Re: [PyMOL] Is it possible in Pymol to determine Individual Bond, Dissociation Energy for any Bond in organic molecules?

Hi Rajib, Probably part of the confusion is due to the meaning of "determine the structure". I understand "determine" can have different meaning in different contexts. In my area of research "determine" generally means to use experimental methods like X-ray crystallography or NMR to establish the

Re: [PyMOL] Pymol spheres/circles

Hi Laura, Read here how to select a single atom using the GUI. Or using the command line and the selection albegra do something like: select

Re: [PyMOL] on save_transformed.py

Dear Smith, The line cmd.extend('save_transformed',save_transformed) adds a new command to PyMOL, this command is named save_transformed and what is does is to call the save_transformed function. This function takes two arguments save_transformed(object, file), hence the newly created command

Re: [PyMOL] on async

Hi Smith, That argument controls if the command runs asynchronously or not. If asyn=0 the command has to finish before the next command is executed if async = 1 the command is going to keep working (until finish) while the next commands are executed. Cheers, Osvaldo. On Sat, Nov 21, 2015 at

Re: [PyMOL] Pymol for inorganic chemists - dealing with bonds

Hi, I think the options that Andreas propose are very good for your needs. Nevertheless, if you what to try, another option will be to use PyMOL CGO Cheers, Osvaldo. On Fri, Nov 20, 2015 at 4:10 PM, Andreas Warnecke <

Re: [PyMOL] what is wrong on my using centroid.py

Hi Smith, There was an error in script, incidentally, I introduce the error, but now is fixed. Please download again the centroid.py script. Cheers, Osvaldo. On Fri, Nov 20, 2015 at 3:00 AM, Smith Liu wrote: > Dear All, > > When I run the centroid.py, I have the

[Open Babel] error compiling openbabel

I am trying to compile openbabel on Ubuntu (to make it work with python3) and I when I execute make I get the following error: error: ‘std::tr1’ has not been declared Cheers, Osvaldo. ​ -- Presto, an open source

Re: [PyMOL] H bonds

u. > > On Wed, Nov 11, 2015 at 11:17 AM, Osvaldo Martin <aloctavo...@gmail.com> > wrote: > >> Hi Amali, >> >> By the =NH group do you mean one of the nitrogens of the guanidine group? >> If that's the case PyMOL is doing the right thing. By default PyMO

Re: [PyMOL] h_add command

Hi Amali, By the =NH group do you mean one of the nitrogens of the guanidine group? If that's the case PyMOL is doing the right thing. By default PyMOL assumes that (Arg, Lys, Glu, Asp) are charged. In general that's a reasonable assumption (if residues are exposed to the solvent or relative

Re: [PyMOL] Stacking Interactions

Hi Amali, I am not aware that PyMOL has this feature implemented out-of-the-box. Nevertheless this can be done with PyMOL. A crude approximation will be to measure the distance between the center of aromatic rings and consider a pi-pi stacking for distances shorter than a threshold value. A

Re: [PyMOL] H bonds

Hi Amali, PyMOL has parameters like h_bond_max_angle that are defined in terms of aceptor-donor-hydrogen, hence if hydrogens are not present PyMOL has to guess the position of hydrogens. If you need to add hydrogens you can use PyMOL’s h_add command,

[PyMOL] Azahar (new plugin announcement)

Hi PyMOL community. We would like to announce the release of a new PyMOL plugin: Azahar . Azahar is a plugin that extends PyMOL’s capabilities to visualize, analyze and model glycans and glyco-conjugates molecules. All input from the community will be

Re: [PyMOL] Common atoms in two selections (and their indices)

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,

Re: [PyMOL] Common atoms in two selections (and their indices)

, 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&q

Re: [PyMOL] superimposing and aligning

Hi Raag, You can use align or super , the main difference is that super does not use sequence information. Cheers, Osvaldo. On Tue, Oct 20, 2015 at 4:04 PM, Raag Saluja wrote: Hi! how

Re: [PyMOL] volume measurement

Hi Smith, I am not sure that there is an out-of-the-box function in PyMOL to compute what you want. May be you would like to check the 3v website. Cheers, Osvaldo. On Sat, Oct 10, 2015 at 10:40 AM, Smith Liu wrote: Dear All, > > If there is a

Re: [PyMOL] change electrostatic ramp color?

