Re: [PyMOL] ColorByRMSD script

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 Bau

Re: [PyMOL] ColorByRMSD script

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

Re: [PyMOL] H bonds

Hi Amali, For adding hydrogens, I have found that PyMOL does an OK job normally, but if you need more accurate placement of hydrogens, I can recommend using Reduce. http://kinemage.biochem.duke.edu/software/reduce.php HTH, Matthew Baumgartner On 11/11/2015 02:06 AM, Osvaldo Martin wrote

Re: [PyMOL] Stacking Interactions

What I've done before is to draw a line between two pseudo-atoms placed at the center of each ring. HTH, Matthew Baumgartner On 11/10/2015 02:08 AM, Albert wrote: I think the major concern is how Pymol depicts the pi-pi stacking Of course we can identify such interaction immediate

Re: [PyMOL] PyMOLWiki: Quick Update

Hi, I googled for the pymol wiki to check it out and I saw a message in the search results that says: "This site may be hacked." Do you know why that is? On 09/09/2015 07:40 AM, Osvaldo Martin wrote: Hi Jason, Thanks very much for the effort! Now the Wiki is far more useful than before! I

[PyMOL] Logging commands errors

Hi, I'm using pymol 1.7.4 from the SVN. When I use the File > Log... feature to log the commands that I use to a file the output commands are not recognized when I do File > Run... in a new session. To reproduce: Open a new pymol session. File > Log... "log.pml" Change the background to white.

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

Hi, I had problems with the retain order setting as well. The autodock vina pulgin turns it on. Unload the plugin to fix it, or manually set it after plugins are loaded. Matt On 4/22/15 8:56 PM, Thomas Holder wrote: > Hi Spencer, > > please check your retain_order setting, it should be off (de

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

pdate past 1.7.4. On 4/8/15 2:38 PM, Thomas Holder wrote: > Hi Matt, > > PyMOL session files are in general not "forward compatible". > > See for example: > https://sourceforge.net/p/pymol/mailman/message/31070268/ > > Cheers, >Thomas > > On 08 Apr 201

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

Hi, I'm running pymol 1.7.5.0 (r4114) from the SVN and I can't load pse files created in 1.7.5.0 in any older version of Pymol. When I create a pymol session file where I fetch a PDB, show as cartoons, and save the session (see https://dl.dropboxusercontent.com/u/22529812/test.pse) and open i

[PyMOL] Compile Errors on SVN 4111

Hi, I'm getting compile errors on the latest SVN build (4111). Any help would be appreciated. Thanks, Matt Baumgartner $ sudo python setup.py build -j 1 fatal: Not a git repository (or any parent up to mount point /home) Stopping at filesystem boundary (GIT_DISCOVERY_ACROSS_FILESYSTEM not set). r

Re: [PyMOL] Problem with h_add hydrogens in sequence viewer

ens in sequence viewer <http://ehc.ac/p/pymol/mailman/message/30647188/>* From: Thomas Holder - 2013-03-26 13:06:08 Hi Matt, use the "sort" command after adding atoms: PyMOL> h_add 1ycr PyMOL> sort See also: http://pymolwiki.org/index.php/Sort Cheers, Thomas Matthe

[PyMOL] Assign secondary structure on group

Hi, I'm using pymol 1.7.4.0. The A> assign sec. struct. command doesn't seem to work when you call it on a group. It works fine on the objects in the group individually, but it doesn't apply the command to the objects when called from a group. Thanks, Matt Baumgartner --

Re: [PyMOL] what color was used?

Hi Adam, You can retrieve them using the iterate method. See: http://pymolwiki.org/index.php/Color#Getting_Atom_Colors HTH, Matt Baumgartner On 2/27/2015 4:28 PM, H. Adam Steinberg wrote: I am creating a new PyMOL session and I have to match the colors that someone else used in a different Py

Re: [PyMOL] Pymol wiki search is not working

Yes, I've been having this problem for a while. I contacted Jason Vertrees about it a while ago, but never heard back from him. However, when I search "color" (an exact article title) I actually do go to the page. In addition, if you search for a something that doesn't have a page in the se

[PyMOL] Bug in Save Molecule dialog box

Hi, I've discovered a (relatively minor) bug in the Save Molecule... dialog box. This happened because I always have tons of windows up on multiple monitors and it got lost. To reproduce: Go to File > Save Molecule... Don't close the window, and do it again Go to File > Save Molecule... Now you

Re: [PyMOL] Alpha setting of CGO spheres

8, -28.181, -15.016, 0.5] cmd.load_cgo(sph2, "sph2", 1) Cheers, Osvaldo. On Tue, Jan 20, 2015 at 7:19 PM, Matthew Baumgartner <mailto:mp...@pitt.edu>> wrote: Hi, I'm having some trouble using CGO spheres. When I create one, it is not visible in the viewer

