Re: [PyMOL] Pymol cavity detection error?

Hi Kanika, Try set two_sided_lighting Cheers, Tsjerk On Jun 28, 2017 17:14, "kanika sharma" wrote: > Dear PyMolers > > I want to see the cavities in my protein using the following steps: > > Setting → Surface → Cavities & Pockets Only. > Show surface > Cavity Detection

Re: [PyMOL] Problem with 'byring' selection

Hi Vijay, It is logic. 'byring elem N' selects all nitrogens and then expands the selection to include the rings in which these participate. 'elem N and byring elem N' does the same, but then intersects (and) to extract only nitrogens. But that is the same as 'elem N'. If you want to have the

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

Dear Rajib, Pymol reads atom labels and positions from a coordinate file. It then determines which atoms are bonded based on distance criteria. That is used to draw the molecule. Pymol also has an internal library of molecules and fragments, with atoms and bonds, which can be used to build bigger

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

Hi Rajib, The bonds are determined based on a distance cutoff. Hope it helps, Tsjerk On Jun 1, 2017 21:15, "Susmita/Rajib" wrote: How come we see structures of molecules in PyMol? https://en.wikipedia.org/wiki/PyMOL

Re: [PyMOL] Pymol fab ss = 4 introduces bends in the structure

Hi Ahmad, Because the chain contains prolines. These typically cause kinks in a chain. Cheers, Tsjerk On Fri, Apr 7, 2017 at 2:26 PM, Ahmad Abdelzaher wrote: > Hello, > > I used cmd.fab('sequence', ss=4) to create 1baz_linear_protein.pdb, > where sequence is the

Re: [PyMOL] Calculating center of mass for the entire protein

Hi Ahmad, The center of mass of an atom is its position. A function like cmd.centerofmass in the context of pymol only makes sense with a selection. E.g.: x,y,z = cmd.centerofmass('byres n. ca') print "COM of protein:", x, y, z Hope it helps, Tsjerk On Thu, Apr 6, 2017 at 6:30 AM, Ahmad

Re: [PyMOL] Scripting coloring method via own calculations

Hey :) Just as sidenote, the spectrum command takes arbitrary color schemes. Just combine colors separated by underscores. Also fun in combination with set_color :) Cheers, Tsjerk On Feb 14, 2017 5:46 PM, "Robert Campbell" wrote: Hello Peleg, I think there are

Re: [PyMOL] Pseudoatom for a cavity

Hi Kanika, That's been quite a while! Nice to see you again and to see you're still your determined self, still a bit impatient, reposting a message within a day :) The issue with the second question is not about center_of_mass, but about center_of_no_mass, which is a bit harder (and I don't

Re: [PyMOL] making a plane

Hi Vitaly, You have several options, but if the loops are nicely bent, the best is probably doing PCA on the coordinate sets of the loops and calculate the angle between the smallest eigenvectors. Is that enough information? Do you insist on drawing the planes? Cheers, Tsjerk On Jan 17, 2017

Re: [PyMOL] default water bond lengths in PyMOL

Hi Tom, Do consider that 1. the PDB format only allows four digits for residue numbers, such that water molecules must get the same number of there are more than of them. 2. periodic boundary conditions may cause water molecules to be split, making water molecules seem to miss an atom or

Re: [PyMOL] how to show PBC box?

Hi Albert, You can do: show cell Cheers, Tsjerk On Dec 7, 2016 8:44 PM, "Albert" wrote: > Hello: > > I am visualizing a MD simulation system in PyMOL. It contains the PBC > information. I am just wondering how can we show the PBC box in PyMOL? > As far as I know the

Re: [PyMOL] Starting PyMol in interactive IPython Session

Hi Leonhard, I would guess it's the formatting setting of numpy in IPython. You can see what one float really is: print(cmd.get_coords("1xyz")[0,0]) Cheers, Tsjerk On Thu, Dec 1, 2016 at 1:40 PM, Leonhard Heizinger wrote: > I guess formatting didn't work out as i

Re: [PyMOL] Scripts don't work any longer after upgrade to v1.8.4

es) > works flawlessly using v1.8.07. > > > > I will be happy about any possibly helpful suggestion. > > > > Best > > Thomas > > > > > > > > *Von:* Tsjerk Wassenaar [mailto:tsje...@gmail.com] > *Gesendet:* Donnerstag, 24. Novembe