Hi Adam, Now that the PyMOL wiki is back, did you find the solution at the Ramp_New Wiki page? Cheers, Osvaldo. On Fri, Oct 16, 2015 at 9:10 PM, H. Adam Steinberg < h.adam.steinb...@gmail.com> wrote: I opened a complex .pse file I created back in 2007 and the electrostatic > ramp is showing

Re: [PyMOL] Remove my email

Hi Sabi, Please follow this link or the link at the bottom of every e-mail from the PyMOL mailing list. Cheers, Osvaldo. On Mon, Oct 19, 2015 at 3:57 PM, Sabi wrote: How can I remove my email from the list I

Re: [PyMOL] lipid membrane help

Hi Nhi, You can use the Rotate . You just need to specify the correct selection. If you have any other doubt, please ask. Cheers, Osvaldo. On Mon, Oct 12, 2015 at 9:45 PM, Tran,Nhi T wrote: I want to rotate the lipid molecules in

Re: [PyMOL] on cartoon representation

Hi Smith, There are several setting you could change to modify the way helices (and loops and beta strands) are rendered. Try with this page and let us know if you find something useful or you have further doubts. Cheers, Osvaldo. On Wed,

Re: [PyMOL] change electrostatic ramp color?

gt; Thanks! > > > On Oct 19, 2015, at 9:14 AM, Osvaldo Martin <aloctavo...@gmail.com> wrote: > > Hi Adam, > > Now that the PyMOL wiki is back, did you find the solution at the Ramp_New > Wiki page? > > Cheers, > > Osvaldo. > > On Fri, Oct 16, 2015 at

Re: [PyMOL] pymol to webGL?

gt; we got from cmd.get_session) has changed in recent upgrades. > I have to rewrite the program. > > Does anyone know if there is a setting to export in the 'old' format? > > Best regards, > > Takanori Nakane > > On 2015/10/18 1:47, Osvaldo Martin wrote: > > That really weir

Re: [PyMOL] pymol to webGL?

item__' > > > If possible, would you please give me some suggestions? > > Thanks a lot > > Albert > > > > > On 10/17/2015 04:36 PM, Osvaldo Martin wrote: > > Hi Albert, > > I do the following steps and I get a .html file as expected. > >1.

Re: [PyMOL] Change bond thickness

Hi Henrique, Given that you are new to PyMOL I just want to add that you can explore all the available settings and their values going to settings --> edit all (on the external GUI). Cheers, Osvaldo. On Sat, Oct 17, 2015 at 9:12 AM, Jame R.Ketudat-Cairns wrote: > Deaer

Re: [PyMOL] pymol to webGL?

Hi Albert, I get the following error 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 "exportToWeb.py", line 138, in dump_rep int(255 * float(bgcolor[1])),

Re: [PyMOL] pymol to webGL?

n I export the scene I always get a black background. Cheers, Osvaldo, On Sat, Oct 17, 2015 at 1:50 PM, Osvaldo Martin <aloctavo...@gmail.com> wrote: Hi Albert, > > I get the following error > > Traceback (most recent call last): > File "/usr/lib/python2.7/dist-packages/

Re: [PyMOL] pymol to webGL?

ou sugguested, and rerun it with command: > > python pymol2glmol.py test.pse > > and there is still nothing new generated > > do you have any further comments? I've attached the files. > > Thanks again > > Albert > > > > On 10/17/2015 02:01 PM, Osvaldo

Re: [PyMOL] help

Hi Clarisa, If I understand correctly you generate the dimer, but you are not able to save it. Wich error did you get? Did you select all the object when saving the file? By the way, may be you will find this wiki page useful. Cheers, Osvaldo. On Wed,

Re: [PyMOL] how to setup environment for APBS?