[PyMOL] Alpha setting of CGO spheres

Hi, I'm having some trouble using CGO spheres. When I create one, it is not visible in the viewer, although there is an (apparently empty) object in the object pane. It is somewhat confusing because with some parameters the spheres ARE visible when ray tracing, although they are still not visi

Re: [PyMOL] Scripting attempts

aves to Image0001.png just fine in the correct location without that directory error. On 7/01/2015 2:11 AM, Matthew Baumgartner wrote: I think that is because that the directory there doesn't exist. I think I made a copy paste error of your directory structure. Please double check, but f

Re: [PyMOL] Scripting attempts

s\Chem Structures\PDBs\2\2HYY - > imatinib\PyMOL movie\Image{}.png".format(str(i).zfill(4)), dpi=300, > ray=1) > > > On 7/01/2015 1:33 AM, Matthew Baumgartner wrote: >> Is it in your for loop? >> >> for i in range(2,61): >> rotate y, 6 >>

Re: [PyMOL] Scripting attempts

> parse > exec(layer.com2+"\n",self.pymol_names,self.pymol_names) > File "", line 1, in > NameError: name 'i' is not defined > > On 7/01/2015 1:03 AM, Matthew Baumgartner wrote: >> cmd.png("C:\Users\Brenton\Documents\C

Re: [PyMOL] Scripting attempts

ScenePNG-Error: error writing ""C:\Users\Brenton\Documents\Chem > Structures\PDBs\2\2HYY - imatinib\PyMOL > movie\Image{}.png".format(str(i).zfill(4)).png"! Please check > directory... > > Thanks for your time, > Brenton > > On 7/01/2015 12:33 AM, Mat

Re: [PyMOL] Selecting specific ligands for colouring

Hi, I just wanted to chime in and add to what Folmer said. Your selection syntax was close, but not quite correct, you are missing a slash. Following you example, you would do /2hyy//A/600 where 600 is the residue id of the ligand. But in general, I would recommend using the syntax that Folmer

Re: [PyMOL] PyMOL png movie creation from command line

Hi, When you ray trace you can specify the dimensions of the resulting image in pixels, eg: ray 600,800 You can also set the resolution when saving the png file: png image.png, dpi=300 HTH, Matt Baumgartner On 01/06/2015 12:39 AM, Brenton Horne wrote: > Hi, > > I'd like to know how to create a

Re: [PyMOL] set size nb_spheres

Hi, Just to chime in, you might need to call 'sort' and/or 'rebuild' after using the alter command to see the changes. Matt Baumgartner On 11/20/2014 08:20 AM, Osvaldo Martin wrote: Hi Erica, I think something like: alter name ca, vdw=10 should help. Change "10" for the value you want. Be

Re: [PyMOL] Optimize plugin throws "NameError: global name 'ob' is not defined"

Hi, Can you check to see if the python bindings are compiled openbabel? On the bash command line, run the command 'python' to get an interactive shell and then run 'import openbabel'. Matt On 11/12/2014 07:14 AM, Douglas Houston wrote: > Hi all, > > I installed Optimize.py, now when I start Pym

Re: [PyMOL] Access API without the GUI

Hi Doug, Check out these pages on integrating PyMOL into a python script. Essentially you will write a python script that imports pymol. From there you can do things like load objects, align them, or anything else. http://www.pymolwiki.org/index.php/Python_Integration http://www.pymolwiki.org/

Re: [PyMOL] run a pymol command using the terminal

Hi Cedric, Check out the "Launching PyMOL from Python programs" section from here: http://www.pymolwiki.org/index.php/Python_Integration HTH, Matt On 10/24/2014 02:02 PM, Cedric wrote: > Hi, > > I know how to write small scripts in pymol and then call them within pymol. > > But I am not sure ho

Re: [PyMOL] Crash on launch with r4098

doing incremental builds). > > Thanks, >Thomas > > On 20 Oct 2014, at 19:10, Matthew Baumgartner wrote: > >> Hi, >> I updated pymol to r4098 and now it crashes on launch. I'm assuming that >> it was something I did, but I can't figure out what. >> Th

[PyMOL] Crash on launch with r4098

Hi, I updated pymol to r4098 and now it crashes on launch. I'm assuming that it was something I did, but I can't figure out what. Thanks for your help, Matt $ pymol Traceback (most recent call last): File "/usr/local/lib/python2.7/dist-packages/pymol/__init__.py", line 71, in import pym

Re: [PyMOL] align and RMSD calculation

Hi, You may want to check out the rms_cur command. http://www.pymolwiki.org/index.php/Rms_cur HTH, Matt Baumgartner On 10/03/2014 02:28 PM, Nat Echols wrote: On Fri, Oct 3, 2014 at 11:17 AM, PC > wrote: Sorry its me again. Can someone tell me where I can f

