATITUDE 3540. It got an Intel and an AMD graphics at > 1605x1050. > > I installed PyMOL-v1.8.0.6-Win32.msi. > But on start there is only flash up the cmd windows and that it was. The MS > error dialog pops up. > > So I tried PyMOL-v1.7.0.5-Win32.msi, but all the same. > > > Mit freundlichen Grüßen > > Joachim Reichelt > > > > Helmholtz-Zentrum für Infektionsforschung GmbH | Inhoffenstraße 7 | 38124 > Braunschweig | www.helmholtz-hzi.de > Das HZI ist seit 2007 zertifiziertes Mitglied im "audit berufundfamilie" > 50 Jahre Spitzenforschung - 50 Jahre HZI: www.helmholtz-hzi.de/50 > > Vorsitzende des Aufsichtsrates: MinDir’in Bärbel Brumme-Bothe, > Bundesministerium für Bildung und Forschung > Stellvertreter: MinDirig Rüdiger Eichel, Niedersächsisches Ministerium für > Wissenschaft und Kultur > Geschäftsführung: Prof. Dr. Dirk Heinz; Franziska Broer > Gesellschaft mit beschränkter Haftung (GmbH) > Sitz der Gesellschaft: Braunschweig > Handelsregister: Amtsgericht Braunschweig, HRB 477 -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. -- Transform Data into Opportunity. Accelerate data analysis in your applications with Intel Data Analytics Acceleration Library. Click to learn more. http://makebettercode.com/inteldaal-eval ___ 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] auto_show_cartoon or similar
Hi all, The "auto_show_classified" feature is now available from the open-source SVN code repository. I've also uploaded pre-compiled builds to http://pymol.org/download (alpha release, not intended for production use). The setting has 3 modes: 0 (off, default), 1 (like Adam suggested), 2 (including the default lines), and 3 (simplified version with ribbon instead of cartoon). See also: http://pymolwiki.org/index.php/auto_show_classified Any feedback will be appreciated. Cheers, Thomas On 08 Feb 2016, at 15:16, H. Adam Steinberg <h.adam.steinb...@gmail.com> wrote: > Every application has to satisfy it's users. > > Thinking out loud… > If you show all lines the new users find it confusing and overwhelming but > they do get to see every atom. Experienced users generally know what atoms > are in a PDB or know how to find them if they are looking for them and > therefore do not need to see all lines. > > The current proposal is to show more structure (cartoon, sticks, spheres) but > leave on all lines behind this structure. My first thought is what would that > look like. So I open a current structure and show both options (attached). If > I leave all lines on it’s still a bit of a mess. I think it looks better with > all lines off. > > > > PM.pdf> > > > >> On Feb 8, 2016, at 1:29 PM, Thomas Holder <thomas.hol...@schrodinger.com> >> wrote: >> >> Adam, Abhinav, Dave, >> thanks for the very useful feedback. >> >> To keep it simple, I propose a "auto_show_classified" setting (will depend >> on "auto_classify_atoms", on by default) which will be equivalent to: >> >> show cartoon, polymer >> show sticks, organic >> show spheres, inorganic >> >> Question: should this automatically hide lines for classified atoms? >> >> By the way, you may also like the "nice" preset (with "x" alias) from psico: >> https://github.com/speleo3/pymol-psico/blob/master/psico/viewing.py >> >> Cheers, >> Thomas >> >> On 08 Feb 2016, at 13:50, Bourgaize David <dbourga...@whittier.edu> wrote: >> >>> My thoughts exactly! >>> >>> Dave Bourgaize >>> >>> On 2/8/16, 9:54 AM, "H. Adam Steinberg" <h.adam.steinb...@gmail.com> wrote: >>> >>>> Every year I teach students PyMOL, and the look on their faces when they >>>> first open a pdb in PyMOL and get a cluster of green sticksŠ yikes! >>>> >>>> YES!!! to the default being secondary structure, ligands as sticks, and >>>> metal ions as spheres! Add - nucleic acids as cartoon. >>>> >>>>> On Feb 8, 2016, at 10:57 AM, Kumar, Abhinav <aku...@intrexon.com> wrote: >>>>> >>>>> Showing metal ions (and FES clusters etc) as spheres would also be >>>>> useful. >>>>> >>>>> Thanks, >>>>> Abhinav >>>>> >>>>> Abhinav Kumar, PhD >>>>> Senior Scientist, Bioinformatics >>>>> Intrexon, Inc. >>>>> 329 Oyster Point Blvd., South San Francisco, CA 94080 >>>>> (650) 597-4072 | aku...@intrexon.com >>>>> >>>>> >>>>> >>>>> From: Thomas Holder [thomas.hol...@schrodinger.com] >>>>> Sent: Monday, February 08, 2016 8:51 AM >>>>> To: Ivan Vulovic; Schubert, Carsten [JRDUS] >>>>> Cc: pymol-users@lists.sourceforge.net >>>>> Subject: Re: [PyMOL] auto_show_cartoon or similar >>>>> >>>>> Hi Ivan and Carsten, >>>>> >>>>> I can take "auto_show_cartoon" as a feature request. It's trivial to >>>>> implement. >>>>> >>>>> What also would be nice: automatically showing sticks for ligands. e.g. >>>>> corresponding to the "not polymer" or the "organic" selection. Thoughts? >>>>> >>>>> Cheers, >>>>> Thomas >>>>> >>>>> On 08 Feb 2016, at 09:07, Schubert, Carsten [JRDUS] >>>>> <cschu...@its.jnj.com> wrote: >>>>> >>>>>> Hi Ivan, >>>>>> >>>>>> you could either try to overload the ³load² function in Pymol (not >>>>>> sure this is supported) or write your own custom load function under a >>>>>> different name, which loads the protein, assigns the name of the >>>>>>
Re: [PyMOL] Selections don't work on structures loaded using 'fetch' command
Hi Timofey, See http://pymolwiki.org/index.php/ignore_case Note: The wiki page mentions 1.8.0.0 (official release), but the SVN repo had the change since 1.7.7.1 (https://sourceforge.net/p/pymol/code/4123/ ). Cheers, Thomas On 29 Feb 2016, at 06:23, Timofey Tyugashev <tyugas...@niboch.nsc.ru> wrote: > Sorry, it's actually part false alarm and part a completely different > problem. > > For false alarm:Structure retrieved by 'fetch' simply lacked residue > numbered 10, why my own file was already repaired and had it fine. > > For different problem: For some reason it turns out that 'select' is > case-sensitive and it's not actually mentioned anywhere on the wiki, so > selectors like 'resn' and 'name' simply silently failed. > Is there a way to disable it? > > 29.02.2016 17:10, Timofey Tyugashev пишет: >> If I load my own pdb file and issue a simple select command like >> 'select resi 10' it works fine, producing something like 'selection >> "sele" defined with 6 atoms'. >> However if I load the same structure using fetch command selections >> stop working, 'select resi 10' results in 'selection "sele" defined >> with 0 atoms'. >> System is Linux. PyMOL is 1.7.7.2 version from svn. -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. -- Site24x7 APM Insight: Get Deep Visibility into Application Performance APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month Monitor end-to-end web transactions and take corrective actions now Troubleshoot faster and improve end-user experience. Signup Now! http://pubads.g.doubleclick.net/gampad/clk?id=272487151=/4140 ___ 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 get an atom coordinates information
Hi Carsten & Albert,
There actually is a function for getting the coordinates of a single atom.
Example:
PyMOL>print cmd.get_atom_coords('first (elem O)')
Cheers,
Thomas
On 25 Feb 2016, at 09:54, Schubert, Carsten [JRDUS] <cschu...@its.jnj.com>
wrote:
> Albert,
>
> there is no command line tool for that purpose per se, however you can use
> the iterate command for that purpose.
> http://pymolwiki.org/index.php/Iterate#Example:_Get_coordinates
>
>
> There are other ways to do this but this will get you going more quickly.
>
> -Original Message-
> From: Albert [mailto:mailmd2...@gmail.com]
> Sent: Thursday, February 25, 2016 12:48 PM
> To: pymol-users@lists.sourceforge.net
> Subject: [PyMOL] how to get an atom coordinates information
>
> Hello:
>
> I would like to know the XYZ information of a specific atom. I am just
> wondering how can we do this? Is there any command line?
>
> thank you very much
>
> Albert
--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.
--
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Re: [PyMOL] PyMOL split_states error on [PDB: 1hho]
This is fixed in SVN rev 4150. Cheers, Thomas On 22 Feb 2016, at 05:53, Thomas Holder <thomas.hol...@schrodinger.com> wrote: > Hi all, > > The bug seems to be that the "pdb_insure_orthogonal" setting is only applied > to the first model. Turning the setting off shows the correct assembly: > > set pdb_insure_orthogonal, off > load 1hho.pdb1 > > If "pdb_insure_orthogonal" is on, PyMOL will apply the SCALE transformation, > which might be necessary to correctly line up with the corresponding electron > density map. > > Ioannis, you can file bug reports on https://sf.net/p/pymol/bugs/ but > reporting a bug here on the pymol-users list is equally effective :) > > Cheers, > Thomas > > On 22 Feb 2016, at 04:44, Ioannis Michalopoulos <imicha...@bioacademy.gr> > wrote: > >> Dear all, >> >> Thank you for your informative answers. >> >> For various reasons, I am not yet willing to move to cif. >> >> Indeed remark 285 of the 1hho header: >> >> http://www.rcsb.org/pdb/files/1HHO.pdb?headerOnly=YES >> >> reads: >> >> REMARK 285 >> >> REMARK 285 THE ENTRY COORDINATES >> REMARK 285 ARE NOT PRESENTED IN THE STANDARD CRYSTAL FRAME. >> >> Rasmol 2.7.5.2 displays both states of the biological structure, but, >> unfortunately, it does not recognise the secondary structure elements of the >> second state. >> >> The fact that Rasmol and the three html embedded viewers in the PDB page: >> >> http://www.rcsb.org/pdb/explore/jmol.do?structureId=1HHO=1 >> >> display the second state, means that Pymol is the one that has the issue, as >> Ezra mentioned. >> >> As PyMOL's failure to recognise non-standard crystal frames is a major >> issue, >> I think I have to report it to PyMOL developers. How do I do a bug report on >> PyMOL 1.8.0.0? I just joined your emailing list and I am not sure how to do >> that. >> >> Thank you in advance. >> >> Best Regards, >> >> Ioannis >> >> On Monday 22 of February 2016 05:53:08 Ezra Peisach wrote: >>> 1hho does have a non-standard crystal frame. (see remark 285) >>> >>> If you load the assembly PDB file in rasmol - it displays properly. Pymol >>> is having the issue. >>> >>> However, if you fetch the cif file in pymol, and ask it to display the >>> assembly - it does the right thing. >>> >>> set assembly, 1 >>> fetch 1hho >>> >>> >>> Ezra >>> >>> On Mon, Feb 22, 2016 at 5:04 AM, Spencer Bliven <spencer.bli...@gmail.com> >>> >>> wrote: >>>> This looks like a bug in the PDB's file, and you should definitely let >>>> them know about it. It's a particularly weird case since the second model >>>> doesn't correspond to any of the valid crystallographic operators. >>>> Probably >>>> it is a problem with the very non-standard crystal frame specified by the >>>> SCALE matrix in the PDB file. These are always problematic, to the point >>>> that some tools (e.g. EPPIC <http://eppic-web.org>) will ignore them >>>> completely. >>>> >>>> While waiting for the PDB to fix the file, you can generate the biological >>>> unit from the symmetry operators using: >>>> >>>> fetch 1hho, async=0 >>>> symexp sym, 1hho, 1hho, 2 >>>> >>>> -Spencer >>>> >>>> On Mon, Feb 22, 2016 at 10:19 AM, Jame R.Ketudat-Cairns <cai...@sut.ac.th> >>>> >>>> wrote: >>>>> Dear Ioannis, >>>>> >>>>> I was wondering about that, too. Given the prominence of hemoglobin >>>>> >>>>> structure and oxygen binding in Biochemistry education, the 1 HHO >>>>> structure >>>>> seems to be a bad biological structure to calculate incorrectly. I guess >>>>> an email to the PDB might be in order (if it is intentional, they could >>>>> at >>>>> least explain it in that case). >>>>> >>>>> Best Regards, >>>>> >>>>> Jim >>>>> >>>>> >>>>> From: Ioannis Michalopoulos <imicha...@bioacademy.gr> >>>>> Sent: Monday, February 22, 2016 4:05 PM &g
Re: [PyMOL] Problem aligning two structures: ExecutiveAlign-Error: atomic alignment failed (mismatched identifiers?)