Re: [PyMOL] Scripts don't work any longer after upgrade to v1.8.4

Hi Thomas, Can you give more information? What is in the script? Is something written in the terminal? FWIW, I have not encountered problems, and certainly not with selections. My guess is that the script breaks before getting to the selection. Cheers, Tsjerk On Thu, Nov 24, 2016 at 2:13 PM,

Re: [PyMOL] External file for writing with multiple data

Hi Daniel, Use \t in stead of \n to separate the numbers from one measurement with tabs, in stead of newlines. Do write one newline before the new series: f.write('\n') However, you might want to be a bit smarter in writing code. So you're trying to get one angle for all states?: f =

Re: [PyMOL] Placing pseudo atom on COM and saving it as pdb

ete('tmp') > > > @Tsjerk: Don't know why I got an error: Selector-Error: Invalid selection > name "pseudo". > pseudo<-- > > Thanks again for the support. > > Best Regards, > Subha > > > > > > On Wed, Oct 12, 2016 at 12:53 PM, Tsjerk Wassen

Re: [PyMOL] Placing pseudo atom on COM and saving it as pdb

Hi Subha, Probably this will get close: for pdb in open('./out').readlines(): pdb = pdb.strip() cmd.load(pdb,'tmp') cmd.pseudoatom('tmp',name='pseudo') cmd.save(pdb[:-4]+'-pseudo.pdb','pseudo') cmd.delete('tmp') cmd.delete('pseudo') ... Just a bit too much for a oneliner

[PyMOL] Leap Motion

Hey :) We've been playing recently with a Leap Motion controller for PyMol and are now wondering how we would emulate a mouse click event, based on the screen coordinates. Does anyone know? Thanks in advance, Tsjerk -- Tsjerk A. Wassenaar, Ph.D.

Re: [PyMOL] ray command

Hi Mohsen, So raytracing is indeed not available in the educational version. I find this a bit strange, as I regarded the educational version the least-changed-with-respect-to-the-original (say 0.99), which did have raytracing available. Also, I like students to give me reports with pretty

Re: [PyMOL] ray command

Hi Mohsen, What happens? What error do you get? Best, Tsjerk On Jul 12, 2016 10:46 AM, "Mohsen Chitsaz" wrote: Hi Pymol users, The “ray command” is not working in my Educational version of Pymol. It seems that educational version does not allow to use this

Re: [PyMOL] post-processing of pdb ensemble

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 wrote: > More precisely I would like to know how to script in pymol the > following

Re: [PyMOL] a special phenomenon on using pymol

Hi Smith, You probably hit the key. Or you clicked the down triangle in the lower right menu. Cheers, Tsjerk On Fri, May 20, 2016 at 7:56 AM, Smith Liu wrote: > Dear All, > > Today as every day I do, I align 2 pdb files by pymol. After a moment, I > find the aligned 2

Re: [PyMOL] How to export secondary structure information from aPDBusing PyMol?

> > So, > L: loop > S: beta-strand > H: alpha-helix > > Is that right? > > Thank you. > > Cheng > > > -- Original -- > *From: * "Tsjerk Wassenaar";<tsje...@gmail.com>; > *Date: * Sat, May 14

Re: [PyMOL] How to export secondary structure information from a PDBusing PyMol?

\PyMOL/modules\pymol\parser.py", line > 464, in parse > exec(layer.com2+"\n",self.pymol_names,self.pymol_names) > File "", line 1, in > TypeError: int argument required > > Can I ask how to modify that? > > Thank you! > > > ---

Re: [PyMOL] How to export secondary structure information from a PDB using PyMol?