Re: [PyMOL] selecting all instead of just one aa

s into that mode? Just curious. /Regards,/ // /Vaheh/ /8-5851/ *From:*Matthew Baumgartner [mailto:mp...@pitt.edu] *Sent:* Thursday, September 25, 2014 2:19 PM *To:* pymol-users@lists.sourceforge.net *Subject:* Re: [PyMOL] selecting all instead of just one aa Hi, Go to the Mouse Menu

Re: [PyMOL] selecting all instead of just one aa

Hi, Go to the Mouse Menu > Selection Mode > Residues Matt Baumgartner On 09/25/2014 01:48 PM, Oganesyan, Vaheh wrote: All, During my PyMOL session I’ve “accidentally” entered into a mode when by clicking one amino acid whole chain becomes selected. How can I turn it off? It is a quite elabo

Re: [PyMOL] AutoDock Vina Plugin

Hi, Did you try restarting pymol? Also, check your startup directory to see if it was moved there. On unix, it's ~/.pymol/startup/ you should see the autodock.py script there. HTH, Matt On 09/25/2014 11:56 AM, Joseph Brown wrote: I am trying to install the autodock vina plugin for PyMOL. I

Re: [PyMOL] measure angles in programming

Hi, you can just use the 'angle' command. cmd.angle('angle1', 'start_point', 'end_point', a) To print the b-factor you can use the iterate command (http://www.pymolwiki.org/index.php/Iterate) cmd.iterate('(a)', 'print b') HTH, Matt Baumgartner On 09/24/2014 06:35 PM, rainfieldcn wrote: > Hi al

Re: [PyMOL] Access to pymol commands from the terminal

osed tar.pdb as the separate pdb (the TMalign is not good because it produce pdb with both merged layers (and its backbone trace only) as the result if -o flagg is provided) Kind regards, Gleb 2014-09-04 16:57 GMT+02:00 Matthew Baumgartner <mailto:mp...@pitt.edu>>: You can use sed

Re: [PyMOL] Access to pymol commands from the terminal

Use the -h flag with grep to suppress the filename. Also, you don't need to pipe to cat, you can write directly to the file. grep -h '^\(ATOM\|HETATM\|END\)' tarr_se.pdb lipids.pdb > merged.pdb On 09/04/2014 10:38 AM, James Starlight wrote: ..and one question about grep (really didn't find

Re: [PyMOL] python script to define an extra pymol function and then use it during the same session

Hi, When you call cmd.extend(), it does not add the function to pymol.cmd. Just call it directly: Change pymol.cmd.align_all_to_all() to align_all_to_all() You may need to import it if you haven't already (and make sure it is in the PYTHONPATH). HTH, Matt Baumgartner On 09/02/2014 10:38 AM

Re: [PyMOL] Problem with finding polar contacts

gt; > On 27 Aug 2014, at 10:30, Matthew Baumgartner wrote: > >> Hi, >> I ran into a bug with the find polar contacts function (distance with >> mode=2) today. The problem arises when I was trying to find the hydrogen >> bonds between a ligand and a receptor that had bee

[PyMOL] Problem with finding polar contacts

Hi, I ran into a bug with the find polar contacts function (distance with mode=2) today. The problem arises when I was trying to find the hydrogen bonds between a ligand and a receptor that had been processed with reduce (http://kinemage.biochem.duke.edu/software/reduce.php). A bug/feature of r

Re: [PyMOL] segfault when loading sdf files

report. We will fix this as soon as possible. >> >> Cheers, >> Thomas >> >> On 23 Jul 2014, at 13:06, Matthew Baumgartner wrote: >>> Hi, I am using pymol from the SVN, and I have run into a problem when >>> using revision 4083. >>> When loadin

[PyMOL] segfault when loading sdf files

Hi, I am using pymol from the SVN, and I have run into a problem when using revision 4083. When loading an sdf file of small molecules, pymol segfaults with the following error: /usr/local/bin/pymol: line 3: 29872 Segmentation fault (core dumped) "/usr/bin/python" "/usr/local/lib/python2.