Hi Max,
If you send me the loop.pdb file then I'll have a look at the issue.
Cheers,
Thomas
On 23 Feb 2016, at 09:03, Ebert Maximilian <m.eb...@umontreal.ca> wrote:
> Hi there,
>
> maybe the subject is a little bit misleading but i couldn’t find any better
> description. Basically I am trying to align two PDB structures, one is from
> the PDB directly and the other one is a file containing conformation
> information about a specific loop of the protein from the PDB. So I try to
> align this loop to the residues 211-220 of the PDB structures. My commands go
> like this:
>
> fetch 1g68
> load loop.pdb
> align 1g68 and chain A and n. CA+N+O+C and i. 211-220, loop
>
> instead of aligning on the 40 atoms as expected I align solely on 8, which
> are the N atoms. If I change the n. selection to O for instance I get
> ExecutiveAlign-Error: atomic alignment failed (mismatched identifiers?). This
> is with the macports compiled version of pymol 1.7.7.2 and the PyMOLX11Hybrid
> 1.7.4. However, doing exactly the same in the Macpymol version 1.7.4 it works
> as expected. To even make it more weird if I use Python:
>
> import __main__
> __main__.pymol_argv = [ 'pymol', ‘-qc'] # Quiet and no GUI -qc
> import pymol
> pymol.cmd.fetch('1g68’)
> pymol.cmd.load('loop.pdb’)
> pymol.cmd.align('loop', ‘1g68 and chain A and n. N+CA+O+C and i. 211-220,
> quiet=0)
>
> it works as well. Does anybody understands what is happening here?
>
> Thank you very much,
>
> Max
>
> PS: If you need the PDB files let me know. I don’t know if this list acceptes
> files
--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.
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Re: [PyMOL] PyMOL split_states error on [PDB: 1hho]
t;> Ioannis >>>> >>>> On Monday 22 of February 2016 02:09:05 you wrote: >>>>> Dear Ioannis, >>>>> >>>>> The 1HHO biological unit seems to be calculated incorrectly (just >>>> >>>> spun >>>> >>>>> around the y-axis 180 degrees). I found that the symexp command works >>>> >>>> for >>>> >>>>> this: symexp sym, 1hho, (1hho), 1 >>>>> Best Regards, >>>>> >>>>>Jim >>>>> >>>>> >>>>> From: Ioannis Michalopoulos <imicha...@bioacademy.gr> >>>>> Sent: Monday, February 22, 2016 3:39 AM >>>>> To: pymol-users@lists.sourceforge.net >>>>> Subject: [PyMOL] PyMOL split_states error on [PDB: 1hho] >>>>> >>>>> Dear PyMOL users, >>>>> >>>>> I run PyMOL 1.8.0.0 for Windows. >>>>> >>>>> I loaded the biological assembly of 1HHO: >>>>> >>>>> http://www.rcsb.org/pdb/files/1HHO.pdb1.gz >>>>> >>>>> When I tried: >>>>> >>>>> split_states 1hho >>>> >>>>> PyMOL failed to produce the proper tetramer that is seen at: >>>> http://www.rcsb.org/pdb/explore/jmol.do?structureId=1HHO=3= >>>> 1 >>>> >>>>> Instead PyMOL shows a weird tetramer. Is it a bug? This approach works >>>>> fine on other cases eg 1SVC. Is there any other way to do it? >>>>> >>>>> Thank you in advance. >>>>> >>>>> Best Regards, >>>>> >>>>> Ioannis >>>>> -- >>>>> Dr Ioannis Michalopoulos >>>>> Staff Research Scientist - Associate Professor Level >>>>> Centre of Systems Biology >>>>> >>>>> Tel: +30 210 6597 127 >>>>> Fax: +30 210 6597 545 >>>>> Email: imicha...@bioacademy.gr >>>>> _ >>>>> Biomedical Research Foundation, Academy of Athens >>>>> Soranou tou Efessiou 4, 115 27 Athens, Greece -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. -- Site24x7 APM Insight: Get Deep Visibility into Application Performance APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month Monitor end-to-end web transactions and take corrective actions now Troubleshoot faster and improve end-user experience. Signup Now! http://pubads.g.doubleclick.net/gampad/clk?id=272487151=/4140 ___ 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 tell from within a script if a plugin is loaded?
Hi Jared,
The plugin system isn't really tuned for API extension. As Tsjerk pointed out,
cmd.extend only registers a command, not a cmd. function. Also, scripts
which are installed as plugins get loaded asynchronously from the external GUI.
I suggest you do the following:
1) Inside your plugin (Python module), do:
from pymol import cmd
def my_func(): ...
cmd.my_func = my_func
cmd.extend('my_func', my_func)
2) The plugin's __init_plugin__ (or __init__) function should only be
responsible for adding Plugin menu entries, not for anything else.
3) Inside your test file, do:
from pymol import cmd
import pmg_tk.startup.my_plugin
# (now cmd.my_func should be available immediately)
Hope that helps.
Cheers,
Thomas
On 17 Feb 2016, at 11:32, Sampson, Jared M. <jms2...@cumc.columbia.edu> wrote:
> Hi Tsjerk -
>
> Thanks for the suggestion. I tried this with:
>
> import time
> from pymol import cmd
> while not hasattr(cmd, 'my_func'):
> time.sleep(0.5)
>
> Unfortunately that also causes everything to hang. I think I might need to
> do this in a separate thread. I'll have to look into how to do that.
>
> Cheers,
> Jared
>
> --
> Jared Sampson
> Columbia University
>
>> On Feb 16, 2016, at 2:47 PM, Tsjerk Wassenaar <tsje...@gmail.com> wrote:
>>
>> Hi Jared,
>>
>> The extend function must set an attribute "my_func" on cmd. You can test for
>> that with hasattr:
>>
>> while not hasattr(cmd, "my_func"):
>> # wait some more
>>
>> Hope it helps,
>>
>> Tsjerk
>>
>> On Feb 16, 2016 20:07, "Sampson, Jared M." <jms2...@cumc.columbia.edu> wrote:
>> To my previous message I should add that it works fine if I do:
>>
>> ```
>> import pmg_tk.startup.my_plugin as mp
>> mp.my_func()
>> ```
>>
>> but I'd like to use the `cmd.my_func()` version, so that `my_func` will work
>> in a .pml script.
>>
>> From `help(cmd)` I found `cmd.kw_list`, but this apparently doesn't include
>> "extended" functions, even after the function is loaded.
>>
>> ```
>> PyMOL>print 'ray' in cmd.kw_list
>> True
>> PyMOL>print 'my_func' in cmd.kw_list
>> False
>> ```
>>
>> Looking forward to any suggestions. Thanks!
>>
>> Cheers,
>> Jared
>>
>> --
>> Jared Sampson
>> Columbia University
>>
>>> On Feb 16, 2016, at 1:50 PM, Sampson, Jared M. <jms2...@cumc.columbia.edu>
>>> wrote:
>>>
>>> Hi PyMOLers -
>>>
>>> Maybe some more experienced users/developers can help me out here. I'm
>>> trying to write some automated test scripts for the plugin I'm writing, but
>>> the test functions end up running before the plugin is loaded. Is there a
>>> way to tell if a plugin has been loaded from within a .pml or .py script?
>>> For example, if the plugin makes commands available via
>>> `cmd.extend('my_func', my_func)`, how can I run `cmd.myfunc()` from a
>>> script and not have it execute before the plugin finishes loading?
>>>
>>> I've tried something like this:
>>>
>>> ```
>>> import time
>>> from pymol import cmd
>>> loaded = 0
>>> while not loaded:
>>> try:
>>> cmd.my_func() # if it's loaded no exception will be raised
>>> loaded = 1
>>> except:
>>> time.sleep(0.5)
>>> ```
>>>
>>> But this just hangs, as apparently `time.sleep()` halts the execution of
>>> all threads, so the plugin won't ever be loaded.
>>>
>>> Thanks,
>>> Jared
>>>
>>> --
>>> Jared Sampson
>>> Columbia University
--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.
--
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Re: [PyMOL] visualizing a transparent surface within a transparent surface
Hi Nasir, Incentive PyMOL 1.7.6 introduced a cross-object order independent transparency mode (transparency_mode=3). The method is a heuristic and not as pretty as ray tracing, but useful since it guarantees that nothing gets accidentally hidden due to rendering method limitations. Not sure if it satisfies your needs for rendering a pretty movie, but worth a try. PyMOL> set transparency_mode, 3 Cheers, Thomas On 16 Feb 2016, at 20:50, Nasir Bashiruddin <nasir...@gmail.com> wrote: > Thanks for the tip Adam! > > However, it would be nice to make movies in the way I requested. > > Nasir > > On Wed, Feb 17, 2016 at 12:41 AM, H. Adam Steinberg > <h.adam.steinb...@gmail.com> wrote: > I get around this by rendering both items separately and then combining the > two images in photoshop. > > Is there a way to do what Nasir is asking directly in PyMOL? > > > > > On Feb 16, 2016, at 8:15 AM, Nasir Bashiruddin <nasir...@gmail.com> wrote: > > > > Hello! > > > > So, I've had this problem for a while now. > > > > I have a ligand that goes deep into a protein. > > > > I have the ligand with stick representation. > > > > I have the protein in cartoon representation. > > > > I have both ligand and protein surfaced with 0.5 transparencies. > > > > The ligand surface is yellow and the protein surface is gray80. > > > > The protein cartoon is set to transparency, 0.5 as well. > > > > I want to show how the ligand goes deep into the binding site of the > > protein. > > > > I can see the ligand surface going into the protein surface but when I Ray, > > the yellow ligand surfaces that go into the protein disappear. > > > > How do I get the Ray quality and keep the ligand surface that is within the > > protein from disappearing? > > > > Hope I explained this well. > > BTW, surface mode is set to 1 to include all atoms > > > > Nasir -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. -- Site24x7 APM Insight: Get Deep Visibility into Application Performance APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month Monitor end-to-end web transactions and take corrective actions now Troubleshoot faster and improve end-user experience. Signup Now! http://pubads.g.doubleclick.net/gampad/clk?id=272487151=/4140 ___ 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] Can't build trans peptides ?