Hi Zhang Cheng, If you replace SELECTION with a proper selection statement (with quotes), then something like: open("ss.dat","w").writelines( ["Residue %d: %s\n"%(a.resi,a.ss) for a in cmd.get_model(SELECTION+" and n. ca").atom] ) It will write the results to a file called ss.dat. Do mind all

Re: [PyMOL] Contact map visualizer

Hi James, You can convert the .xpm file to .png/.jpg using tools like convert (imagemagick) and Gimp. Convert doesn't always get the Gromacs .xpm right, but it's an easy one to try. Cheers, Tsjerk On May 11, 2016 2:40 PM, "James Starlight" wrote: > Dear Pymol users! >

Re: [PyMOL] Bash scripting and pymol

Hi, You need for i in ${pdb_array[@]} do ... done Cheers, Tsjerk On Apr 27, 2016 4:44 PM, "James Starlight" wrote: > so As I tried to do it but it was not worked :-O) > > #pdbs list > pdb_array=("1UBI" "1IGD" "1G33" "1CC7" "4LGJ" "5A2H") > #where to save >

Re: [PyMOL] -- selection --

Hi Leila, Have a look at selection syntax (help selections), in particular 'within ... of ...' Hope it helps, Tsjerk On Mar 2, 2016 06:46, "leila karami" wrote: > Dear all > > I have a complex (protein-ligand). I want to have only those residues > (from protein) with

Re: [PyMOL] How to tell from within a script if a plugin is loaded?

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." wrote: > To my previous message I

Re: [PyMOL] PyMOL-users Digest, Vol 116, Issue 15

nts would love to have easy access to that! > > Thanks! > > Adam > > On Feb 2, 2016, at 1:39 AM, Tsjerk Wassenaar <tsje...@gmail.com> wrote: > > Hi Annemarie, > > It's actually quite simple to generate a real membrane around your protein > and, e.g., to show the head gr

Re: [PyMOL] PyMOL-users Digest, Vol 116, Issue 15

Hi Annemarie, It's actually quite simple to generate a real membrane around your protein and, e.g., to show the head groups. Do you have a PDB ID for the protein, or are they in-house models? Cheers, Tsjerk On Mon, Feb 1, 2016 at 10:57 PM, Julian Heinrich wrote: > Hi

Re: [PyMOL] Testing if a .pml script is run in command line mode

Hey Folmer, You can check if '-c' not in invocation._argv Of course, you'd also need to check combinations, so it would be matching -.*c.* on the elements in _argv. There probably is a way to check for the GUI directly though. Hope it helps, Tsjerk On Wed, Jan 27, 2016 at 11:49 AM, Folmer

Re: [PyMOL] pdb edition

Hi Pascual, The PDB file does not really have information on bonds. If atoms are closer than some cutoff a bond is drawn. Unbonding and saving will not change the distance, so the bond will be drawn again when loaded again. What is your aim? Cheers, Tsjerk On Tue, Jan 19, 2016 at 12:15 PM,

Re: [PyMOL] pdb edition

te.edu> wrote: > > > On 01/19/2016 03:11 PM, Tsjerk Wassenaar wrote: > >> Hi Pascual, >> >> The PDB file does not really have information on bonds. If atoms are >> closer than some cutoff a bond is drawn. Unbonding and saving will not >> change the distance,

Re: [PyMOL] Drawing grid of cubes

't suit my project. > Indeed, I would like to get a script that describe your second guess! > > D > Le 11/12/15 17:12, Tsjerk Wassenaar a écrit : > > > Hi Damien, > > Do you mean replacing the atoms by cubes, or by binning the atoms on a 3D > grid and show these cubes if

Re: [PyMOL] Drawing grid of cubes

Hi Damien, Do you mean replacing the atoms by cubes, or by binning the atoms on a 3D grid and show these cubes if filled? Cheers, Tsjerk On Fri, Dec 11, 2015 at 4:51 PM, Damien Clavel wrote: > Good evening pymol users, > > I would like to represent a protein with a

Re: [PyMOL] how to close displaying a molecule

Hi Smith, You can delete the object: delete B Cheers, Tsjerk On Fri, Dec 11, 2015 at 8:19 AM, Smith Liu wrote: > Dear All, > > Suppose by pymol I have opened A.pdb abd B.pdb. Is anyway I close B.pdb > and have only A.pdb displayed? > > Smith > > > > > > >

Re: [PyMOL] Brownian motion in movie?

