Re: [PyMOL] slab mode fine-tuning

Hi, On Tue, 29 Mar 2011 6:12 AM Nadine Utz [mailto:nad...@mmb.pcb.ub.es] wrote: > > Dear pymol users, > > > > I am looking for a way to "zoom in" a molecule, like the slab mode when > > you are rolling the scroll wheel. The reason why rolling the scroll > > wheel does not work in my case is that

Re: [PyMOL] change transparency for only a selection

Hi Nick, On Wed, 2011-05-18 11:39 EDT, Nicolas Bock wrote: > Hello list, > > I would like to change the stick_transparency for a selection but it > doesn't seem to work. I am using the xyz file from the wiki: > > http://www.pymolwiki.org/index.php/Visualizing_a_computed_structure_-_a_comment

Re: [PyMOL] Pymol: Cartoon representation for .pdb file with multible entries

Hi Alexander, On Wed, 2011-10-26 12:53 EDT, Alexander Schulz wrote: > Hi Thomas, > > thank you very much for the answer, I'm beginning to understand the > actual problem now. > > dss state=1 > helps, but it changes the problem: I would like to see the secondary > structure that corresponds

Re: [PyMOL] Forced Linux/Python upgrade, killed PyMol, please help!

Hi John, On Wed, 2011-12-21 11:12 EST, John Ladasky wrote: > Hello everyone. It has been a while since I posted here. Apologies to > the admins, I tried to subscribe again, and I forgot that I was already > subscribed. > > For some non-PyMol work, I was obligated to upgrade my operating s

Re: [PyMOL] about super_all.py Plugin installation.

Dear Pavan, On Tue, 27 Dec 2011 00:15:38 +0530, PAVAN PAYGHAN wrote: > Dear PyMol Users, > > I am using PyMol +v0.97 version on Windows XP .I have downloded > super_all.py > and tried to install the plugin by using install Plugi

Re: [PyMOL] sequence file extraction

Hi Thomas, On Tue, 2012-07-24 12:57 EDT, Thomas Holder wrote: > Hi Stefano, > > this is a known bug and it has not been fixed yet. A workaround is to > only save one object at a time to fasta format. > > See bug report: > http://sourceforge.net/tracker/?func=detail&aid=3466472&group_id=4546

Re: [PyMOL] drawing a bond between the same Calpha atom in different states

Hi Jon, On Thu, 2012-12-13 16:09 EST, Jonathan Grimes wrote: > Hi All, > >I have 2 different states of the same molecule..different > conformations generated from MD, so the same number of Calpha atoms, with > a direct 1:1 mapping between Calphas with the same residue numbering. >

Re: [PyMOL] drawing a bond between the same Calpha atom in different states

Hi, (replying to my own message) On Thu, 2012-12-13 15:52 EST, Robert Campbell wrote: > Hi Jon, > > On Thu, 2012-12-13 16:09 EST, Jonathan Grimes > wrote: > > > Hi All, > > > >I have 2 different states of the same molecule..different > &

Re: [PyMOL] About draw_links.py by Dr. Robert Campbell

Hi Anasuya, On Thu, 21 Feb 2013 17:10:40 +0530 Anasuya Dighe wrote: > > Hi, > > I have been trying to use the script draw_links.py at > http://pldserver1.biochem.queensu.ca/~rlc/work/pymol/ to view links > between each pair of c-alpha atoms present in an atom selection. > Once I load a PDB (1

Re: [PyMOL] Splitting a PDB file into its constituent chains, and making multiple (smaller) PDB files

Hello Anasuya, On Thu, 2013-04-04 15:49 EDT, Anasuya Dighe wrote: > Hello, > > I wanted to know if its possible in PyMOL to split a PDB file with > multiple chains,into its component chains and make smaller PDB files > corresponding to each chain. > > For eg: I have a pdb file, 1a55.pdb, hav