Hi Charbel, After you opened the builder panel, you can change the "secondary_structure" setting to 4 before you start building: PyMOL> set secondary_structure, 4 You may also like the "fab" command to build peptides: http://pymolwiki.org/index.php/Fab Extended poly-ALA example: PyMOL> fab , ss=4 Cheers, Thomas On 11 Feb 2016, at 06:48, R. Charbel MAROUN <charbel.mar...@inserm.fr> wrote: > Hello Pymolers, > > When trying to build a polypeptide chain with the Build Residue command, > I find no "trans" conformation for the phi and psi angles, only Helix > and Beta sheet. Is there a simple way of building a chain in the trans > (extended) conformation ? > > Thanks in advance. > > -- > R. Charbel MAROUN, Ph.D., H.D.R. > UMR-S INSERM U1204/UEVE > Structure et activité des biomolécules > normales et pathologiques > Université d'Evry-Val d'Essonne > Bâtiment Maupertuis > Rue du Père Jarlan > 91000 EVRY > FRANCE > Tél: +33 1 69 47 76 64 > FAX: +33 1 69 47 02 19 > e-mail charbel.mar...@inserm.fr -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. -- Site24x7 APM Insight: Get Deep Visibility into Application Performance APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month Monitor end-to-end web transactions and take corrective actions now Troubleshoot faster and improve end-user experience. Signup Now! http://pubads.g.doubleclick.net/gampad/clk?id=272487151=/4140 ___ 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] weird behavior with renitialize
Hi Blaine,
I confirm, this is a regression bug in PyMOL 1.6.
This will only happen when using PyMOL commands, not when doing the same thing
with a Python script. Here is an equivalent replacement for your alias:
python
from pymol import cmd, preset
@cmd.extend
def q1():
cmd.reinitialize()
cmd.fetch('3v6d', 'HIVrt', type='pdb')
preset.ball_and_stick("c. P and i. 822")
cmd.zoom('c. P and i. 822')
cmd.rock()
python end
Cheers,
Thomas
On 11 Feb 2016, at 09:55, Mooers, Blaine H.M. (HSC) <blaine-moo...@ouhsc.edu>
wrote:
> Dear PyMOLers,
>
> I am using incentive version 1.8.0.5. I made the following python script
> with an alias
>
> from pymol import *
> cmd.alias('q1', 'delete all;fetch 3v6d, HIVrt, type=pdb,
> async=0;preset.ball_and_stick("c. P and i. 822");zoom c. P and i. 822;rock')
>
> Repeated entry of the alias name changes the color scheme of the atoms and
> toggles on and off the rocking motion.
> Apparently, the settings are not reset with "delete all".
>
> If I replace "delete all" with "remove all" or 'reinitialize", the command
> history windows shows thepdb file haveing been fetched but no molecular
> object show ups in the internal gui. In version 1.55, reinitialize works as
> expected.
>
> It seems that the reinitialize needs a "pause until completed signal" like
> "async=0 " in fetch or theunix "&&".
>
> Best regards,
>
> Blaine
>
> Blaine Mooers, Ph.D.
> Assistant Professor
> Director of the Laboratory of Biomolecular Structure and Function
> Department of Biochemistry and Molecular Biology
> University of Oklahoma Health Sciences Center
> S.L. Young Biomedical Research Center Rm. 466
> 975 NE 10th Street, BRC 466
> Oklahoma City, OK 73104-5419
--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.
--
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Re: [PyMOL] ignore_case in next PyMOL version
Hi Spencer, Very good question. In short, the "ignore_case" setting affects all text matching in the selection language, including operators. The next official release and current latest SVN will exclude chain and segi from that, and handle them with "ignore_case_chain". Correct, the idea is case-insensitive element symbols (that's ignore_case=on) and case-sensitive chains (ignore_case_chain=off). For all normal use cases, there should be no reason to change these settings. In detail, these are the affected selectors: - single-word selectors (http://pymolwiki.org/index.php/Single-word_Selectors ) - selection operators (http://pymolwiki.org/index.php/Selection_Algebra ) - object and selection names - values of: - chain (up to 1.8.0) - segi (up to 1.8.0) - resn - resi (insertion code) - name - alt - element - ss - rep - byca operator (CA name matching) - in operator (resn, resi, name matching; up to 1.8.0 also chain and segi) - like (resi and name matching) Besides the selection language, case insensitive matching is hard coded for atom sorting (affects resi, resn, name; up to 1.7.0 also segi). I'm not sure yet whether we want to do anything about that. I don't see a reason why atom sorting should be case insensitive. Case insensitive matching was also hardcoded for matching two selections with the following commands: fit, rms, rms_cur and update. Latest SVN considers "ignore_case" and "ignore_case_chain" with these commands. Cheers, Thomas On 10 Feb 2016, at 02:58, Spencer Bliven <spencer.bli...@gmail.com> wrote: > Restoring the old ignore_case behaviour seems pragmatic. > > Can you explain the difference with the new ignore_case_chain setting? Is the > idea that we would want case-insensitive element symbols (ignore_case=off) > but case-sensitive chains (ignore_case_chain=on)? Are there other places > where case is important in the selections or structures (e.g. insertion > codes)? > > -Spencer > > On Tue, Feb 9, 2016 at 4:18 PM, Thomas Holder <thomas.hol...@schrodinger.com> > wrote: > Hi all, > > Quick update on the "ignore_case" issue: > > - ignore_case=on default restored in PyMOL 1.8.0.5 and latest SVN > - latest SVN introduces new "ignore_case_chain" setting > > Cheers, > Thomas > > On 02 Feb 2016, at 14:38, Thomas Holder <thomas.hol...@schrodinger.com> wrote: > > > Greetings, > > > > I like to let you know that we plan another change for the "ignore_case" > > setting behavior. We want to restore the old default (ignore_case=on) and > > introduce a new setting "ignore_case_chain=off", which will affect the > > "chain" and "segi" identifiers. > > > > As you may (or should) know, we changed the default of the "ignore_case" > > setting in PyMOL 1.8 from "on" to "off". The rationale was to have default > > settings which properly support PDB files which mix upper and lower case > > chain identifiers (e.g. 3a0b). Users who still prefer a case insensitive > > selection language can put a "set ignore_case" line in their pymolrc file. > > > > However, we now realized that this is not very practical. One reason is > > that too many scripts and code samples use lower case resn and name > > selections, fixing those historic resources is often not feasible or > > desirable. Another reason is that PyMOL inconsistently stores element > > symbols, for example chlorine is "CL" when loaded from a PDB file, but "Cl" > > when loaded from SDF. The logical conclusion is that PyMOL should handle > > chain and segi different from resn, name and elem. > > > > See also: http://pymolwiki.org/index.php/ignore_case > > > > Any kind of feedback regarding the planned change will be appreciated. > > > > Cheers, > > Thomas -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. -- Site24x7 APM Insight: Get Deep Visibility into Application Performance APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month Monitor end-to-end web transactions and take corrective actions now Troubleshoot faster and improve end-user experience. Signup Now! http://pubads.g.doubleclick.net/gampad/clk?id=272487151=/4140 ___ 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] ignore_case in next PyMOL version
Hi all, Quick update on the "ignore_case" issue: - ignore_case=on default restored in PyMOL 1.8.0.5 and latest SVN - latest SVN introduces new "ignore_case_chain" setting Cheers, Thomas On 02 Feb 2016, at 14:38, Thomas Holder <thomas.hol...@schrodinger.com> wrote: > Greetings, > > I like to let you know that we plan another change for the "ignore_case" > setting behavior. We want to restore the old default (ignore_case=on) and > introduce a new setting "ignore_case_chain=off", which will affect the > "chain" and "segi" identifiers. > > As you may (or should) know, we changed the default of the "ignore_case" > setting in PyMOL 1.8 from "on" to "off". The rationale was to have default > settings which properly support PDB files which mix upper and lower case > chain identifiers (e.g. 3a0b). Users who still prefer a case insensitive > selection language can put a "set ignore_case" line in their pymolrc file. > > However, we now realized that this is not very practical. One reason is that > too many scripts and code samples use lower case resn and name selections, > fixing those historic resources is often not feasible or desirable. Another > reason is that PyMOL inconsistently stores element symbols, for example > chlorine is "CL" when loaded from a PDB file, but "Cl" when loaded from SDF. > The logical conclusion is that PyMOL should handle chain and segi different > from resn, name and elem. > > See also: http://pymolwiki.org/index.php/ignore_case > > Any kind of feedback regarding the planned change will be appreciated. > > Cheers, > Thomas -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. -- Site24x7 APM Insight: Get Deep Visibility into Application Performance APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month Monitor end-to-end web transactions and take corrective actions now Troubleshoot faster and improve end-user experience. Signup Now! http://pubads.g.doubleclick.net/gampad/clk?id=272487151=/4140 ___ 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 tracing max_threads
Hi all, Quick summary after off-line discussion with Jesper: The max of 32 threads was hard coded in PyMOL. The latest SVN update increases this limit to 125. If you ever need a higher limit, look for PYMOL_MAX_THREADS in the code. Cheers, Thomas On 22 Jan 2016, at 03:27, Jesper Lykkegaard Karlsen <je...@mbg.au.dk> wrote: > Hi, > > I am doing some heavy duty ray tracing in PyMOL. > > I realize spreading the job over multiple nodes in a PBS requires MPI > integration in PyMOL, but this is run on a single machine with 36 > physical CPU cores and 72 logical threads. > Although, during PyMOL ray tracing CPU usage maxes-out at 32 treads. > > I have even tried setting max_treads to 72, but PyMOL refuses to use any > more than 32 threads. > > Why this limitation? and is the a way to overcome it? > > Thanks > > Jesper > > -- > Jesper Lykkegaard Karlsen > Scientific Computing > Centre for Structural Biology > Department of Molecular Biology and Genetics > Aarhus University > Gustav Wieds Vej 10C > 8000 Aarhus C > > E-mail: je...@mbg.au.dk -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. -- Site24x7 APM Insight: Get Deep Visibility into Application Performance APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month Monitor end-to-end web transactions and take corrective actions now Troubleshoot faster and improve end-user experience. Signup Now! http://pubads.g.doubleclick.net/gampad/clk?id=272487151=/4140 ___ 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] auto_show_cartoon or similar