Hi Adam, That type of motion is typically the result of MD simulation. Some of the examples were just showing the motion on very short time scales and others were over longer times, using a smoothing filter. In addition, there was an example of structure morphing without dynamics. If you want, I

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

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., >&

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

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 cou

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

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,

[PyMOL] CGO segmentation fault

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 :)

Re: [PyMOL] Ploting coordinates

Hi Suzanne, I'll make the guess that it's position and color. Are there any lines to be ignored? Probably this will work anyway... Save this in a script called holecgo.py: def holecgo(filename,radius=0.1,name="hole"): data = [ i.split() for i in open(filename) ] data = [ [ float(i) for

Re: [PyMOL] pymol crashes when try opening a file created by gromacs

Hi Raag, Did pymol crash (quit) with a PDB file written by Gromacs? That can (I think) only happen if the PDB file is corrupted, for example by coordinates going out of bound during a simulation. What did you do to obtain the PDB file? Cheers, Tsjerk On Tue, Sep 15, 2015 at 7:20 AM, Raag

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

Hi, AFAIK, pseudoatom puts a new atom on the center of mass (or geometry) of the selection. So, import glob from pymol import cmd for pdb in glob.glob("*.pdb"): cmd.pseudoatom(pdb[-3:],"{} and resn LIGANDNAME".format(pdb)) Or along those lines. Be creative :) Cheers, Tsjerk On Tue, Sep 15,

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

can be used interchangeably since they could be numerically similar. > > Cheers, > Osvaldo. > > > > > On Tue, Sep 15, 2015 at 3:36 PM, Tsjerk Wassenaar <tsje...@gmail.com> > wrote: > >> Hi, >> >> AFAIK, pseudoatom puts a new atom on the center of

Re: [PyMOL] spectrum and the default minimum and maximum values

Hi Emily, No, it takes them from the selection. Cheers, Tsjerk On Jul 7, 2015 4:09 PM, Emilia C. Arturo (Emily) ec...@drexel.edu wrote: To be extra clear/redundant: The default value passed is None. If Pymol finds that the argument is None, it takes the minimum/maximum value from the

Re: [PyMOL] spectrum and the default minimum and maximum values

Hi Emily, The default value passed is None. If Pymol finds that the argument is None, it takes the minimum/maximum value from the list of values, otherwise it will take the value provided. The interpolation is indeed linear. Hope it helps, Tsjerk On Tue, Jul 7, 2015 at 4:11 AM, Emilia C.

Re: [PyMOL] efficiency assigning b-factors

Hi Jordan, Yes, although I don't have the answer at hand, it has been given on the user list several times. You can find it in the archives. Cheers, Tsjerk On Jun 16, 2015 08:16, Jordan Willis jwillis0...@gmail.com wrote: Hi, I have a dictionary that has a bunch of values I want to assign

Re: [PyMOL] efficiency assigning b-factors

everyone is pointing to this ( http://www.pymolwiki.org/index.php/Color#Reassigning_B-Factors_and_Coloring) which I somehow missed. However, they seem to be altering one residue at a time like I’m doing. Jordan On Jun 15, 2015, at 11:59 PM, Tsjerk Wassenaar tsje...@gmail.com wrote: Hi Jordan

Re: [PyMOL] time bar in a movie done with pymol

Hi Stéphane, You could use four pseudoatoms A,B,C,D and have bonds between A/B and C/D. Then you show them as sticks with A/B in red and C/D in white and let B+C move from position A to position D. Alternatively, you can use CGO. Cheers, Tsjerk On Wed, May 27, 2015 at 3:30 PM, ABEL Stephane

Re: [PyMOL] how to highlight some residues and make other residues being as background?

Hi Yeping Sun, In such cases, I usually use light colors with little contrast (white, wheat, grey, pastel) for the surroundings (on a white background) and bright, contrasting colors (chartreuse, orange, hotpink, marine) for what you want to highlight. In addition, you may want to play around

Re: [PyMOL] on color based on b-factor spectrum

Hi Smith, The colors are interpolated linearly from the minimum to the maximum value. 'spectrum' allows specifying the extreme values, which is handy when you need a symmetric scale. If you color green_yellow_blue, you get a green to yellow gradient from min to (min+max)/2 and a yellow to blue

Re: [PyMOL] sticks do not connect to the backbone

Hi Yeping Sun, Try: set cartoon_flat_sheets, 0 set cartoon_smooth_loops, 0 Cheers, Tsjerk On Mon, May 18, 2015 at 10:23 AM, sunyeping sunyep...@aliyun.com wrote: Dear all, I find that when I show the protein as cartoon representation in pymol, and select some residues to show as