Hi Albert, As far as I know you can set the environmental variables APBS_BINARY_DIR, APBS_PSIZE_DIR and APBS_PDB2PQR_DIR or just set the values for this variable inside the plugin. Anyone knows any other method? Cheers, Osvaldo On Thu, Oct 8, 2015 at 4:54 PM, Albert

Re: [PyMOL] Fwd: visualization problems with pymol

do On Sat, Oct 3, 2015 at 3:16 AM, Carolina Stephania Castro Segura < stephania.castro.seg...@gmail.com> wrote: > It works !!! > > I will check my pymol version. > > Thanks a lot :D > Carolina > El sep 30, 2015 12:51 PM, "Osvaldo Martin" <aloctavo...@gm

Re: [PyMOL] Fwd: visualization problems with pymol

Hi Carolina, Can you reproduce the problem with other sdf files? (for example with the one attached). Could your file be corrupted? Cheers, Osvaldo, On Tue, Sep 29, 2015 at 8:15 PM, Carolina Stephania Castro Segura < stephania.castro.seg...@gmail.com> wrote: > > -- Forwarded message

Re: [PyMOL] loop through many pdb files and show their centre of masses

> > Cheers, > > Tsjerk > > > On Tue, Sep 15, 2015 at 12:25 AM, Osvaldo Martin <aloctavo...@gmail.com> > wrote: > >> Hi Zakir, >> >> The following script computes the Center Of Mass (or alternative the >> geometric center) and then draws a ps

Re: [PyMOL] can we show ligand in 2D?

Hi Albert, Probably you should check Pose_View Cheers, Osvaldo. On Mon, Sep 14, 2015 at 11:52 AM, Albert wrote: Hello: > > I've got a 3D coordinate in 3D. I am just wondering is it possible to > show it in 2D diagram in

Re: [PyMOL] loop through many pdb files and show their centre of masses

Hi Zakir, The following script computes the Center Of Mass (or alternative the geometric center) and then draws a pseudoatom . I think you could adapt the script to your needs if you find difficulties, don’t hesitate to contact the list again (your

Re: [PyMOL] PyMOLWiki: Quick Update

Hi Jason, Thanks very much for the effort! Now the Wiki is far more useful than before! I have been trying the fixed-features and everything is working properly. I will let you now if I found a problem. Cheers, Osvaldo. On Wed, Sep 9, 2015 at 2:02 AM, Jason Vertrees

Re: [PyMOL] any hotkey?

Hi Albert, You can use Set_Key , to bind any function (predefined or defined by you) to any “hotkey/shorcut” Cheers, Osvaldo. On Thu, Sep 3, 2015 at 5:57 AM, Albert wrote: Hello: > > I am just wondering is there any hotkey in

Re: [PyMOL] new to pymol

Hi Celestine, Welcome to the PyMOL community! I am not sure what is your problem, could you please provide more details? Cheers, Osvaldo. On Fri, Aug 28, 2015 at 6:00 AM, Chi Celestine chi.celest...@phys.chem.ethz.ch wrote: Hi, I am very new in pymol and will like to know how know the

Re: [PyMOL] Need help to get SASA for individual Amino Acids

Dear Vinod, One option is to call PyMOL function from Python script. import __main__ __main__.pymol_argv = ['pymol','-qc'] import pymol from pymol import cmd, stored pymol.finish_launching() cmd.set('dot_solvent', 1) cmd.set('dot_density', 3) cmd.load('pdb.file') # use the name of your pdb

Re: [PyMOL] transparent figure

Hi Vaheh, Yes, figures can have transparent backgrounds http://www.pymolwiki.org/index.php/Ray_opaque_background With the GUI Display → background → (un-tick) opaque or using the command line set ray_opaque_background, 0 Then if you raytrace and save the image you will get a transparent

Re: [Open Babel] atom types force field

Thanks, I realized the atom types in OpenBabel are not enough for what I want, hence what I did was to ask openbabel for several atom properties and use those properties to assign the atom types I need. Cheers, Osvaldo On Thu, Jul 30, 2015 at 1:55 PM, Geoffrey Hutchison

Re: [PyMOL] [Pymol] Set scale of vacuum electrostatic potential

Hi Victor, You should never use the build-in generate vacuum electrostatic potential function for any real analysis. The theoretically correct approach is to use the Poisson-Boltzman equation (as implemented for example in the APBS plugin). Other approaches like generalized Born models or SASA