Hi Ivan and Carsten, I can take "auto_show_cartoon" as a feature request. It's trivial to implement. What also would be nice: automatically showing sticks for ligands. e.g. corresponding to the "not polymer" or the "organic" selection. Thoughts? Cheers, Thomas On 08 Feb 2016, at 09:07, Schubert, Carsten [JRDUS] <cschu...@its.jnj.com> wrote: > Hi Ivan, > > you could either try to overload the “load” function in Pymol (not sure this > is supported) or write your own custom load function under a different name, > which loads the protein, assigns the name of the object, hides lines and > shows the cartoon. > > Sorry, this is a rather generic answer but should point you in the right > direction. > > Cheers, > > Carsten > > From: Ivan Vulovic [mailto:i...@uw.edu] > Sent: Saturday, February 06, 2016 8:18 PM > To: pymol-users@lists.sourceforge.net > Subject: [PyMOL] auto_show_cartoon or similar > > Hello > > Is there a way to make cartoon the default representation, something akin to > "auto_show_lines", but for cartoon? There was some dicussion of this in 2010 > (link below) but I haven't found anything more recent that does what I'd like. > > http://www.mail-archive.com/pymol-users%40lists.sourceforge.net/msg07734.html > > Thanks > Ivan -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. -- Site24x7 APM Insight: Get Deep Visibility into Application Performance APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month Monitor end-to-end web transactions and take corrective actions now Troubleshoot faster and improve end-user experience. Signup Now! http://pubads.g.doubleclick.net/gampad/clk?id=272487151=/4140 ___ 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] ignore_case in next PyMOL version
Greetings, I like to let you know that we plan another change for the "ignore_case" setting behavior. We want to restore the old default (ignore_case=on) and introduce a new setting "ignore_case_chain=off", which will affect the "chain" and "segi" identifiers. As you may (or should) know, we changed the default of the "ignore_case" setting in PyMOL 1.8 from "on" to "off". The rationale was to have default settings which properly support PDB files which mix upper and lower case chain identifiers (e.g. 3a0b). Users who still prefer a case insensitive selection language can put a "set ignore_case" line in their pymolrc file. However, we now realized that this is not very practical. One reason is that too many scripts and code samples use lower case resn and name selections, fixing those historic resources is often not feasible or desirable. Another reason is that PyMOL inconsistently stores element symbols, for example chlorine is "CL" when loaded from a PDB file, but "Cl" when loaded from SDF. The logical conclusion is that PyMOL should handle chain and segi different from resn, name and elem. See also: http://pymolwiki.org/index.php/ignore_case Any kind of feedback regarding the planned change will be appreciated. Cheers, Thomas -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. -- Site24x7 APM Insight: Get Deep Visibility into Application Performance APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month Monitor end-to-end web transactions and take corrective actions now Troubleshoot faster and improve end-user experience. Signup Now! http://pubads.g.doubleclick.net/gampad/clk?id=267308311=/4140 ___ 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] drawing trajectory files
Hi Mike, These bonds have bond order zero. Incentive PyMOL 1.8 renders those as dashed lines and sticks. Previous versions of PyMOL had no proper support for zero-order bonds, they did render as solid lines, but had no stick representation. You can set all bond orders to 1 with: PyMOL>valence 1, *, * Or PyMOL can guess the bond orders for you, if double bonds matter: PyMOL>valence guess, *, * I will look into the amber topology loading code to see if we are importing those bonds wrong. Cheers, Thomas On 01 Feb 2016, at 07:08, Michael F. Summers <summ...@umbc.edu> wrote: > Colleagues, > > When I load an amber topology file and associated trajectory file, the lines > for all heteroatoms are drawn as dashed lines (but bonds to hydrogens drawn > as solid lines). > I can’t seem to find a flag that would turn this feature off… I’d rather see > all bonded atoms connected as solid lines. I couldn’t find an explanation on > the WIKI (earlier versions of pymol didn’t behave this way). Everything else > works fine (movie plays as it normally would). Any advice would be > appreciated. > > Thanks, > > Mike -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. -- Site24x7 APM Insight: Get Deep Visibility into Application Performance APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month Monitor end-to-end web transactions and take corrective actions now Troubleshoot faster and improve end-user experience. Signup Now! http://pubads.g.doubleclick.net/gampad/clk?id=267308311=/4140 ___ 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] ColorByRMSD script
Hi Guilherme, Simply remove the __future__ import line from the script. The script will work just fine in PyMOL 1.3. Cheers, Thomas On 29 Jan 2016, at 09:00, Guilherme Souza <gsouza...@gmail.com> wrote: > Yes, it seems that this is exactly the problem. I'm using PyMOL 1.3, and the > Python version it is using is 2.5.4... > Is there any way of fixing it without uninstalling my current version of > PyMOL? > > 2016-01-29 11:57 GMT-02:00 Matthew Baumgartner <mp...@pitt.edu>: > What version of Pymol are you using? Pymol ships with it's own version of > python that is separate from your system python. > In the pymol command line, run: > > import sys > print sys.version > > That will tell you what python version pymol is using. > > HTH, > Matt > > > On 01/29/2016 08:55 AM, Guilherme Souza wrote: >> I've searched about this kind of error, and in every site I look, it seems >> that it is caused by using Python <= 2.5, which is not my case. Is there any >> chance that my PyMOL is using and older version of Python? >> >> 2016-01-29 11:46 GMT-02:00 Guilherme Souza <gsouza...@gmail.com>: >> Okay. I did it, and kind of got the same error: >> >> PyMOL>run colorbyrmsd.py >> Traceback (most recent call last): >> File "C:\Program Files (x86)\PyMOL\PyMOL/modules\pymol\parser.py", line >> 338, in parse >> parsing.run_file(path,self.pymol_names,self.pymol_names) >> File "C:\Program Files (x86)\PyMOL\PyMOL/modules\pymol\parsing.py", line >> 455, in run_file >> execfile(file,global_ns,local_ns) >> SyntaxError: future feature print_function is not defined (colorbyrmsd.py, >> line 10) >> >> 2016-01-29 11:41 GMT-02:00 Matthew Baumgartner <mp...@pitt.edu>: >> Hi, >> You run the command 'run colorbyrmsd.py' in the Pymol command line. That >> initializes the function in pymol. If everything goes well, you shouldn't >> see anything (no errors). Then to use the command, type just 'colorbyrmsd >> [args...]' into the command line. >> >> You can see the usage instructions in the wiki. >> >> HTH, >> >> Matt Baumgartner >> >> >> On 01/29/2016 08:36 AM, Guilherme Souza wrote: >>> I'm sorry.. Where exactly am I supposed to type 'run colorbyrmsd.py'? >>> And should I expect to see my both protein structures colored in the PyMOL >>> interface? >>> >>> Thank you! >>> >>> 2016-01-29 11:36 GMT-02:00 Guilherme Souza <gsouza...@gmail.com>: >>> I'm sorry.. Where exactly am I supposed to type 'run colorbyrmsd.py'? >>> And should I expect to see my both protein structures colored in the PyMOL >>> interface? >>> >>> 2016-01-29 11:35 GMT-02:00 Guilherme Souza <gsouza...@gmail.com>: >>> I'm sorry.. Where exactly am I supposed to type 'run colorbyrmsd.py'? >>> And should I expect to see my both protein structures colored in the PyMOL >>> interface? >>> >>> Thank you! >>> >>> 2016-01-29 11:09 GMT-02:00 Schubert, Carsten [JRDUS] <cschu...@its.jnj.com>: >>> Hi Guilherme, >>> >>> >>> the script is not a plugin, so you cannot install it since it is missing >>> some software infrastructure to work as a plugin. Simply put the script >>> into the directory you are working in and run it via ‘run colorbyrmsd.py’ . >>> This will add the command to the scripting interface and you can run the >>> command like any other pymol command. See the wiki for the details in that >>> regards. >>> >>> >>> HTH >>> >>> >>> Carsten >>> >>> >>> From: Guilherme Souza [mailto:gsouza...@gmail.com] >>> Sent: Friday, January 29, 2016 7:07 AM >>> To: pymol-users@lists.sourceforge.net >>> Subject: [PyMOL] ColorByRMSD script >>> >>> >>> Hi. >>> >>> >>> I'm a starter in PyMOL, and I'm trying to use this script, ColorByRMSD >>> (http://www.pymolwiki.org/index.php/ColorByRMSD). >>> However, I'm getting the following error >>> message, when I initialize PyMOL after installing the plugin: >>> >>> >>> Exception in plugin 'colorbyrmsd' -- Traceback follows... >>> >>> Traceback (most recent call last): >>> >>> File "C:\Program Files (x86)\PyMOL\PyMOL/modules\pmg_tk\PMGApp.py", line >>> 313, in initializePlugins &g
Re: [PyMOL] regarding show_bumps
Hi Spencer & Priyan,
I've updated the show_bumps script to work with multi-state objects. Please
re-download.
Cheers,
Thomas
On 28 Jan 2016, at 06:15, Spencer Bliven <spencer.bli...@gmail.com> wrote:
> You can automate generating the bump objects:
>
> split_states *,prefix=split_
> for n in cmd.get_object_list("(split_*)"): show_bumps(n, "bump_"+n);
>
> However, unfortunately the bump cgo objects don't seem to be able to be
> combined into a multi-state object (e.g. with `for n in
> cmd.get_object_list("(split_*)"):
> cmd.create("bumps","bump_"+n,target_state=-1)`). Thus you might have to
> generate your movie using some python loops to enable/disable the bumps for
> each frame, if you want to automate it.
>
> -Spencer
>
> On Thu, Jan 28, 2016 at 11:25 AM, ccp4 pymol <ccp4.py...@gmail.com> wrote:
> Dear Spencer
>
> Thank you for the suggestion. Well, I actually wanted to do it as a part of
> making a movie, so would have liked some automation.
>
> Thank you.
>
> Best Regards
> Priyan
>
> On Thu, Jan 28, 2016 at 2:39 PM, Spencer Bliven <spencer.bli...@gmail.com>
> wrote:
> Priyan–
>
> You can use the split_states command to divide it into multiple objects, then
> run the script on each state individually.
>
> -Spencer
>
> On Thu, Jan 28, 2016 at 3:45 AM, ccp4 pymol <ccp4.py...@gmail.com> wrote:
> Hi
>
> I have a multi-state object loaded in PyMOL which represents transition of a
> domain from one orientation to the other. I tried using "show_bumps.py" to
> bring up clashes during the transition but the cgo that is written out shows
> clashes only for the first state. Am I doing something wrong or should we
> pass additional commands to show clashes for all states. Kindly post your
> replies with help/suggestions in this regard.
>
> Thank you
>
> Best Regards
> Priyan
--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.
