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 Radius 5A > > But I se

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 nitr

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 sequence extracted from 1baz.p

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 Abdelz

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 other possibilities, but my dat

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 thin

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 1

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 hy

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 PBC box can be shown in V

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 expected. So once again and

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

t; 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. November 2016 15:36 > *A

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, w

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 = open('NE_S_

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

e('ligCOM') > > cmd.delete('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 > > > >

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 picture

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 command. Does anyone have a sol

Re: [PyMOL] post-processing of pdb ensemble

... of course 8-o :p T. On May 25, 2016 18:32, "Thomas Holder" wrote: > or simply: > > alter bound_combined, chain = chr(ord(chain) - 1) > > Cheers, > Thomas > > On 25 May 2016, at 11:06, Tsjerk Wassenaar wrote: > > > Hi James, > >

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 alteration fo the chains

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 molecules start to rock

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";; > *Date: * Sat, May 14, 2016 07:49 PM > *To: * "Z

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 pa

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! > > I am in charge with the

Re: [PyMOL] Bash scripting and pymol

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

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 special distance relative

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 should add that it works fine if

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

> > Thanks! > > Adam > > On Feb 2, 2016, at 1:39 AM, Tsjerk Wassenaar wrote: > > 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

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 Annemarie, > > Have you t

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 Fred

Re: [PyMOL] pdb edition

; > > 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, so the bond will

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, Pasc

Re: [PyMOL] cgo bug during ray tracing?

Hi Vincent, 25.0 is not a cylinder, but a sausage. Since it has a spherical end, it also has a highlight/phong, which is rendered white and therefore disappears against your background. This won't just happen, but I guess that you've set the raytrace and light settings such that it only gives the

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 superimposed 3D grid of cub

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)

> > 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 > wrote: > > Hi Osvaldo, >> >> I could have been more clear I gu

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

erence > 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 > wrote: > > >> Hi Thomas e.a., >> >> Given two selections, would

[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, Tsjer

[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 :) C

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 i

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

changeably since they could be numerically similar. > > Cheers, > Osvaldo. > > > > > On Tue, Sep 15, 2015 at 3:36 PM, Tsjerk Wassenaar > wrote: > >> Hi, >> >> AFAIK, pseudoatom puts a new atom on the center of mass (or geometry) of >>

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] 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 Saluja

Re: [PyMOL] secondary structure disappears

Hi Adam, You can use iterate to get the secondary structure designation, and then use alter to apply it to the other chains. secstruc=[] iterate model1 and n. ca, secstruc.append(ss) s1=list(secstruc) alter model2 and n. ca, ss=s1.pop(0) The last two lines need to be repeated, including the cop

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)" 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 list of

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. Arturo

Re: [PyMOL] efficiency assigning b-factors

veryone 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

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" wrote: > Hi, > > I have a dictionary that has a bunch of values I want to assign to > b-factors in

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 17

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 with

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 gra

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 wrote: > > Dear all, > > > I find that when I show the protein as cartoon representation in pymol, > and select some residues to show as sticks, then the stic

Re: [PyMOL] how to connect to atoms?

rcherInstitute of Biochemistry and > BiophysicsUniversity of TehranTehran, Iran* > > *Email: karami.le...@ut.ac.ir > * > *Tel: +98 9193155894 <%2B98%209193155894>* > > On Tue, May 12, 2015 at 12:27 AM, Tsjerk Wassenaar > wrote: > >> Hi Leila, >> >&g

Re: [PyMOL] how to connect to atoms?

Hi Leila, Are the peptides already positioned correctly? Then there's nothing you can do with Pymol to help out with Gromacs. With Gromacs, you'll have to make a special bond to account for the link between the peptides, and you have to merge the two peptides during the processing with pdb2gmx. Ch

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 it

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 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 ray tracing, the > bla

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

is with the proper selection > > > > E.g > > PyMOL>select not-relevent, b > 0 > > results only in small atoms selected > > > > and > > PyMOL>select ss, b = 0 > > Selector-Error: Invalid selection. > > b<-- > > > > > > Regard

Re: [PyMOL] Labelling ligands and amino acids

, "Ser403" > > with and w/o the "n. and" part. > > On 7/04/2015 6:28 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, >

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 wrote: > Hi, > > I have skimmed the Label page on > PyMOL Wiki and it