Re: [PyMOL] visualize autodock vina results

Hi Leila, I can't reproduce your error. Your code works for me. Did you try the following save obj3.pdb, obj1_0001, obj2 Cheers, Osvaldo On Tue, Jul 14, 2015 at 5:02 AM, leila karami karami.lei...@gmail.com wrote: Dear pymol users, I am visualizing autodock vina results using PyMOL:

Re: [PyMOL] visualize autodock vina results

Both methods work for me. Are you sure you are opening the correct obj3.pdb file? Maybe you are saving the obj3.pdb file to a different directory and opening an old obj3 file. Wich PyMOL version are you using and on which operating system? On Tue, Jul 14, 2015 at 10:25 AM, leila karami

[Open Babel] atom types force field

Hi, I need to get the atom types from molecules. I am using a Python/PyMOL script. I have the following code def get_atom_type(selection): pdb_string = cmd.get_pdbstr(selection) mol = ob.OBMol() obconversion = ob.OBConversion() obconversion.SetInAndOutFormats('pdb', 'pdb')

Re: [PyMOL] Optimize Geometry {rpblem

I Stephen I am confused, the problem is with Avogadro, or with the PyMOL's optimize plugin http://www.pymolwiki.org/index.php/Optimize? I tried to replicate the problem (with the plugin) and I get the correct answer (the chair conformation) Cheers, Osvaldo On Fri, Jul 10, 2015 at 11:04 AM,

Re: [PyMOL] How to find RMSD values using fitting.py using Shell script

Hi Gazal, Generally when I want to do batch operations using PyMOL I wrote a Python script and I call PyMOL from within that script. I prefer this way because I think is more flexible and simple than using PyMOL from the command line. In those cases I start the Python script with the following

Re: [PyMOL] how to measure the distance of 2 hydrophobic residues

Hi Smith, If you want to measure the distance between two residues (hydrophobic or not) you could choose and atom from each residue and measure the distance between those two atoms. Is this what you want to do, or something more complex? Could you provide more details about your problem?

Re: [PyMOL] how to measure the distance of 2 hydrophobic residues

? Best regards. Smith At 2015-07-09 00:52:32, Osvaldo Martin aloctavo...@gmail.com wrote: Hi Smith, If you want to measure the distance between two residues (hydrophobic or not) you could choose and atom from each residue and measure the distance between those two atoms

Re: [PyMOL] Change thickness of hydrogen bonds?

Hi, Jorge The setting you need to change is the width of the dashes http://www.pymolwiki.org/index.php/Dash_width Cheers, Osvaldo. On Thu, Jul 2, 2015 at 5:26 PM, Jorge Fernandez de Cossio Diaz cos...@cim.sld.cu wrote: Hi all, How can I change the thickness of hydrogen bonds in Pymol?

Re: [PyMOL] Race condition when running scripts in stdin mode

Hi MIchael, I can reproduce the error on a machine with Ubuntu 15.04 (64 bits) and PyMOL 1.7.2 On Tue, Jun 23, 2015 at 7:13 PM, Michael Banck mba...@debian.org wrote: Hi, on Debian, we got a bug report which looks like the bug reported here as well:

Re: [PyMOL] visualize mode

Hi, Do you want to do something similar to porcupine plots? If so, check the porcupine function in this Ipython notebook https://github.com/aloctavodia/SBioA/blob/master/English/04_Comparing_structures.ipynb . Cheers, Osvaldo. On Thu, Jun 18, 2015 at 5:07 PM, Command Line

Re: [PyMOL] Batch processing

. On Sat, Jun 6, 2015 at 2:42 AM, Osvaldo Martin aloctavo...@gmail.com wrote: Hi Praz, When I want to process several files, do complex or repetitive tasks I prefer to write a Python script and access the PyMOL functions using the PyMOL API, as in the code below. This example will upload all

Re: [PyMOL] Batch processing

. For example, I put set light_count,8 and that results in the before-mentioned error message. On Mon, Jun 8, 2015 at 2:22 PM, Osvaldo Martin aloctavo...@gmail.com wrote: Hi Praz, Sorry. Please use this new version of the script. import __main__ __main__.pymol_argv = ['pymol','-qc'] import