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Re: [PyMOL] iterate names in group
Hi Jared and Jordan,
Just want to clarify that dots for hierarchical grouping is optional. Any name
can be put into a group, with the "group" command. Grouping can happen
automatically with dots, depending on the "group_auto_mode" setting.
Relevant settings for dotted name handling:
group_auto_mode
group_full_member_names
Group command:
http://pymolwiki.org/index.php/Group
There is no proper API to get the (first-order) children of a group. You can
get all molecular object children (including children from nested groups) by:
cmd.get_object_list('(groupname)')
Hope that helps.
Cheers,
Thomas
On 25 Jan 2016, at 17:33, Sampson, Jared M. <jms2...@cumc.columbia.edu> wrote:
> Hi Jordan -
>
> Grouped object names use dots to indicate group inheritance ("groupA.obj1"),
> so maybe try something like this:
>
> ```
> from pymol import stored
>
> stored.group_names = []
> group_name = "groupA"
> for obj in cmd.get_names():
> if obj[0:len(group_name)] == group_name:
> # either add them to a list to use later
> stored.group_names.append(obj)
> # or run your `iterate` command here
> #cmd.iterate(...)
> print sorted(stored.group_names)
>
> ```
>
> For me the printed dummy output looks like:
> ['groupA', 'groupA.obj1', 'groupA.obj2', ... ]
>
> Hope that helps.
>
> Cheers,
> Jared
>
>> On Jan 25, 2016, at 2:34 PM, Jordan Willis <jwillis0...@gmail.com> wrote:
>>
>> Hi,
>>
>> Is there a way to iterate through the names that have been grouped?
>>
>> iterate
>>
>> doesn’t seem to do it because it kills my pymol app.
>>
>> Jordan
--
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PyMOL Principal Developer
Schrödinger, Inc.
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Re: [PyMOL] Displaying sticks on RNA bases only
Hi Maria, The following shows filled rings and sticks for the nucleosides: set cartoon_ring_finder, 1 set cartoon_ring_mode, 3 as cartoon To not show filled rings for the nucleobases, you can hide cartoon for the sidechain selection, and show sticks instead (the sidechain selection keyword was introduced in PyMOL 1.7.0): hide cartoon, sidechain show sticks, sidechain extend 1 See also: http://pymolwiki.org/index.php/Overview_of_nucleic_acid_cartoons Hope that helps. Cheers, Thomas On 20 Jan 2016, at 10:10, COSTA Maria <maria.co...@i2bc.paris-saclay.fr> wrote: > Hello, > > I am using Pymol to visualize nucleic acid structures ( I'm a new user) and I > would like to be able to display the functional groups of bases A, G, T/U, C > with sticks while using the cartoon mode : cartoon_ring_finder, 1 or 2 for > the ribose_phosphate backbone of the molecule. Can you please tell me how to > achieve that ? > For the moment the only thing I found was to display the 'cartoon' and the > 'stick' modes at the same time to get the sticks corresponding to the > functional groups of the bases but then I also visualize all the sticks of > the riboses and phosphates which makes my drawings 'overloaded'. I hope I was > clear enough. > > Many thanks in advance for your answers, > > Maria > > CNRS > France -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. -- Site24x7 APM Insight: Get Deep Visibility into Application Performance APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month Monitor end-to-end web transactions and take corrective actions now Troubleshoot faster and improve end-user experience. Signup Now! http://pubads.g.doubleclick.net/gampad/clk?id=267308311=/4140 ___ 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 + APBS plugin
Hi Matic, 1. If you have conflicting (non-unique) file names, you have two options: a) Specify an object name with the "load" command (load foo_1.dx, foo_1_map) b) Set the "auto_rename_duplicate_objects" setting 2. The APBS GUI update bug has been fixed in the PyMOL SVN repository two days ago. If you don't want to recompile, you can also install the updated plugin manually from here: http://pymolwiki.org/index.php/Apbsplugin 3. Use the "matrix_copy" command to transfer the transformation matrix from the molecular object to the map object after alignment (matrix_copy foo_1, foo_1_map) Hope that helps. Cheers, Thomas On 13 Jan 2016, at 13:19, Matic Kisovec <matic.kiso...@ki.si> wrote: > Dear all, > > I wish to report two issues (numbered 1. and 2.) with APBS plugin in Pymol. I > use Xubuntu 14.04 (Xubuntu is a flavour of Ubuntu) and opensource Pymol > 1.8.0.0. > > • First I tried to perform a couple of APBS calculations through the > APBS plugin window and all went great. Then I did a batch pdb2pqr > transformation on my local machine and then a batch apbs calculation also on > my local machine. Both directly in terminal (no connection with Pymol). I > more or less followed these instructions: http://jamiebaxter.com/blog/?p=890 > . After the calculations I ended up with all the standard files (.in, .pqr > and .dx). The issue was that I was not able to load them in Pymol. After > loading .pqr and .dx the tab 'Visualization' in APBS plugin windows kept > saying to load a molecule and a map. And after clicking the button 'Update' > nothing happened. There was no error reported. First I thought there has to > be something wrong with the manual procedure of generating .pqr and .dx > files. More or less by accident I figured out the problem is in the names of > files. I generated them to be identical and the only difference was the > extension (for example foo_1.pqr and foo_1.dx). If I changed one of the names > (I just tried .dx for now) and added or deleted a single character everything > went smoothly once loaded in Pymol. Is this a problem/bug only in my case > since the APBS plugin also creates temporary files with identical names? > • Another possible bug is present in the 'Visualization' tab of APBS > plugin. If one uses the button 'Update' in the 'Maps and Molecules' field > (the one marked in orange in this image: > https://app.box.com/s/wztcwondd0fiqqczdyekhnd3ltfo0nxa) then one slowly loses > the option to use the fields 'Positive Isosurface', 'Neg. Isosurface' and > 'Molecular Surface'. They keep on moving downwards until you loose the from > the screen (see the image in the previous link to see this). 'Field lines' > fields keep appearing after each click on the 'Update' button. Of course one > can restrain from using the mentioned 'Update' button since it seems to me > that it is not really necessary at all. But still it is a strange behaviour. > • This is just a question not an issue really. Is there an easy way to > visualise multiple aligned proteins with their electrostatic surfaces > simultaneously? I tried 'set grid_mode' and it works but not if I do an > alignment after loading the pqr structure and the APBS map. I suppose I > could/should align them before doing the calculations but since I didn't it > would be great if it is possible to do this during visualization. > Hopefully somebody can look into this or at least find this through googling > and in this way save a couple of minutes or hours. > All the best, > Matic Kisovec -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. -- Site24x7 APM Insight: Get Deep Visibility into Application Performance APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month Monitor end-to-end web transactions and take corrective actions now Troubleshoot faster and improve end-user experience. Signup Now! http://pubads.g.doubleclick.net/gampad/clk?id=267308311=/4140 ___ 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] OBJECT argument in ALIGN command - color
Hi Tim and Carsten, I wonder what exactly you have tried so far to change the color of the alignment object. In fact, the "color" command should do the job. Example: fetch 1oky 1t46, async=0 align 1oky, 1t46, object=aln color blue, aln I don't think that two-color gradients were ever intended, and I don't remember which version of PyMOL created them. That might have been a bug. Cheers, Thomas On 11 Jan 2016, at 09:19, Schubert, Carsten [JRDUS] <cschu...@its.jnj.com> wrote: > Hi Tim, > > I ran into the same issue a while back as well. I gets complicated very > quickly when you dive deeper into the subject. Your are right the colors of > the CGO lines seem to be hardcoded. A way to get around this is to extract > the matching residues with cmd.get_raw_alignment(alignment_object). The > result is a tuple of tuples of matching atoms as determined by the alignment > algorithm. You could then take these atoms pairs and draw distance lines > between them. These distance lines can be customized with color, linewidth, > etc. > > It has been a while since I worked on this, but I believe that the assignment > of pairs is a non-trivial issue and sometimes fraught with mismatches. So > manual checking against a sequence alignment is always a good idea especially > for rather unrelated proteins. > > I do have a script which can accomplish this, it is based on > “colorbyrmsd.py”. However it is not ready for primetime, but I can share this > with you if there is interest. Contact me offline to arrange something. > > Cheers, > > Carsten > > From: Timothy Umland [mailto:uml...@gmail.com] > Sent: Sunday, January 10, 2016 9:08 PM > To: pymol-users@lists.sourceforge.net > Subject: [PyMOL] OBJECT argument in ALIGN command - color > > > > Hi: > > I am trying to use the Alignment Objects (i.e., lines between the paired > aligned atoms) created by using the OBJECT argument of the ALIGN command to > illustrate domain movement between the superimposed ligand-bound and unbound > forms of an enzyme. > > I successfully made the basic aligned image, and now I want to tweak it. > > Is it possible to change the color of the Alignment Object lines between > paired atoms? For me, they display only in yellow. From what I have read > online these lines are CGO objects with the color hardwired in upon creation, > and so it can’t be changed in PyMol latter on. However, I haven’t been able > to find a way to assign a color upon creation. Is there a way to assign a > specific color? > > Additionally, I have seen this type of image where the lines between the > paired aligned atoms are two colors, with half of the line in one color (say > blue) and the other half another color (say red) to better illustrate which > protein is the origin of each end of the connecting line. I haven’t > discovered a way to make these bi-colored lines in ALIGN. Any ideas? > > I have tried the open source version 1.8.0, plus several earlier versions > from various origins (all on Macs) with similar results. > > > Thanks much for any ideas. > > Tim > > Tim Umland, Ph.D. > Hauptman-Woodward Institute -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. -- Site24x7 APM Insight: Get Deep Visibility into Application Performance APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month Monitor end-to-end web transactions and take corrective actions now Troubleshoot faster and improve end-user experience. Signup Now! http://pubads.g.doubleclick.net/gampad/clk?id=267308311=/4140 ___ 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] Quick PyMOLWiki Update
Hi Jason, This is great, thanks for your work. One thing I noticed: On the main page, the "Did you know..." random article seems to be frozen. It does however show random articles when doing "Edit > Show preview". Does the wiki use a server side cache? Cheers, Thomas On 03 Jan 2016, at 01:21, Jason Vertrees <jason.vertr...@gmail.com> wrote: > Greetings PyMOLers, > > Traffic on the PyMOLWiki continues to grow. It serves far over 100k page > views/month. In 2015 we got traffic from almost every country on the planet. > Very cool. > > While operating well, the site, schemas, and plugins were outdated. So, I > went through and upgraded everything (and reinstalled a few previously > omitted plugins). Because of the scope of the changes, something may go > wrong. If it does, please let me know. > > Also, curiously, today my provider let me know that the PyMOLWiki was being > DDoS'd. I can imagine more productive use of one's time. If you encounter > issues, please let me know. > > Happy New Year! I hope everyone enjoyed their holiday(s). > > Cheers, > > -- Jason -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. -- ___ 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] Version question -- PSE session file format