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

[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 Date: Sat, Apr 4, 2015 at 9:14 PM Subject: Re: [PyMOL] Displaying covalent bonds between amino acids (within protein) and ligand To: Bre

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 wrote: > Hi, > > In the structure that goes by the PDB ID

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 amino

[PyMOL] scipy problem

n this device. 2015-02-19 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

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 :) Floris

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" wrote: > Dear all, > > My question i

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 wrote: > Be sure to reply to the list so everyone can benefit from the questions > and answers. > > Ah, as Tsjerk mentioned, you ne

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 you

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 wrote: > Does anyone know why PyMoL renders the PDBs 3U2S and 3U4E without > conne

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 Sun

Re: [PyMOL] Is it possible to move different subunits independently using Pymol

Hey :) PyMOL>help translate DESCRIPTION "translate" translates the atomic coordinates of atoms in a selection. Alternatively, is modifies the matrix associated with a particular object or object-state. USAGE translate vector [, selection [, state [, camera [, object ###

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 wrote: > Dear all, > > Is it possible to get the color code of each residue if I color the whole > molecule

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 wrote: > Dear All, > > > > I wonder if anyone can help with this issue? I am c

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,

[PyMOL] Color according to RMSD

Hey :) In response to an earlier question regarding coloring objects according to per residue RMSD, I wrote a small routine to color according to atom RMSD, after an alignment. Maybe it'll be of any use to someone... The script performs an alignment and then gets the corresponding atoms, for whic

Re: [PyMOL] [gmx-users] constraint and restraints

ch. You are always ready to help. > > I have understood and taken your note : "Whether it makes sense is another > question. The dynamics is usually coupled throughout the protein." > > With very best regards, > > Niyaz > > - Original Message - > *From:* T

Re: [PyMOL] align and RMSD calculation

Maybe this is related to http://www.biopython.org/pipermail/biopython-dev/2010-October/008361.html Cheers, Tsjerk On Fri, Oct 3, 2014 at 8:37 PM, PC wrote: > Hi Tsjerk and others, > > Thank you, I did use PYMOL with cycles=0 > > Online tools I used were: > 1) Superpose > 2) RMSDCalc from ht

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 wrote: > Hi, > > Sorry its me again. Can someone tell me where I can find t

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

onsole, but > the script proceeds anyhow. > Is there anyway of intercepting/silencing this output? > > Thanks, > > Andreas > > On Fri, Oct 3, 2014 at 1:46 PM, Tsjerk Wassenaar > wrote: > >> Hi Andreas, >> >> A try/except block is actually a very py

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] 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] = numpy.linalg.eig

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 commerciall

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 probably

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" | se

Re: [PyMOL] Shell utilities for structural bioinformatics

#x27;ve tried to do it > > csplit -b "%04d.pdb" my_docking.pdb /^MODEL/ {*} | grep -v '^ENDROOT' | > grep -v '^TORSDOF 0' | sed -e 's/^ENDMDL/TER/g' > > but the resulted files still consist of unused lines > > BTW might the csplit be use

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, Ja

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 wrote: > should to add > > than I've used both TMali

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

ne which should be deleated before it merging (in my case it's the > HEADER lala.pdb). could you suggest me the combination of grep sed command > which should be used to deleate the first line from both pdbs and than > merge it in one-command method? > > Many thanks, > > J

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

Hi James, You can use pymol -cd "pymolcommands". See http://www.pymolwiki.org/index.php/Command_Line_Options However, the first part is much easier with grep or sed. To remove all solvent molecules: grep -v "^ATOM.*SOL" in.pdb > out.pdb To remove NA+/CL- too grep -v "ATOM.*\(SOL\|NA+\|CL-\)" i

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 wrote: > Dear PyMol Users, > > > I am a PyMol-Gromacs plugin ( > http://www.pymolwiki.org/inde

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 wrote: > Jared, > > For now, we are using different colors to indicate the SS assignments but > it's not pretty. We would prefer to show the SS f

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 al

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")) Che

Re: [PyMOL] Pymol cannot load pdb file

Hi Jacky, Do you encounter the same error with other PDB files? If not, can you check the file? If you don't find anything obviously wrong, can you post this PDB file somewhere where we can access it? If you do get the same error with other files, but you didn't have it before, you may have corrup

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