Re: [PyMOL] PyMOL ray tracing errors

Hi Brenton The script seems to work for me A couple of questions: - Why aren’t you installing PyMOL from the repository? sudo apt-get install pymol - Are you sure that the name of the pdb file is correct? (remember that names are case sensitive) Cheers, Osvaldo On Fri,

Re: [PyMOL] Batch processing

Hi Praz, When I want to process several files, do complex or repetitive tasks I prefer to write a Python script and access the PyMOL functions using the PyMOL API, as in the code below. This example will upload all the pdb files in the folder where the script is located, one file at a time, save

Re: [PyMOL] create bonds between selections within cutoff radius

Hi Tobias, One possible solution will be to run the following code. import pymol from pymol import cmd, stored stored.pd = [] stored.pairs = [] cmd.iterate('name pd', 'stored.pd.append(index)') for i in stored.pd: cmd.iterate('name si within 2.5 of index %s' % i, 'stored.pairs.append((%s,

Re: [PyMOL] create bonds between selections within cutoff radius

cmd.find_pairs: http://pymolwiki.org/index.php/find_pairs Cheers, Thomas On 28 May 2015, at 09:06, Osvaldo Martin aloctavo...@gmail.com wrote: Hi Tobias, One possible solution will be to run the following code. import pymol from pymol import cmd, stored stored.pd = [] stored.pairs

Re: [PyMOL] Printing Protein Surface residues

Hi Vinod The exposed residues are stored in the selection “exposed_res_02”. You can iterate http://www.pymolwiki.org/index.php/Iterate this selection to get several properties like the residues names, for example the command: iterate exposed_res_02, resn will return the name of the residues,

[PyMOL] assigning atom types

Hi, I need to assign atom types for glycans and organic molecules. I can't relly on the atom types in the pdb, since in general there is not atom type information (e.g. all carbons are equal). Does PyMOL offers some feature to make this assignment easier? like checking the hybridization and

[PyMOL] get_sasa atom vs hetatm

Hi, I have noticed that computing the SASA using the PyMOL function get_area returns a reasonable value if the PDB has the record ATOM and a larger value (about 1 order of magnitude larger) if the record is HETATM. Is this a bug, or some intended feature? Other people in my group were able to

Re: [PyMOL] How to Highlight B-Values of Side Chains?

Hi Angelo, As far as I understand the putty representation takes the values from the b-factor of the Ca atom. Probably you should store your fluctuation values either on the Ca (leaving all the others atoms with 0.0 or any other value) or just set the same b-factor for all the atoms of a given

Re: [PyMOL] Is cyclododecene in the database of PyMol?

Hi Rajib Yuktimmana, I found this paper that describes the conformational preferences of trans-cyclododecene. http://pubs.acs.org/doi/abs/10.1021/jo990628w I hope it helps. Cheers, Osvaldo. On Thu, May 7, 2015 at 5:51 PM, Tsjerk Wassenaar tsje...@gmail.com wrote: Hi Rajib Yuktimmana,

Re: [PyMOL] RMS or RMSD for two structures

Hi Dmitry, You have to load both molecules and then you could use the command fit x-mol, dft-mol You can find more examples and options on the PyMOL wiki, http://www.pymolwiki.org/index.php/Fit Cheers, Osvaldo. El may 7, 2015 6:00 a.m., Dmitry B. Eremin e...@ioc.ac.ru escribió: Hello

Re: [PyMOL] Modified DNA bases

Hi Rachel, You can do it using the PyMOL built-in Builder http://www.pymolwiki.org/index.php/Builder Cheers, Osvaldo. On Tue, May 5, 2015 at 2:18 PM, Werther, Rachel A rwert...@fredhutch.org wrote: Is there a way to mutate a cytosine to 5-methylcytosine in Pymol? Can it be done using the

Re: [PyMOL] Superimpose small non-protein molecules?