Hi Bob, Nothing has changed here in 1.8. I assume you used MacPyMOL recently? As far as I know, MacPyMOL never stored the "main" dictionary item. Or if you export a session with partial=1, it will also not store the viewport. Cheers, Thomas On 23 Dec 2015, at 19:12, Robert Hanson <hans...@stolaf.edu> wrote: > I have a question about the PSE file format. > > Newer PSE files, perhaps those created using PyMOL 1.8, seem to have no > indication of the desired viewport width and height. These were in the "main" > dictionary item. Is there any way in these new files to find out the original > viewport size? > > Bob > > -- > Robert M. Hanson > Larson-Anderson Professor of Chemistry > Chair, Department of Chemistry > St. Olaf College > Northfield, MN > http://www.stolaf.edu/people/hansonr > > If nature does not answer first what we want, > it is better to take what answer we get. > > -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. -- ___ PyMOL-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] Announcing Julian Heinrich as PyMOL Open Source Fellow
Greetings PyMOL users, Please join me in congratulating Dr. Julian Heinrich, who has been awarded the Warren L. DeLano Memorial PyMOL Open Source Fellowship for 2015–2016. Julian will work on automated view selection for molecular structures. Setting up a view (camera orientation) which maximizes the visibility of relevant features is critical when creating figures and movies. An automated view selection will improve the output of automated figure generation pipelines, it can assist the user when manually searching for the best view, and it can be used to generate automatic tour movies with the N best views. Julian will also help maintaining the PyMOLWiki and pymol-users mailing list. You can reach Julian at jul...@joules.de. The Warren L. DeLano Memorial PyMOL Open-Source Fellowship is awarded by Schrӧdinger to supplement the income of an outstanding member of the PyMOL open-source community so that s/he can continue to develop free resources to help scientific progress and the community as a whole. You can read more about the PyMOL Open Source Fellowship Program and the fellows at http://pymol.org/fellowship. Cheers, Thomas & the PyMOL Team at Schrödinger -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. -- ___ 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 with Python 3
Hi Justin, Thanks a lot for working on the repo. I converted isoslider.py and frame_slider.py, they work fine for me with Python 2 and 3. Will check them in shortly. Cheers, Thomas On 07 Dec 2015, at 07:00, Justin Lecher <j.lec...@fz-juelich.de> wrote: > On 07/12/15 10:42, Justin Lecher wrote: >> On 07/12/15 10:23, Spencer Bliven wrote: >>> Nice work! It will be very nice to have python3 compatibility in the future. >>> >>> It would be nice to organize a section of the pymol-script-repo for >>> python3-compatible scripts once this gets merged to SVN. >>> >> >> I think, we can make most of the scripts work on py2 and 3 >> simultaneously. I will create a new branch in the repo. I someone likes >> to help, you are very welcome to send PRs. Please send one PR per script >> for the ease of reviews. >> >> Justin > > Hi, > > I updated all scripts except of two for python2 and 3 compatibility. > > isoslider.py and frame_slider.py are using tk. Although 2to3 is able to > convert the code I am not familiar with implementing it in a cross ABI > compatible way. So contributions are welcome here. > > Justin -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. -- ___ 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] RMSD calculations for a group of structures
Hi Daniel,
You say you used "split_states", so all your conformations have the same
topology (are the same molecule). In that case, I suggest to use cmd.rms
instead of cmd.align, which will be more efficient. You also don't need to
split the structures, but call the function with the correct "mobile_state" and
"target_state" arguments. The cmd.rms() function returns the RMSD. Note that it
by default calculates the all-atom RMSD, vs. cmd.align which does outlier
rejection.
Example:
python
from pymol import cmd
f=open('rmsd.txt','w')
cmd.fetch('1nmr')
for state in range(2, cmd.count_states() + 1):
r = cmd.rms('1nmr and name CA',
'1nmr and name CA', 1, state)
f.write('State: %3d RMS: %5.2f\n' % (state, r))
f.close()
python end
Hope that helps.
Cheers,
Thomas
On 03 Dec 2015, at 17:13, Daniel Munoz Escudero <dmun...@unal.edu.co> wrote:
> Hi!
>
> I have a group of structures (168 in total) and I want to align all of them
> to the first one in order to know the RMSD calculation. For that purpose I
> use the following:
>
> f=open('rmsd.txt','w')
> rms2=cmd.align('structure_0002 and name ca','structure_0001 and name ca')
> .
> . (NOTE: I got all of these structures by the command split_states somename)
> .
> rms9=cmd.align('structure_0009 and name ca','structure_0001 and name ca')
>
> How do I get the output with the number of each RMSD into the text file
> rmsd.txt? What other way can I use to do so?
>
> Thanks in advance,
> D.
--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.
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[PyMOL] PyMOL with Python 3
Hi all, We have refactored Open-Source PyMOL to work with Python 3. If you are interested, the patched code and the patch itself are currently available from the sourceforge download page: https://sf.net/projects/pymol/files/pymol/1.8/ pymol-v1.8.0.0-r4145-py3.tar.bz2 (patched code) pymol-v1.8.0.0-r4145-py3.patch (diff agains current SVN) Disclaimer: If you have no particular interest in Python 3, then this is not for you. Most currently available PyMOL plugins and Python scripts will not work with this version, they will need to be refactored as well. If you find any bugs or unexpected behavior, please let us know. In Python 3, all strings (type "str") are unicode, while in Python 2 "str" is an alias for "bytes". This difference is probably the most significant one for PyMOL. Once the patch looks rock solid and also proves to still work fine with Python 2, we will check it in to SVN. Cheers, Thomas -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. -- Go from Idea to Many App Stores Faster with Intel(R) XDK Give your users amazing mobile app experiences with Intel(R) XDK. Use one codebase in this all-in-one HTML5 development environment. Design, debug & build mobile apps & 2D/3D high-impact games for multiple OSs. http://pubads.g.doubleclick.net/gampad/clk?id=254741911=/4140 ___ 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] MacPymol
Hi Young-Jin, The latest MacPyMOL works fine on El Capitan. XQuartz is not required, unless you use the "MacPyMOLX11Hybrid" interface. Which version do you have installed? In my tests, all MacPyMOL versions newer than 1.4 work on El Capitan (not heavily tested, but they open and render something). Some of them only open if you select "Allow apps downloaded from: Anywhere" in the Security & Privacy System Preferences. Some older versions also might have problems with multiple or external displays. Cheers, Thomas On 02 Dec 2015, at 18:01, Young-Jin Cho <yj...@wavelifesci.com> wrote: > Hi, > By accident(!) I upgraded my Mac OS to El Captain. The problem is now I > cannot open my MacPymol that was fine up to previous or lion. > I downloaded XQuartz but still somehow doensn’t open my old MacPymol. Has > some one experienced or solved this problem? > > Thanks in advance. > Young-Jin -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. -- Go from Idea to Many App Stores Faster with Intel(R) XDK Give your users amazing mobile app experiences with Intel(R) XDK. Use one codebase in this all-in-one HTML5 development environment. Design, debug & build mobile apps & 2D/3D high-impact games for multiple OSs. http://pubads.g.doubleclick.net/gampad/clk?id=254741911=/4140 ___ 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] light reposition
Hi Darya and Carsten, The "regular display mode" (real-time OpenGL graphics) does take lights into account, and their position can be updated in real-time. A neat way to play around with lights is in lights mouse mode (new in PyMOL 1.5). From the menu, select "Mouse > 3 Button Lights" Now hold down the SHIFT key on the keyboard, press the left mouse button and drag (just like rotating the molecule, but now it rotates the light position). The "edit_light" setting controls which light get updated. The effect is most obvious with spheres representation. Note that "light_count=2" corresponds to one specular light, the first light is ambient only. Cheers, Thomas On 30 Nov 2015, at 13:56, Schubert, Carsten [JRDUS] <cschu...@its.jnj.com> wrote: > Darya, > > I have never used that feature, but do you see a difference when raytracing > or drawing the scene? Could be that the regular display mode does not take > these feature into account (this is a wild guess though) > > Cheers, > > Carsten > > From: Дарья Николаева [mailto:daranikola...@gmail.com] > Sent: Monday, November 30, 2015 9:58 AM > To: pymol-users@lists.sourceforge.net > Subject: [PyMOL] light reposition > > Hello, > > I want to change the position of my light sources. > > First I set the number of light sources: > >set light_count, 3 > > Then I attempt to reposition the light source, e.g., #2: > >set light2, [x, y, z] > > The problem is - I see no changes to the scene. > > The question: How to use the "set light(2-8)" command or is there any > other way to reposition light sources? > > Thank you, > Darya -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. -- Go from Idea to Many App Stores Faster with Intel(R) XDK Give your users amazing mobile app experiences with Intel(R) XDK. Use one codebase in this all-in-one HTML5 development environment. Design, debug & build mobile apps & 2D/3D high-impact games for multiple OSs. http://pubads.g.doubleclick.net/gampad/clk?id=254741911=/4140 ___ 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_transformed.py
Smith, Let's take this off-list. I will reply to you directly. We can send a summary to the list once it's working for you. Cheers, Thomas On 29 Nov 2015, at 22:13, Smith Liu <smith_liu...@163.com> wrote: > Dear Thomas, > > I do not know I still do something wrong. > > First I load a PDB in pymol, then I input orient (with orient input the > molecule really moved significantly in display), then I input > transform_by_camera_rotation, then I input save /tmp/withneworientation.pdb, > the withneworientation.pdb was really saved, but the newly saved > withneworientation.pdb has the all atom orientations (x,y,z) exactly same as > those of the original PDB I initially input to the pymol for the process I > obtained the withneworientation.pdb. > > Smith -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. -- Go from Idea to Many App Stores Faster with Intel(R) XDK Give your users amazing mobile app experiences with Intel(R) XDK. Use one codebase in this all-in-one HTML5 development environment. Design, debug & build mobile apps & 2D/3D high-impact games for multiple OSs. http://pubads.g.doubleclick.net/gampad/clk?id=254741551=/4140 ___ 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_transformed.py
Nov 27, 2015, at 9:08 PM, Smith Liu <smith_liu...@163.com> wrote:
>>>>>
>>>>>
>>>>> Dear All,
>>>>>
>>>>> Osvaldo is new here for this question, so I repeat it a little. By pymol
>>>>> I open a pdb and orient it and I want to save the oriented pdb. First I
>>>>> input command "orient" after load the pdb, then I input command "run
>>>>> save_trannsforme.py all, newpdb.pdb". I have tried to locate the
>>>>> newpdb.pdb by locate newpdb.pdb or find newpdb.pdb, even as the root
>>>>> user, but I cannot find the outpur newpdb.pdb. My pymol is Linux
>>>>> Open-Source PyMOL 1.6.X.
>>>>>
>>>>> I am looking forward to getting a reply from you on how to get the
>>>>> oriented pdb, which should be different from the original PDB I load.