Re: [PyMOL] Faster installation of plugins during development

; if you have a menu item for your GUI, that might still launch the old (not > reloaded) version. > > Cheers, >Thomas > > On 18 Jul 2014, at 14:12, Matthew Baumgartner wrote: > >> Hi, >> It is possible for users to run without a GUI, but it has a GUI and when I &

Re: [PyMOL] Faster installation of plugins during development

http://kong.med.nyu.edu/ On Jul 18, 2014, at 1:47 PM, Matthew Baumgartner <mailto:mp...@pitt.edu>> wrote: Hi, Thank you for you suggestions. However, I was looking for a way to do it without restarting pymol if possible. Currently, restarting is the fastest solution, but it still

Re: [PyMOL] Faster installation of plugins during development

Just beware: removing a installed plugin may physically delete the file. So be sure to backup your script should you decide to remove scripts or paths that were added to the Plugin Manager. Hope this will relieve some of the frustration. Cheers, Andreas On Fri, Jul 18, 2014 at 5:41 PM, Matthew Bau

[PyMOL] Faster installation of plugins during development

Hi, So i am working on a pymol plugin (shameless plug ) and I have been annoyed how difficult it is to reinstall my plugin so I can see the effect of the changes I have made. Currently, the process is: Plugin Menu > Plugin Manager > Install New

Re: [PyMOL] Script from command line invoking plugins

Hi, If you don't need the GUI you can access your command using the extend command. In your script, put something like: from pymol import cmd def foo(bar): print bar cmd.extend('foo', foo) Then in pymol first use the 'run' command to have pymol read your script, and then call the funct

[PyMOL] Pymol and Oculus Rift

Hi, Has anyone tried to get pymol working with the Oculus Rift? I just got my hands on one and I think it would be awesome to use it with pymol? Thanks, Matthew Baumgartner -- -- CenturyLink Cloud: The Leader in

[PyMOL] Accessing progress bar

Hi, My google-fu didn't find anything, but is it possible to access the progress bar in pymol (the one that comes up when ray tracing) in a script? I have a script that is a little long running and it would benefit from giving users feedback on progress. Thanks, Matt -- ---

Re: [PyMOL] restricting selection to the current frame

to specify the state. > > So if the waters of interest are in state 1,40: > > python > for i in range(1,41): > cmd.select("wat_"+i,"byres in within 6 of > ",state=i) > python end > > J > > >> 'sele wats, byres res >> WAT in

[PyMOL] restricting selection to the current frame

Hi, Is it possible to force a selection to only apply to the specific frame rather then across frames? I'm running in to a problem where I have some (~40) frames from an explicit solvent MD that I want to look at. What I want to do is look at water molecules around a specific residue at each fra

Re: [PyMOL] Problems with Pymol v 1.6.0.0

Hi, Adding to thread. I'm using pymol 1.6 (built from svn yesterday) on Ubuntu 13.04. I've noticed that the selection indicators are not working properly. Steps to reproduce: #launch ignoring the config file pymol -k #in pymol >fetch 1YCR Then open sequence viewer and select a range of residue

[PyMOL] Possible hydrogen addition bug

Hi, I may have found a bug in the way pymol interprets connectivity of atoms. I noticed this in one pdb structure that I am working with 1RV1. Steps to reproduce: fetch 1RV1 #extract one of the ligands to it's own object extract 'lig', /1RV1//A/110 #add hydrogens h_add lig Now look at atom C2

[PyMOL] Problem with h_add hydrogens in sequence viewer

Hi, When I fetch a new structure (1YCR, for example) then run 'h_add 1ycr' the hydrogens are added to the structure as expected, but they are put in the sequence viewer as their own residue with the same chain. This is problematic for several reasons, one is that it breaks selections, when I cl

Re: [PyMOL] PyMOL script with a parameter ?

Hi Tim, You can use two dashes on the command line, like: pymol -r get_neighbors.py -- ALA And then access them using sys.argv in your script. For example: save the following as tmp_pymol.py and run: 'pymol -r tmp_pymol.py -- ALA' ( without quotes) from pymol import cmd import sys def

Re: [PyMOL] wire-mesh spheres?

something in the meantime that resembles a mesh sphere (but is > not exact) you can create your CGO spheres and then do, > > set cgo_debug, 1 > > No, it won't ray trace like that either -- they'll be converted to full > spheres. > > Cheers, > > -- Jason > > &g

Re: [PyMOL] wire-mesh spheres?

23, 2012 at 4:16 PM, Matthew Baumgartner wrote: Hi, Is it now possible to have wire mesh cgo object spheres in pymol? I found this thread from a while ago (2004) but googleing, I didn't find anything more recent. The one sort of work around that I though of was to create pseudo-atoms

Re: [PyMOL] wire-mesh spheres?

Hi, Is it now possible to have wire mesh cgo object spheres in pymol? I found this thread from a while ago (2004) but googleing, I didn't find anything more recent. The one sort of work around that I though of was to create pseudo-atoms and somehow modify their radius and then show them as mesh.

[PyMOL] Importing simplejson in pymol on OSX

Hi, I wrote a short script that I am going to use in pymol. I need to parse a json file and then display the contents in some manner. It works just fine in Ubuntu 12.04, but when I try it on OSX, it doesn't work. The problem that I am having is that when I try `import simplejson` or `import js