Hi Jorge, You are right align is only for proteins. You can use the Fit http://www.pymolwiki.org/index.php/Fit command Cheers, Osvaldo. On Tue, May 5, 2015 at 3:38 PM, Jorge Fernandez de Cossio Diaz cos...@cim.sld.cu wrote: How can I superimpose two small non-protein molecules in PyMol? I

Re: [PyMOL] Ray Trace of Icosahedral Viral Capsids using NVIDIA GE Force

Hi, Did you try with this recipe http://www.pymolwiki.org/index.php/Huge_surfaces? Did you try doing the ray-traicing from a script (and not using the GUI)? Cheers, Osvaldo. On Tue, Apr 28, 2015 at 11:46 AM, Rallapalli, Pavithra pavithra.rallapalli...@ucl.ac.uk wrote: Hi all I am trying

Re: [PyMOL] Problem with How do I change the font in the Tck/Tk external GUI window?

Hi Saverio, The file is the correct one. Inside the file ./python2.7/dist-packages/pmg_tk/PMGApp.py find the line def initializeTk_unix(self): pass and change it to make it look like def initializeTk_unix(self): self.root.option_add('*Font', 'Lucida 10')

Re: [PyMOL] Cartoon putty in pymol

Hi, Wenfu The putty representation uses the values on the b-factor column of the pdf file and your file has the same value for each atom (0.0), hence the error. If you want to have residues with different width you need different b-factor values for different residues. If, on the other hand you

Re: [PyMOL] pymol crash when ray

Hi Wenfu, Did you get the same error if you do the raytraicing from a script? Probably you could try with this http://www.pymolwiki.org/index.php/Huge_surfaces approximation to render your molecule. Cheers, Osvaldo. On Tue, Apr 14, 2015 at 5:12 PM, m...@mskcc.org wrote: Hi pymol users, I

Re: [PyMOL] Cartoon visualization of per-residue txt data

Hi James, I think what you want to do is to load your data to the b-factor column of the pdb file and then ask PyMol to color the protein according to the b-factor values. Try with this http://www.pymolwiki.org/index.php/Color#B-Factors example from the PyMol wiki and let us know if you find some

Re: [PyMOL] creating selections without launching GUI

Hi Irem, You could use __main__.pymol_argv = ['pymol','-qc'] the c suppress the GUI. Cheers, Osvaldo. On Sun, Mar 8, 2015 at 9:32 PM, Irem Altan irem.al...@duke.edu wrote: Hi, I have recently started to play with PyMOL and using python scripts. Is it possible to create a new

Re: [PyMOL] ? about polarpairs.py script

Hi Suzanne, How are you calling the script? Try doing something like pairs = polarpairs(‘sel1’, ‘sel2’) and then for pair in pairs: print pair Alternative you can try with this http://www.pymolwiki.org/index.php/Dehydron plugin, that returns a list of backbone hydrogen bonds, both as a

Re: [PyMOL] Is it possible to find pi-pi interactions and cation-pi interactions of a PDB?

Hi Surya, I do not think these features are implemented yet, although there has been some discussion http://sourceforge.net/p/pymol/mailman/message/32715572/ about it. ​ Cheers, Osvaldo. On Mon, Feb 9, 2015 at 8:48 AM, Seera Suryanarayana paluso...@gmail.com wrote: Dear Users, I have one pdb

Re: [PyMOL] Alpha setting of CGO spheres

Hi Matt, Try removing the BEGIN sph1 = [ALPHA, 0.5, COLOR, 1.0, 1.0, 1.0, SPHERE, -3.818, -28.181, -15.016, 0.5] cmd.load_cgo(sph1, sph1, 1) sph2 = [ALPHA, 1.0, COLOR, 1.0, 1.0, 1.0, SPHERE, -3.818, -28.181, -15.016, 0.5] cmd.load_cgo(sph2, sph2, 1) Cheers, Osvaldo. On Tue, Jan 20, 2015 at

Re: [PyMOL] Unable to select correct ligand

Dear Gabriel, You should try something like this sele ligand, not polymer and resn leu notice that ligand is just a variable name it has no special meaning if you do sele asdf, not polymer and resn leu You will get the same result. The selection is defined by the portion after the coma.

Re: [PyMOL] Cel shading in PyMOL

Hi Jacob, What about the Goodsell-like representation from here http://www.pymolwiki.org/index.php/Gallery? Cheers, Osvaldo. On Tue, Jan 13, 2015 at 7:29 AM, Jacob Lewis jl...@uowmail.edu.au wrote: Hi all, Has anyone figured out a good way to do Cel shading in pymol? Or even the sort of

Re: [PyMOL] APBS_problem

Hi Monica, I think the problem ObjectMapLoadDXFile-Error is because the spaces in the names of the files. The problem ValueError: invalid literal for float() is caused because a python script is trying to read 1.00105.23 as a number but it could not because have two . you ca fix this by changing

Re: [PyMOL] Is it possible to set the number of frames in a movie?