Re: [PyMOL] SS in a trajectory

Hi, On Wed, 2013-04-24 10:31 EDT, Jianghai Zhu wrote: > Hi, > > I have a trajectory file, in which two short helices would merge into one > long helix. However, when I play the trajectory in Pymol as cartoon, the > long helix would still be shown as two helices with a loop in between. > Is t

Re: [PyMOL] PyMOL-users Digest, Vol 82, Issue 1

Hello Bachar, On Fri, 2013-05-10 14:29 EDT, Bachar Cheaib wrote: > Dear pymol users, > > I have wondered whether someone know how to know if a such structure in > pdb file is multi-mer or mono-mer biologically speaking? Somehow in the > related publication of structure this information is pr

Re: [PyMOL] PyMOL-users Digest, Vol 82, Issue 1

Hello Bachar, On Fri, 2013-05-10 14:29 EDT, Bachar Cheaib wrote: > Dear pymol users, > > I have wondered whether someone know how to know if a such structure in > pdb file is multi-mer or mono-mer biologically speaking? Somehow in the > related publication of structure this information is pr

Re: [PyMOL] PyMOL 1.6 pre-release announcement

Hello Thomas and David, Was there any resolution of this? I've just compiled the latest version from SVN and I have the same problem opening files created under version 1.5.0. This is on Debian testing (32-bit). Cheers, Rob On Fri, 2013-04-26 19:15 EDT, David Hall wrote: > Hi Thomas, > >

Re: [PyMOL] Problem Compiling v 1.6.0.0 in 64 bit Debian Testing

Hi Stephen, On Tue, 2013-06-25 09:16 EDT, "Stephen P. Molnar" wrote: > I have just installed the 64 bit Debian Testing distribution in an > Oracle VM on my laptop as a test bed. > > I successfully compiled v 1.6.0.0 in my 6 bit Debian Wheezy production > OS. > > I didn't get any error messag

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

On Tue, 2014-01-07 12:05 EST, Jed Goldstone wrote: > Check out Robert Campbell's Pymol script repository. > I think align_all_to_all.py should do what you want, including exporting > RMSD values. > > http://pldserver1.biochem.queensu.ca/~rlc/work/pymol/ Actually, I think Om only wants to ali

Re: [PyMOL] combining multiple objects into one multistate object

Hi Jed, On Thu, 2014-01-16 10:28 EST, Jed Goldstone wrote: > I know this seems silly, but I can't figure out how to combine multiple > separate objects into one multistate object. I have a set of Modeler > models loaded from a single pdb file, automagically separated into > separate objects

Re: [PyMOL] ccp4 question

Dear Stefan, On Tue, 2014-02-04 14:44 EST, Stefan Ivanov wrote: > Dear Pymolers, > > I tried to run ncont on a pdb structure and got a .ncont file as output, > but the only thing the file contains is an error message (see below). I > tried copying default.def into the working directory, but c

Re: [PyMOL] command question RE printing out distances to text file

Hi Suzanne, You can also get the distance printed in the external GUI or terminal window by using the "cmd.distance" version of the command. So either you can assign the distance to a variable and print it or you can print the result directly. Assuming you have two selections, sele1 and sele2 sp

Re: [PyMOL] command question RE printing out distances to text file

Hi Suzanne, You can also get the distance printed in the external GUI or terminal window by using the "cmd.distance" version of the command. So either you can assign the distance to a variable and print it or you can print the result directly. Assuming you have two selections, sele1 and sele2 sp

Re: [PyMOL] Fwd: color by RMSF or RMSD

Hello Hidhi, On Wed, 2014-07-23 16:39 EDT, Nidhi Jatana wrote: > Dear Sir/Madam > I have generated five models for a protein and I wanted to check how the > models align to each other and color them by RMSD/RMSF. I wanted to know > what should be the ideal way to do it. Shall I use RMSF or RMS

Re: [PyMOL] Backbone RMSD

Hello Amita, On Wed, 2014-09-10 09:41 EDT, Amita Rani Sahoo wrote: > Dear Pymol users, > > I want to calculate backbone RMSD of proteins having two different > conformations (For example 2RH1 and 1F88). With the align command it > calculates the executive RMSD, but i need backbone RMSD. Pleas