Re: [PyMOL] how to connect to atoms?

of TehranTehran, Iran* *Email: karami.le...@ut.ac.ir karami.le...@ut.ac.ir karami.le...@ut.ac.ir* *Tel: +98 9193155894 %2B98%209193155894* On Tue, May 12, 2015 at 12:27 AM, Tsjerk Wassenaar tsje...@gmail.com wrote: Hi Leila, Please ask this question on the gromacs mailing list. But first

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

Hi Rajib Yuktimmana, Cyclododecene has twelve carbon atoms in a ring, and one of the bonds is a double bond. This means that there are two forms, cis and trans. Neither is wrong, if not specified explicitly. For the rest, the structure is very flexible, so there is not a single structure, but

Re: [PyMOL] cylinder fuzzy color when ray traced

Hey Doug, Does set ray_trace_mode, 3 do what you want? Cheers, Tsjerk On Fri, May 1, 2015 at 5:20 PM, Douglas Kojetin douglas.koje...@gmail.com wrote: Hi All, I am trying to highlight a specific residue (black color) in a helix (orange color) displayed in cylinder mode. When I perform

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

according to the B-factor value? Here the issue is with the proper selection E.g PyMOLselect not-relevent, b 0 results only in small atoms selected and PyMOLselect ss, b = 0 Selector-Error: Invalid selection. b-- Regards, James 2015-04-10 21:12 GMT+02:00 Tsjerk

Re: [PyMOL] Labelling ligands and amino acids

Hi Brenton, Add a specific atom, at which you want the label, to the selection. You can pick one to get to know its name. Cheers, Tsjerk On Mon, Apr 6, 2015 at 10:03 PM, Brenton Horne brentonho...@ymail.com wrote: Hi, I have skimmed the Label http://pymolwiki.org/index.php/Label page on

Re: [PyMOL] Labelling ligands and amino acids

:28 AM, Tsjerk Wassenaar wrote: Hi Brenton, Add a specific atom, at which you want the label, to the selection. You can pick one to get to know its name. Cheers, Tsjerk On Mon, Apr 6, 2015 at 10:03 PM, Brenton Horne brentonho...@ymail.com wrote: Hi, I have skimmed the Label http

Re: [PyMOL] Zoom animation

Hi Brenton, cmd.zoom(r. pnm, 20) You forgot the quotes: r. pnm Cheers, Tsjerk -- Dive into the World of Parallel Programming The Go Parallel Website, sponsored by Intel and developed in partnership with Slashdot

Re: [PyMOL] Displaying covalent bonds between amino acids (within protein) and ligand

Hi Brenton, You will also need to show the sticks for the sidechain of residue 62: fetch 1pwc hide show cartoon show sticks, r. pnm show sticks, resi 62 and not name c+n+o Cheers, Tsjerk On Sat, Apr 4, 2015 at 3:52 PM, Brenton Horne brentonho...@ymail.com wrote: Hi, In the structure that

[PyMOL] Fwd: Displaying covalent bonds between amino acids (within protein) and ligand

Oh, and always use 'reply-to-all' if this is follow-up on a post. Cheers, Tsjerk -- Forwarded message -- From: Tsjerk Wassenaar tsje...@gmail.com Date: Sat, Apr 4, 2015 at 9:14 PM Subject: Re: [PyMOL] Displaying covalent bonds between amino acids (within protein) and ligand

Re: [PyMOL] Colouring nucleic acids, without changing the colouring of amino acids

Hi Brenton, Jared, For RNA, the residue names are A, C, G, and U (not R*). However it's also possible to specify the nucleic acid, using: set cartoon_color, green, resn G and byres name C1' This way, you filter the selection on an atom of the ribose, that is in all nucleic acids, and in no

[PyMOL] scipy problem

-02-19 17:36:38.356 MacPyMOL[46379:507] HID: Tsjerk Wassenaar’s Mouse 2015-02-19 17:36:38.356 MacPyMOL[46379:507] HID: Counted 2 buttons on this device. 2015-02-19 17:36:38.357 MacPyMOL[46379:507] HID: Apple Internal Keyboard / Trackpad 2015-02-19 17:36:38.357 MacPyMOL[46379:507] HID: Counted 3