Hi Brenton, Have you tried using the EMovie-plugin http://www.pymolwiki.org/index.php/EMovie? Cheers, Osvaldo. On Mon, Dec 22, 2014 at 10:47 AM, Brenton Horne brentonho...@ymail.com wrote: Hi, I've just started using PyMOL and although I rather like the movie-making function I would like

Re: [PyMOL] CGOs

Hi Robert, I do not have a proper answer to your question, but two other resources to try to learn about CGO in PyMOL are. http://www.pymolwiki.org/index.php/Category:CGO the folder examples/devel/ in your PyMOL installation On Sun, Dec 21, 2014 at 3:06 PM, Robert Hanson hans...@stolaf.edu

Re: [PyMOL] plugin errors in pymol 1.7.2.1

Hi Hena, Regarding Optimize plugin. You need to install OpenBabel and OpenBabel Python bindings (see instructions here http://openbabel.org/wiki/Get_Open_Babel). As far as I know for Windows there is not a 64 bit version of OpenBabel and hence if you want to use openbabel and optimize plugin on a

Re: [PyMOL] plugin errors in pymol 1.7.2.1

wrote: Try the 64 bit version of OpenBabel at http://www.lfd.uci.edu/~gohlke/pythonlibs/#openbabel Christoph On 12/20/2014 1:12 PM, Osvaldo Martin wrote: Hi Hena, Regarding Optimize plugin. You need to install OpenBabel and OpenBabel Python bindings (see instructions here http

Re: [PyMOL] moving large flexible loops

Hi Jacob, I recommend using specific tools to perform docking. Some options are: http://rosie.rosettacommons.org/docking/ https://salilab.org/imp/ http://haddock.chem.uu.nl/ Also you could check the Capri http://www.ebi.ac.uk/msd-srv/capri/ home page, to have and idea of the different methods

Re: [PyMOL] making liposomes

Hi Marcelo, You should check packmol http://www.ime.unicamp.br/~martinez/packmol/. Packmol creates an initial point for molecular dynamics simulations by packing molecules in defined regions of space. The packing guarantees that short range repulsive interactions do not disrupt the simulations.

Re: [PyMOL] CONECT card and STATES / damien

Hi Damien, I am not sure if I understood you problem correctly. Have you tried the following commands? set connect_mode, 2 (or other number) load your_pdb_file_name.pdb, discrete=1 Cheers, Osvaldo. On Fri, Nov 28, 2014 at 12:23 PM, Clavel dcla...@ibs.fr wrote: Hello PyMOL users, I am

Re: [PyMOL] Announcing Osvaldo Martin as PyMOL Open Source Fellow

As Thomas already said to all of you feel free to contact me for anything you want or need. Cheers, Osvaldo. On Wed, Nov 26, 2014 at 6:13 PM, Thomas Holder thomas.hol...@schrodinger.com wrote: Greetings PyMOL users worldwide, Please join me in congratulating Dr. Osvaldo Martin, who has been

Re: [PyMOL] Super, algorithm

, Spencer Bliven sbli...@ucsd.edu wrote: I would also be interested if there is any documentation about the super algorithm and the differences to align. -Spencer On Fri, Nov 14, 2014 at 10:25 PM, Osvaldo Martin aloctavo...@gmail.com wrote: Hi, Exactly which algorithm is behind

Re: [PyMOL] set size nb_spheres

Hi Erica, I think something like: alter name ca, vdw=10 should help. Change 10 for the value you want. Best Regards, Osvaldo. On Wed, Nov 19, 2014 at 11:16 AM, Erica Valentini er...@embl-hamburg.de wrote: Dear all, I would like to change the size of nonbonded spheres. They are nonbonded

Re: [PyMOL] how to add an oxygen atom in carbonyl group?