Re: [PyMOL] efficiency assigning b-factors

Hi Jordan et al., Yes one can use the alter command with a whole selection at once and it is much faster. I hadn't realized that until Thomas Holder helped fix my script that appears to do what you were wanting to do: http://pldserver1.biochem.queensu.ca/~rlc/work/pymol/data2bfactor.py The B-fa

Re: [PyMOL] secondary structure disappears

Hi Adam, I think you also want to make sure that each strand as a distinct chain ID if you want the cartoon representation to work correctly. Unfortunately that means you have to use "alter" but to change the chain IDs on the objects created by the split_states command before merging them all int

Re: [PyMOL] question on cctbx and pymol

Hi, * Jianghai Zhu [2005-08-24 01:59] wrote: > > I could not get cctbx work under either MacPymol or PymolX11Hybrid in > Mac OS X. Anywhere I can find some instructions to get cctbx work in > OS X? There is a page on the cctbx with special instructions for using it on the Mac: http://cc

Re: [PyMOL] [colors frozen for rendering modes defined in .pymolrc]

Sebastien, * Sebastien Moretti [2005-10-17 08:41] wrote: > >Sebastien, > > > >>I cannot > >>change the color for rendering modes I defined. > > > >I do not understand what you mean by this. > > > >Cheers, > >Warren > > I mean that the color, for cartoon view, is unchangeable when 'set > carto

Re: [PyMOL] Listing secondary structure assignments

* J. Evan Sadler [2005-11-23 13:08] wrote: > I need a list of the secondary structure assigned to each residue by dss in > pymol. Is there a simple way to write this information to a file, or dump it > to the screen? To dump it to the screen, try: iterate & n. ca, print resn,resi,ss Cheers,

Re: [PyMOL] Re: New spectral color pallette

Alexander, * alexander.paut...@bc.boehringer-ingelheim.com wrote: > > > > I would like to color my protein according to B-factor with a self-defined > > spectral palette (In this case I have put sequence conservation into the > > Bfactor this column). I found that > > spectrum b, blue_whit

Re: [PyMOL] What residues have I selected?

Hi Aaron, * Aaron New [2006-02-09 09:36] wrote: > I have selected atoms near an object of interest, and extended this via > byres to a selection of the other atoms that are part of the same residue. > Is there any way to output a file that would have the coordinates of the > atoms I have selected

Re: [PyMOL] delete/create bonds in pymol

Hi Vanessa, * Vanessa Oklejas [2006-02-10 11:18] wrote: > Hi All, > > Does anyone know how to delete bonds between atoms in PyMol? You can use the "unbond" command: PyMOL>unbond ? Usage: unbond [ atom1 [, atom2 ]] You can pick the two atoms with the mouse (such that they are selected and

Re: [PyMOL] a scaling question

Hi Fei, * Fei Xu [2006-04-19 11:55] wrote: > Hi!: > I met a scaling problem. > I created many pdb files along one trajectory of DNA movement. I loaded > each pdb file in pymol to create a picture, that is, one frame of the > trajectory. Pymol shows each molecule in an optimal size automatically >

Re: [PyMOL] D-ala

Hi Orla, * Orla O'Sullivan [2006-04-28 11:37] wrote: > > Is there any way to change an L-alanine to a D-alanine in pymol Sure. In the "build" menu there is an entry: Invert (pk2)-(pk1)-(pk3) [Ctrl-E] pk1 is the atom whose configuration is to be inverted. pk2 and pk3 are the two atoms atta

Re: [PyMOL] That _cmd thing

Hello Atro, * Atro Tossavainen [2006-05-05 11:10] wrote: > > I've built pymol 0.99 manually according to the INSTALLATION VIA COMPILATION > instructions. I don't want to have a second copy of all the dependencies > which I already have anyway, and I want to have pymol for multiple flavours > of