>>>>>
>>>>> Smith
>>>>>
>>>>>
>>>>> At 2015-11-28 00:44:07, "Shane Caldwell" <shane.caldwel...@gmail.com>
>>>>> wrote:
>>>>> Hi Smith,
>>>>>
>>>>> It will be in whatever folder pymol is launched from. If you launched
>>>>> pymol from a specific place, it will be that folder. If not, it might be
>>>>> in the system files for pymol, which will depend on your operating system
>>>>> and architecture.
>>>>>
>>>>> Shane
>>>>>
>>>>>
>>>>> Shane Caldwell
>>>>> McGill University
>>>>>
>>>>> On Fri, Nov 27, 2015 at 12:59 AM, Smith Liu <smith_liu...@163.com> wrote:
>>>>> Dear All，
>>>>>
>>>>> Once a molecule displayed in pymol, first I input command "orient", then
>>>>> I input command "run save_trannsforme.py all, newpdb.pdb", I cannot get
>>>>> the oriented newpdb.pdb.
>>>>>
>>>>> Will you please show me how to get the oriented newpdb.pdb?
>>>>>
>>>>> Smith
>>>>>
>>>>>
>>>>>
>>>>> At 2015-11-26 18:58:48, "Spencer Bliven" <spencer.bli...@gmail.com> wrote:
>>>>> Smith–
>>>>>
>>>>> The code is intended to be saved to a file ("save_transformed.py") and
>>>>> then loaded into pymol using `run /path/to/save_transformed.py`. There's
>>>>> some general info on running pymol scripts: Simple_Scripting
>>>>> Running_Scripts
>>>>>
>>>>> The script defines a new command which can be run e.g. `save_transformed
>>>>> , `. You don't have to replace anything in the script
>>>>> yourself.
>>>>>
>>>>> Note that the save_transformed command modifies the object it's run on,
>>>>> so you might want to run it on a backup copy by first calling `create
>>>>> _backup, `
>>>>>
>>>>> -Spencer
>>>>>
>>>>> On Thu, Nov 26, 2015 at 8:33 AM, Smith Liu <smith_liu...@163.com> wrote:
>>>>> Dear All,
>>>>>
>>>>> For get view, we get something like
>>>>>
>>>>> set_view (\
>>>>>0.999876618, -0.000452542, -0.015699286,\
>>>>>0.000446742,0.99821, -0.000372844,\
>>>>>0.015699454,0.000365782,0.999876678,\
>>>>>0.0,0.0, -150.258514404,\
>>>>>11.842411041, 20.648729324,8.775371552,\
>>>>>118.464958191, 182.052062988,0.0 )
>>>>>
>>>>> For save trasformed pdb file, we need sonething like
>>>>>
>>>>> ttt = [m[0], m[1], m[2], 0.0,
>>>>>m[3], m[4], m[5], 0.0,
>>>>>m[6], m[7], m[8], 0.0,
>>>>>0.0, 0.0, 0.0, 1.0]
>>>>> Will you please show me how to replace m[0], m[1] from what we get by
>>>>> get_view? Which item is which item?
>>>>>
>>>>> In addition, for the save_transformed.py, the last sentence is
>>>>> "cmd.extend('save_transformed',save_transformed)". Should we replace the
>>>>> second save_transformed with something, for example *.pdb? Ortherwise how
>>>>> to get the output modified PDB?
>>>>>
>>>>>
>>>>> I am looking forward to getting a reply from you.
>>>>>
>>>>> Smith
>>>>>
>>>>>
>>>>>
>>>>> At 2015-11-26 14:24:15, "Andreas Forster" <docandr...@gmail.com> wrote:
>>>>> http://www.pymolwiki.org/index.php/Modeling_and_Editing_Structures
>>>>>
>>>>>
>>>>> Andreas
>>>>>
>>>>>
>>>>> On Thu, Nov 26, 2015 at 2:24 AM, Smith Liu <smith_liu...@163.com> wrote:
>>>>> Dear Shane,
>>>>>
>>>>>
>>>>> get_view is a nice command. Is any way to change the original PDB based
>>>>> on what we get by set_view to get the new pdb?
>>>>>
>>>>> Smith
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> At 2015-11-26 03:54:32, "Shane Caldwell" <shane.caldwel...@gmail.com>
>>>>> wrote:
>>>>> Hi Smith,
>>>>>
>>>>> You can type
>>>>>
>>>>> >get_view
>>>>>
>>>>> and copy the output into a txt file for later use. The output set_view
>>>>> command will return the window to the same camera settings
>>>>>
>>>>> Shane
>>>>>
>>>>> Shane Caldwell
>>>>> McGill University
>>>>>
>>>>> On Tue, Nov 24, 2015 at 9:45 PM, Smith Liu <smith_liu...@163.com> wrote:
>>>>> Dear All,
>>>>>
>>>>> Suppose the original PDB was not oriented. Once we have it oriented by
>>>>> pymol, is any way we can save the new PDB oriented?
>>>>>
>>>>> Smith
--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.
--
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Re: [PyMOL] can we clone representation?
Hi Albert,
This functionality is not built-in to PyMOL, but is rather simple to implement
with a script. See attachment. The script adds a "clone_reps" command which
takes two selections (just like the VMD plugin).
Example:
run clonerep.py
fetch 1a00 1hbb, async=0
as cartoon, 1a00
spectrum count, rainbow, 1a00
# clone color and representations
clone_reps 1a00, 1hbb
# clone only color
clone_reps 1a00, 1hbb, props=color
# clone from chain A to all other chains
clone_reps 1a00 & chain A, all, match=resi name
Cheers,
Thomas
from pymol import cmd
@cmd.extend
def clone_reps(fromsele, tosele, match='chain resi name', props='reps color'):
'''
DESCRIPTION
Clone color and representation from one selection to another.
ARGUMENTS
fromsele = str: source selection
tosele = str: target selection
match = str: space separated list of atom identifiers to use for
matching the two selections {default: chain resi name}
props = str: space separated list of atom properties to clone
{default: reps color}
EXAMPLE
fetch 1a00 1hbb, async=0
as cartoon, 1a00
spectrum count, rainbow, 1a00
clone_reps 1a00, 1hbb
SEE ALSO
scene, iterate, alter
'''
match = '(' + ','.join(match.split()) + ')'
props = '(' + ','.join(props.split()) + ')'
space = {'_lookup': {}}
cmd.iterate(fromsele, '_lookup[' + match + '] = ' + props, space=space)
cmd.alter(tosele, props + ' = _lookup.get(' + match + ', ' + props + ')', space=space)
cmd.rebuild(tosele)
On 21 Nov 2015, at 10:04, Albert <mailmd2...@gmail.com> wrote:
> Hello:
>
> I've shown an object as cartoon and displaced sticks with various
> colors. I am just wondering, can we clone all representation from object
> 1 to object 2 with some command in Pymol? As far as I known, this is
> possible in VMD:
>
> http://www.ks.uiuc.edu/Research/vmd/plugins/clonerep/
>
> Thank you very much
>
> Albert
--
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PyMOL Principal Developer
Schrödinger, Inc.
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Re: [PyMOL] default fetch format
Hi Albert,
Unfortunately the default fetch type can't be configured. But you can override
the fetch command. Example which you could place in your ~/.pymolrc file:
python
from pymol import cmd
def fetchpdb(*args, **kwargs):
if 'type' not in kwargs:
kwargs['type'] = 'pdb'
return cmd.fetch(*args, **kwargs)
cmd.extend('fetch', fetchpdb)
python end
However, if you don't have a compelling reason to work with PDB instead of
mmCIF, then I recommend to give the new mmCIF default a try.
Cheers,
Thomas
On 19 Nov 2015, at 13:47, Albert <mailmd2...@gmail.com> wrote:
> Hello:
>
> I noticed that if we run command:
>
> fetch 2ac1
>
> to get PDB into pymol in Version 1.8.0, it downloaded .cif file by
> default. I am just wondering is it possible to change the default format
> as .pdb file?
>
> thanks a lot
>
> Albert
--
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PyMOL Principal Developer
Schrödinger, Inc.
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Re: [PyMOL] default fetch format
Hi Albert, > May I ask is there any superior features of mmCIF format against PDB format? It solves all the identifier limitations of the PDB format, like number of chains, number of residues, and number of atoms. Besides that, the PDB format will be phased out by the wwPDB in favor of the mmCIF format, which is the new standard since 2014. See also http://mmcif.wwpdb.org/docs/faqs/pdbx-mmcif-faq-general.html Cheers, Thomas -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. -- ___ 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 1.8.0.0 requires ZLIB 1.2.3.5?
Hi Roger, Please run ./setup.sh which will activate a more recent libz library which is bundled with the build. Please also see the INSTALL.txt for similar troubleshooting solutions. Cheers, Thomas On 19 Nov 2015, at 11:01, Roger Rowlett <rrowl...@colgate.edu> wrote: > Pymol 1.8.0.0 (64 bit linux) is throwing an error about a ZLIB > requirement (v 1.2.3.5). The latest Ubuntu 12.04 LTS version through > apt-get is 1.2.3.4. Is there supposed to be a local version of zlib.1.so > in the pymol install package? > > ___ > Roger S. Rowlett > Gordon & Dorothy Kline Professor > Department of Chemistry > Colgate University > 13 Oak Drive > Hamilton, NY 13346 > > tel: (315)-228-7245 > ofc: (315)-228-7395 > fax: (315)-228-7935 > email: rrowl...@colgate.edu > > ------ -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. -- ___ 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 of pymol 1.8
Hi Albert, It seems that you have a lot of plugins installed, you likely don't need them or maybe don't even know that they are installed. Please open the Plugin Manager from the "Plugin" menu and uncheck "Load on startup" for all plugins that you don't need or don't know what they do. Cheers, Thomas On 18 Nov 2015, at 17:29, Albert <mailmd2...@gmail.com> wrote: > Hi Thomas: > > thanks a lot for helpful advice. > > HOwever, I got something new warnings: > > No module named cPluginManager > Unable to initialize plugin 'xPyder' (pmg_tk.startup.xPyder). > No module named backend_wxagg > Unable to initialize plugin 'mtsslPlotter' (pmg_tk.startup.mtsslPlotter). > > I google it, and cannot find any helpful information > > > thanks again > > ALbert > > > On 11/18/2015 11:16 PM, Thomas Holder wrote: >> Hi Albert, >> >> These messages come from third-party plugins that you have installed, see: >> http://pymolwiki.org/index.php/MtsslDock >> http://pymolwiki.org/index.php/MtsslTrilaterate >> >> Cheers, >> Thomas -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. -- ___ 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 1.8.0 released
Greetings, We are happy to announce the release of PyMOL v1.8.0! Official PyMOL sponsors can download ready-to-use installers from http://pymol.org/download . The open-source code has been pushed to sourceforge svn (revision 4142). This release finalizes our mmCIF support roadmap. Important: We changed the default of the “ignore_case” setting to off. This setting has effect on the selection language and atom sorting. While it’s convenient to select chain A with “chain a”, it’s not practical when you work with large structures and run out of uppercase chain identifiers (note: PyMOL does support multi-letter chain identifiers, but this doesn’t help when you want to export to PDB format). Be prepared that your old scripts might depend on ignore_case, in that case either fix them, or put an “set ignore_case” at the top of the script or in your pymolrc file. The “fetch” command now by default downloads mmCIF files (type=cif). This release fixes the issues with ATI R9 graphics cards on OS X. Find the complete release notes on: http://pymol.org/features We welcome any feedback and bug reports. Cheers, - The PyMOL Team at Schrödinger -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. -- ___ 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 of pymol 1.8
Hi Albert, These messages come from third-party plugins that you have installed, see: http://pymolwiki.org/index.php/MtsslDock http://pymolwiki.org/index.php/MtsslTrilaterate Cheers, Thomas On 18 Nov 2015, at 17:08, Albert <mailmd2...@gmail.com> wrote: > Hello: > > I've installed the open source code version pymol 1.8 in my Linux OS. > > > However, when I start pymol, it always showed the following messages: > > No module named tkintertable.Tables > Unable to initialize plugin 'mtsslDockGui' (pmg_tk.startup.mtsslDockGui). > No module named wx > Unable to initialize plugin 'mtsslTrilaterate' > (pmg_tk.startup.mtsslTrilaterate). > > I am just wondering how can we solve the problem? I've already installed > python PMW in my machine. > > thank you very much. > > Albert -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. -- ___ 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] 1.7.6.6 does not display a 1.7.4.4 .pse ifle.