Re: [PyMOL] Clip surface only

Hey :) If you want to do it using only Pymol in just a few minutes, try this: set auto_zoom, 0 scale=1.0 import numpy M=numpy.array(cmd.get_view()).reshape(6,3) cmd.pseudoatom(dummy,pos=list(M[4,:]-scale*numpy.dot(M[:3,:3],M[3,:]))) hide everything, (not ligand) within 150 of dummy Adjust the

Re: [PyMOL] raytracing a transparant surface, with reflections only on the cofactors inside

Hi Thomas, Thanks for chiming in. I guess this would be a step towards textures/finishes. I would really like to see more extended support for those in Pymol. Of course that would mostly serve artistic purposes, but I'd gladly raise the suggestion that it can do wonders for highlighting :)

Re: [PyMOL] raytracing a transparant surface, with reflections only on the cofactors inside

Hi Floris, I'm not entirely sure whether these are object/selection or global properties. But have you tried specifying the selection? set spec_reflect, 0, protein Haven't tried it myself, though. Cheers, Tsjerk On Jan 9, 2015 4:07 PM, Floris van Eerden f.j.van.eer...@rug.nl wrote: Dear

Re: [PyMOL] Scripting attempts

Hi :) You can use for-loops in pml files, but it's a bit tricky. Usually you will want to enclose the code in a python .. python end block, indicating that the lines are pure python: python for i in range(2,61): ... python end Also mind that range runs UP TO (excluding) the last number, so

Re: [PyMOL] Scripting attempts

Hey :) Image{}.png.format(str(i).zfill(4)) can also be written Image{:04d}.png.format(i) Cheers, Tsjerk On Tue, Jan 6, 2015 at 4:52 PM, Matthew Baumgartner mp...@pitt.edu wrote: Be sure to reply to the list so everyone can benefit from the questions and answers. Ah, as Tsjerk

Re: [PyMOL] sulfated tyrosine's losing connection

Hi Jordan, A quick look shows that there is no bond between the adjacent phosphotyrosines. Apparently they are too far apart for Pymol's bond check. Cheers, Tsjerk On Tue, Dec 23, 2014 at 6:20 AM, Jordan Willis jwillis0...@gmail.com wrote: Does anyone know why PyMoL renders the PDBs 3U2S and

Re: [PyMOL] CGOs

Hi Bob, Unfortunately, there is little documentation on CGO objects. You can have a look in modules/cgo.py and in the example scripts in examples/devel/ in the pymol directory to get some more information. If there is something specific you want to do, please let us know. Cheers, Tsjerk On

Re: [PyMOL] Get the color code of each residue when using spectrum?

Ni hao Chen Zhao, This works for me: col=[] iterate n. ca, col.append((chain,resi,name,cmd.get_color_tuple(color))) print col Cheers, Tsjerk On Sat, Oct 18, 2014 at 4:57 AM, Chen Zhao chenzhaoh...@gmail.com wrote: Dear all, Is it possible to get the color code of each residue if I color

Re: [PyMOL] Problems setting bg_rgb_top / bg_rgb_bottom

Hi James, Can you try: cmd.set(bg_rgb_bottom,cmd.get_color_tuple(bottom)) The number refers to a color index, so that should probably work. Hope it helps, Tsjerk On Wed, Oct 8, 2014 at 9:27 AM, James Davidson j.david...@vernalis.com wrote: Dear All, I wonder if anyone can help with

Re: [PyMOL] Color according to RMSD

Hi Cedric, The first part is numeric inaccuracy. You get all atomic rmsds in the range of 0 - 1e-12 or so. Spectrum colors according to the extent of this range. For the other one, note that the RMSD (mean sum of MSDs) is pretty low. Usually, it's due to a few residues that don't align perfectly,

Re: [PyMOL] Testing for incentive vs. open-source in scripts

Hi Andreas, A try/except block is actually a very pythonic way of dealing with such issues. You can catch the error with an except clause, that allows executing some code in case the other thing didn't work out. Make sure to only catch the error that is raised by what you're trying, otherwise you

Re: [PyMOL] Testing for incentive vs. open-source in scripts

. Is there anyway of intercepting/silencing this output? Thanks, Andreas On Fri, Oct 3, 2014 at 1:46 PM, Tsjerk Wassenaar tsje...@gmail.com wrote: Hi Andreas, A try/except block is actually a very pythonic way of dealing with such issues. You can catch the error with an except clause