Hi Tumpa, What about using the builder http://www.pymolwiki.org/index.php/Builder. Is this what you need? Osvaldo. On Thu, Nov 20, 2014 at 4:02 AM, t.sadhuk...@chem.iitb.ac.in wrote: Hi, I am a new user of pymol. My question is how to add an oxygen atom in carbonyl group? Thanks, Tumpa

Re: [PyMOL] how to solvate a protein in a box with water?

Hi, I am not aware of the possibility to do that using PyMOL (unless someone has implemented a plugin/script to do so). I guess you want solvate a molecule to perform a Molecular Dynamics simulation, in that case you could use Gromacs to solvate and simulate your system. You could also use this

Re: [PyMOL] How to build imedazole by using builder

Hi Surya, I don't know exactly what problem are you experiencing (I tried to do something similar without any problem). I guess that maybe the problem is that when you are rebuilding the ring, you are positioning the atoms in a not very good position and maybe PyMOL is having trouble to

[PyMOL] Super, algorithm

Hi, Exactly which algorithm is behind the super command? How the outliers pairs are defined? The is some scientific paper related to super or it is really an experimental idea? Thanks. -- Comprehensive Server Monitoring

[PyMOL] Pymol python 3.

Hi, I just want to know if there have been some discussion about porting PyMOL to python 3. Osvaldo. -- Want excitement? Manually upgrade your production database. When you want reliability, choose Perforce Perforce

[PyMOL] Using pymol with Ipython

I was trying to use pymol within Ipython notebook, but I can get all the functionality of PyMOL and/or Ipython, let me explain. I tried the following two options: A) Like a normal script 1) I lauch PyMOL (inside the ipython notebook) import pymol from pymol import cmd, stored

Re: [PyMOL] Using pymol with Ipython

Osvaldo, A3) PyMOL captures sys.stdout, but you can reclaim it: import sys, pymol stdout = sys.stdout pymol.finish_launching() sys.stdout = stdout B4) cmd is your ServerProxy instance, so don't import anything from pymol Cheers, Thomas On 24 Aug 2014, at 13:36, Osvaldo Martin aloctavo

Re: [PyMOL] disable all screen output

for the suspend_updates setting. Cheers, Thomas On 19 May 2014, at 15:10, Osvaldo Martin aloctavo...@gmail.com wrote: Hello everyone! I working on a PyMOL plugin that performs a lot of selections and operations. I would like to avoid updating the screen until the script finish (mainly

[PyMOL] disable all screen output

Hello everyone! I working on a PyMOL plugin that performs a lot of selections and operations. I would like to avoid updating the screen until the script finish (mainly to increase the performance of the plugin) I tried with something like this cmd.disable('all') Some code cmd.enable('all') The

Re: [PyMOL] pymol does not free-up the RAM when objects are deleted

. Cheers, Thomas On 02 Apr 2014, at 20:30, Osvaldo Martin aloctavo...@gmail.com wrote: Hi, I need to run an script based on PyMOL for a thousands of proteins. The problem is that even when I delete all object the RAM usage keeps increasing. I am using PyMOL 1.7 on ubuntu 14.04 (beta 2

[PyMOL] pymol does not free-up the RAM when objects are deleted

Hi, I need to run an script based on PyMOL for a thousands of proteins. The problem is that even when I delete all object the RAM usage keeps increasing. I am using PyMOL 1.7 on ubuntu 14.04 (beta 2). my script looks like this. import __main__ __main__.pymol_argv = ['pymol','-qc'] import

[PyMOL] quiet copy

When I run a script, like this import __main__ __main__.pymol_argv = ['pymol','-qc'] import pymol from pymol import cmd pymol.finish_launching() cmd.copy('mol_copy','mol_ori') I get the message Executive: object mol_copy created. in the terminal. It is posible to keep the copy comand quiet?

Re: [PyMOL] quiet copy

Thank you Thomas! On Fri, Jan 24, 2014 at 1:06 PM, Thomas Holder thomas.hol...@schrodinger.com wrote: Hi Osvaldo, http://pymolwiki.org/index.php/Feedback PyMOL feedback disable, executive, actions Cheers, Thomas On 24 Jan 2014, at 13:33, Osvaldo Martin aloctavo...@gmail.com wrote

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