Hi Mark,
Thanks for the bug report. The stack trace is sufficient for us to reproduce
the problem, no need to send the file.
Checking the code revealed: PyMOL never supported spaces in scene names. All
versions before 1.7.6 silently ignored the problem but also couldn't restore
the scene.
We can fix this in the next version to not throw an error.
Workaround: Open your file in 1.7.4, rename the scenes to not contain spaces,
and save it again. Then 1.7.6 should load it without problems.
Cheers,
Thomas
On 05 Nov 2015, at 20:20, Mark A Saper <sa...@umich.edu> wrote:
> I guess this is for Schrodinger representative.
>
> I have a .PSE file (21.8 Mbyte) that does not open properly in 1.7.6.6. The
> file has about 10 scenes in it.
>
> Here are the errors:
> Executive: Loading version 1.744 session...
> Selector-Error: Invalid selection name "on".
> ?_scene_EcLpoA HTH1 on 4gpk HTH2 with 4gpk peptide_lines<--
> Traceback (most recent call last):
> File "/Applications/MacPyMOL.app/Contents/pymol/modules/pymol/__init__.py",
> line 262, in exec_deferred
>cmd.load(a, quiet=0)
> File "/Applications/MacPyMOL.app/Contents/pymol/modules/pymol/importing.py",
> line 912, in load
>partial=partial,steal=1)
> File "/Applications/MacPyMOL.app/Contents/pymol/modules/pymol/importing.py",
> line 96, in set_session
>if not apply(a,(session,),{'_self':_self}): # don't stop on errors...try
> to complete anyway
> File "/Applications/MacPyMOL.app/Contents/pymol/modules/pymol/viewing.py",
> line 1296, in session_restore_scenes
>_convert_legacy_scene(key, data, _self)
> File "/Applications/MacPyMOL.app/Contents/pymol/modules/pymol/viewing.py",
> line 1341, in _convert_legacy_scene
>_self.show(rep_name, "?_scene_" + key + "_" + rep_name)
> File "/Applications/MacPyMOL.app/Contents/pymol/modules/pymol/viewing.py",
> line 593, in show
>if _self._raising(r,_self): raise QuietException
> pymol.parsing.QuietException: 0x110905f38>
>
> Suggestions? Do you want to examine the file? If so contact me off list.
>
> -Mark
> _
> Mark A. Saper, Ph.D.
> Associate Professor of Biological Chemistry, University of Michigan
> Currently on sabbatical:
> Laboratory of Susan Buchanan, Ph.D.
> NIDDK, National Institutes of Health, Bethesda, MD 20892-8030
> sa...@umich.edu mobile (734) 276-6505
--
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PyMOL Principal Developer
Schrödinger, Inc.
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Re: [PyMOL] Common atoms in two selections (and their indices)
Hi Tsjerk, Spencer, Osvaldo,
cmd.get_raw_alignment() might be what you are looking for.
http://pymolwiki.org/index.php/Get_raw_alignment
Cheers,
Thomas
On 27 Oct 2015, at 12:49, Spencer Bliven <spencer.bli...@gmail.com> wrote:
> Tsjerk–
>
> You might be able to extract the ids of the aligned residues from an
> alignment object:
>
> cmd.align(sele1,sele2copy,object="aln")
> [a.id for a in cmd.get_model('aln').atom]
>
> Since the alignment is sequential, I think this should contain all the
> aligned atoms from sele1 concatenated with the aligned atoms from sele2.
> However, as far as I know the internals of the alignment objects aren't
> documented, so I'm not sure if this can be relied upon.
>
> -Spencer
>
>
> On Tue, Oct 27, 2015 at 12:22 PM, Tsjerk Wassenaar <tsje...@gmail.com> wrote:
> Hi Osvaldo,
>
> Probably that's the trick, although I'd need the indices, but that's simple
> enough.
> The 'equivalence' one is still standing though :)
>
> Thanks,
>
> Tsjerk
>
> On Tue, Oct 27, 2015 at 11:44 AM, Osvaldo Martin <aloctavo...@gmail.com>
> wrote:
> So, you want to know the best way to do this?
>
> Z = [at_x for at_x in X for at_y in Y if at_x.id == at_y.id
> ]
>
> Or am I still not getting it right?
>
> Cheers,
> Osvaldo.
>
> On Tue, Oct 27, 2015 at 10:56 AM, Tsjerk Wassenaar <tsje...@gmail.com> wrote:
>
>
>
> Hi Osvaldo,
>
> I could have been more clear I guess. First of all, let's say I have obtained
> the atom list of a selection:
>
> X = cmd.get_model(selection1).atom
>
> I'm doing stuff with that (PCA, to be exact), but now I want to display the
> result only for a subselection. Probably getting the intersection of the
> selections and then check which atoms there match with the original selection
> is an approach. The question there is what the best way is for checking
> identity of the atoms.
>
> The second issue is when there is no intersection of the selections, but
> there may be correspondence, as in alignment.
>
> Thanks for thinking along,
>
> Tsjerk
>
> On Tue, Oct 27, 2015 at 10:44 AM, Osvaldo Martin <aloctavo...@gmail.com>
> wrote:
> Hi Tsjerk,
>
> Do you mean something like this?
>
> cmd.index("sel_1 and sel_2")
>
> I do not get the differences between your two cases. Whats the difference
> between “atoms which are both in selection 1 and 2” and “matching atoms in
> the two selections”
>
> Cheers,
>
> Osvaldo.
>
> On Mon, Oct 26, 2015 at 10:33 AM, Tsjerk Wassenaar <tsje...@gmail.com> wrote:
>
>
>
>
> Hi Thomas e.a.,
>
> Given two selections, would there be an easy way to
>
> 1. find the atoms which are both in selection 1 and 2, and the indices of
> those in the selections
>
> and
>
> 2. find the matching atoms in the two selections, like align does, and the
> indices of those in the selections
>
> Thanks,
>
> Tsjerk
>
> --
> Tsjerk A. Wassenaar, Ph.D.
--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.
--
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Re: [PyMOL] CGO segmentation fault
Hi Tsjerk, Thanks for reporting, we'll look into that. Cheers, Thomas On 23 Oct 2015, at 05:14, Tsjerk Wassenaar <tsje...@gmail.com> wrote: > Hi Thomas, > > Not sure if I ever reported this already, but when cmd.load_cgo gets an > argument that is not a list of values, Pymol (1.7.4.0 incentive, Mac) halts > with a segmentation fault. I know it's my bad for feeding a still nested > list, but a segmentation fault is a harsh way of complaining :) > > Cheers, > > Tsjerk > > -- > Tsjerk A. Wassenaar, Ph.D. -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. -- ___ 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] pdbml
Hi Arthur, The script I sent you earlier had one Incentive PyMOL specific line and won't work in Open-Source PyMOL unless you delete that line. My apologies. However, if you are compiling the latest code from SVN you don't need the script, I already have incorporated it into the code base! Simply load files with .xml or .pdbml extension. I have to add that loading 4v50 in PDBML format into PyMOL is a rather bad idea. PDBML is utterly bloated, the uncompressed file for 4v50 is over 300MB, and the in-memory xml representation will explode into the gigabytes. You should really use mmCIF format instead, PyMOL loads 4v50.cif in 2 seconds. Cheers, Thomas On 22 Oct 2015, at 12:38, Arthur Zalevsky <aozalev...@fbb.msu.ru> wrote: > Hi Thomas! > > I've tried your parser with pymol 1.4.1 from ubuntu 12.04 repos and > freshly compiled 1.7.7.2 from svn with no luck at all. I've tried to > load PDB ID 4V50 (full E.coli ribosome). Pymol simply hangs with 100% > cpu usage. > > From 1.4.1 i've got following traceback (after i left it overnight): > > Traceback (most recent call last): > File "/usr/lib/python2.7/dist-packages/pymol/parser.py", line 254, in > parse > self.result=apply(layer.kw[0],layer.args,layer.kw_args) > File "/home/domain/silwer/Downloads/load_pdbml.py", line 80, in > load_pdbml > atom.properties['entity_id'] = child.text or '' > File "/usr/lib/python2.7/dist-packages/chempy/__init__.py", line 59, > in __getattr__ > raise AttributeError(attr) > AttributeError: properties > > Any help would be appreciated. > > > Regards, > Arthur > > > On 25.09.2015 01:50, Thomas Holder wrote: >> Hi Arthur & Jerome, >> >> I wrote a basic PDBML importer for PyMOL, see attached script which >> adds a "load_pdbml" command. I meant to assess the complexity of such >> a project and ended up writing the entire thing. So far, this only >> reads atoms and symmetry information. If you find this useful we can >> include that in the next PyMOL release. >> >> Cheers, >> Thomas >> >> >> >> On 23 Sep 2015, at 03:27, Arthur Zalevsky <aozalev...@fbb.msu.ru> >> wrote: >> >>> Sorry for bumping old thread, but is support for pdbml still >>> unimplemented? In such case i think it's a good project for our >>> students. >>> >>> Regards, >>> Arthur >>> >>>> From: Thomas Holder <speleo3@us...> - 2013-12-02 19:23:18 >>>> Hi Jerome, >>>> >>>> I think the simple reason is that nobody ever wrote a PDBML parser >>>> for >>>> PyMOL. Is that a good reason? >>>> >>>> Cheers, >>>> Thomas >>>> >>>>> On 28 Nov 2013, at 13:21, Jerome BENOIT <g6299304p@...> wrote: >>>>> Hello List, >>>>> >>>>> is there any good reason why PyMOL can not read PDBML data files ? >>>>> >>>>> Cheers, >>>>> Jerome -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. -- ___ 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