Re: [PyMOL] align and RMSD calculation

Hi Patrick, What other tool do you compare to and how large is the difference? There are different ways to calculate the RMSD, and they may have some rounding errors. Cheers, Tsjerk On Fri, Oct 3, 2014 at 8:17 PM, PC patrick.coss...@inbox.com wrote: Hi, Sorry its me again. Can someone

Re: [PyMOL] Align C-alpha based backbone

Hi Jianhui Song, With a bit of scripting it's not that hard: ## python code from pymol import cmd import numpy def princalign(obj): R = numpy.zeros((4,4)) x = numpy.array(cmd.get_model(obj).get_coord_list()) R[3,:3] = -x.mean(axis=0) x += R[3,:3] R[:3,:3] =

Re: [PyMOL] Academical position in field of macromolecular visualization

Hi James, There are some research groups around that focus on scientific visualization. I recall there was someone talking about it at the Biophysical Society meeting this spring, but I don't immediately remember a name to go with it. I do know that some have taken up this kind of work

Re: [PyMOL] Shell utilities for structural bioinformatics

Hi James, These are the sort of questions that'll be answered elsewhere. Most notably on stackoverflow: http://stackoverflow.com/questions/18364411/using-regex-to-tell-csplit-where-to-split-the-file csplit -b %04d.pdb file.pdb /^MODEL/ {*} Cheers, Tsjerk On Fri, Sep 12, 2014 at 11:25 AM,

Re: [PyMOL] Shell utilities for structural bioinformatics

'^TORSDOF 0' | sed -e 's/^ENDMDL/TER/g' but the resulted files still consist of unused lines BTW might the csplit be used to extract only ONE (e,g first) model from the multi-pdb file? James 2014-09-12 11:39 GMT+02:00 Tsjerk Wassenaar tsje...@gmail.com: Hi James, These are the sort

Re: [PyMOL] Shell utilities for structural bioinformatics

csplit -b %03d.pdb test.pdbqt /^MODEL/ {0} somelog.log man csplit: csplit -f blabla -b %03d.pdb test.pdbqt /^MODEL/ {1} But you want only the first frame anyway, so no real use for csplit... sed /^ENDMDL/q my_docking.pdb | grep -v ^ROOT\|^ENDROOT\|^TORSDOF 0\|^MODEL\|^REMARK | sed -e

Re: [PyMOL] PyMol Dynamics plugin config

Hi Niyaz, The author of the package will have the best answers to these questions. But you should be able to find in the source files where the mdp file is written. There you can make changes, to make sure that coulombtype is set to PME and tcoupltype is set to v-rescale. In addition, you

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

Hi James, I have a light version for fitting gromacs' gro files. No time to adapt that now for PDB, but it's not too hard. ./qfit.py source.gro target.gro output.gro Hope it helps, Tsjerk On Fri, Sep 5, 2014 at 12:31 PM, James Starlight jmsstarli...@gmail.com wrote: should to add than

Re: [PyMOL] PyMol_Gromacs plugin

Hi Niyaz, You can install a version of Gromacs yourself. The script detects which version is active (and installs one if none is found). Cheers, Tsjerk On Thu, Aug 28, 2014 at 2:09 AM, niyaz.sabir niyaz.sa...@gmail.com wrote: Dear PyMol Users, I am a PyMol-Gromacs plugin (

Re: [PyMOL] Visualize Sheets from C-alpha Only Structure

Hi Sean, Maybe this is useful: http://sourceforge.net/p/pymol/mailman/message/31618301/ Cheers, Tsjerk On Wed, Jun 4, 2014 at 10:17 PM, Sean Law magic...@hotmail.com wrote: Jared, For now, we are using different colors to indicate the SS assignments but it's not pretty. We would prefer

Re: [PyMOL] Multiple pdb simulation data

Hi Ritesh, Assuming you want the PDB files to end up in one object and they are numbered like file0.pdb .. file1000.pdb for i in range(0,1000,100): cmd.load(file%d.pdb%i,traj) You can set the step size from 100 to 50, 25, ... One thing that you may want to ask yourself is whether you need all

Re: [PyMOL] How to automate RMSD calculation for large no of structures

If the Wild-Type is called wildtype: rmsds = [(i,cmd.align(i,wildtype)[0]) for i in cmd.get_object_list(not wildtype)] print rmsds or, writing out the results directly open(rmsds.dat,w).writelines(%s %f\n%(i,cmd.align(i,wildtype)[0]) for i in cmd.get_object_list(not wildtype)) Cheers, Tsjerk

Re: [PyMOL] Count_states command

Hi Katherine, You explain some of how you want to do it, but you don't explain what you're trying to do. What is the objective? It may well be that there's an easier way. As a sidenote, create can also make an object with multiple states. Check the help. Hope it helps, Tsjerk On Wed, Dec 18,

Re: [PyMOL] rmsd sicechains super

Hi Osvaldo, The problem can be understood from the description of 'super'. #- PyMOLhelp super DESCRIPTION NOTE: This feature is experimental and unsupported. super performs a residue-based pairwise alignment followed by a structural superposition,

Re: [PyMOL] CGO rotate vs quaternion

Hi Pawel, Have a look here: http://euclideanspace.com/maths/algebra/realNormedAlgebra/quaternions/index.htm It should provide some insight into what quaternions are and how you can use them to rotate or obtain an axis-angle representation. Cheers, Tsjerk On Sun, Nov 24, 2013 at 11:31 PM,

Re: [PyMOL] How to make outlines to spheres drawn in PyMOL ?

Hi Anasuya, And for the other part of your question, check out ray_trace_color: set ray_trace_color, hotpink The thickness can be controlled with ray_trace_gain: set ray_trace_gain, 2 Hope it helps, Tsjerk On Tue, Nov 19, 2013 at 5:21 PM, Jason Vertrees jason.vertr...@schrodinger.com

[PyMOL] Secondary structure for C-alpha only and coarse-grained models

Hey :) I thought there was a post recently about showing secondary structure in C-alpha only models. I can't find it anymore, but in any case it's something popping up now and again. For reconstruction of high-resolution models out of coarse-grained ones, I came up with a very simple algorithm

Re: [PyMOL] alignment of metal coordination

Hi, I'd say that align would be a good start with a selection like: align byres protein1 within 5 of metalion1, byres protein2 within 5 of metalion2 And from there you can see if further refinement is needed. The 5A is arbitrary :p Cheers, Tsjerk On Sat, Nov 9, 2013 at 1:24 PM, Mike

[PyMOL] Molecular models with LEGO

Hey :) What if you could hold the molecules you view in your hands? Ever thought of using LEGO to build molecular models? It may happen if we raise 10 000 votes for my LEGO chemistry project at http://lego.cuusoo.com/ideas/view/51273 Please consider forwarding this mail to anyone you think would

Re: [PyMOL] Molecular models with LEGO

of its representatives. From: Tsjerk Wassenaar tsje...@gmail.commailto:tsje...@gmail.com Date: Friday, October 18, 2013 2:05 PM To: pymol-users pymol-users@lists.sourceforge.netmailto: pymol-users@lists.sourceforge.net Subject: [PyMOL] Molecular models with LEGO Hey :) What if you could hold

Re: [PyMOL] How to visualize coarse-grained pdb file with CONECT ?

Hi Aiqun Huang, It puzzled me for a while. I found that renaming all 'K' atoms to 'C' the bonds are drawn correctly. That still puzzles me, but at least it offers a way to get the desired view. Are you actually running simulations with this model? And are you interested in converting the CG

[PyMOL] Fwd: issue with the allign command

For the record... -- Forwarded message -- From: Pascal Auffinger p.auffin...@ibmc-cnrs.unistra.fr Date: Wed, Sep 4, 2013 at 3:54 PM Subject: Re: [PyMOL] issue with the allign command To: tsje...@gmail.com Hi Tsjerk, Apparently, the problem comes from the fact that I used set

Re: [PyMOL] issue with the allign command

Hi Pascal, What platform is this, and what version of pymol are you using. Also, it works if you type the command, but does it work if you run the script from the terminal? Is it possible that the editor inserted some (invisible) control characters? Cheers, Tsjerk On Sat, Aug 31, 2013 at 3:16

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