Re: [PyMOL] loosen secondary structure

Hi, * O. J. Ganesh [2006-05-18 16:09] wrote: > > Hey PyMOL gurus: > > I have a 'perfect' helix. Is there some way to 'loosen' all of the > angles in the helix so instead of 3.6 residues per turn, I could > have, say, 8 residues per turn. My goal is to make the helix more > 'coil-like'. Is thi

Re: [PyMOL] Problem loading chempy objects to pymol

Hello Raúl, * Raúl Mera [2006-06-07 04:32] wrote: > Hello all, > > I'm writing a Pymol plugin which creates many chempy > objects (of the class Indexed) and displays the > objects as diferent states of a structure. The atoms > in the objects are not standar (they are dummy atoms > to represent a

Re: [PyMOL] debian: error in opening pymol

Hi Arvind, * Arvind Marathe [2006-06-09 00:14] wrote: > Hi all, > my system is a newly installed debian-3.1 linux. 'pymol' seems to be part > of the installed package. But when I try to open pymol, I get the > following error: > > -

Re: [PyMOL] sphere_scale problem

Hi Vladimir, * Vladimir Potapov [2006-07-10 12:05] wrote: > Hi everyone, > > I need to set different sphere radius in my task - large CA and small CB > atoms. I use commands: > set sphere_scale=1.5, name ca > set sphere_scale=0.5, name cb > > What I see, that command affects all atoms, not jus

Re: [PyMOL] align states

Hi, * Joel Tyndall [2006-07-15 14:29] wrote: > Hi andrea, > > you can easily do this by > > split_states my_struct > dele my_struct > > > for the NMR ensemble, then I would use the action menu, align function > and align them to state_1. This is in effect aligning the separate > states as

Re: [PyMOL] How can I change the surface_quality of an electron density map surface?

Hi Jonathan, * Jonathan Stuckey [2006-08-15 12:03] wrote: > How can I change the surface_quality of an electron > density map surface? set surface_quality=-1 does not > do anything. The surface_quality parameter affects the quality of molecular surfaces, not isosurfaces. To change the smoothnes

Re: [PyMOL] Paths to loaded objects

Hi folks, * Michael Lerner [2006-08-21 12:26] wrote: > I think he means for you to have a "Load" button as part of your > plugin. That button would first record the path to the file and then > call through to cmd.load(). Perhaps what Ron needs to do is not use the cmd.load() function but use hi

Re: [PyMOL] problem getting kabsch.py to run

Hello Margaret, * Margaret Luk-Paszyc [2006-10-15 14:07] wrote: > Hello -- > > Can someone please advise me? > I'm a new user of PyMol trying to get the kabsch alignment > script to work. I only installed the main pymol installer > (v 0.99r6), and I have copied the kabsch.py script as the > w

Re: [PyMOL] mesure line width

Hi Andrea, * andrea carotti [2007-02-02 14:13] wrote: > Hi all, > is there the possibility to change the line width of the distance > measure between two atoms? set dash_width, 3 If you like using a white background like I do, you can also change the dash color using the "Setting... -> Color.

Re: [PyMOL] simple cgo question

Hi Richard, * Richard Gillilan [2007-02-19 10:22] wrote: > > I'm probably making a simpler mistake here, or perhaps there is > something wrong with my installation or paths. > I'm trying to load and display the simple cgo example in the manual. > I created a file named "arrows" containing th

Re: [PyMOL] Question about electron density map with mtz file

Hi Adiphol * adi di [2007-05-11 10:26] wrote: > Dear all, > > I am trying to put on the electron density. I only > have .mtz file but I have a look at the manual and the > program need XPLOR file. How can I get the XPLOR file > or do I need to convert the mtz file to this - if so > how can I do

Re: [PyMOL] APBS

Hi Vaheh, * Oganesyan, Vaheh [2007-05-30 09:45] wrote: > I did not get much luck with those recommendations either. I was doing > exactly the same. Something is phishy with my pymol and/or APBS installation. > I did check for different pdb files, so it is not pdb related. The roor > message is

Re: [PyMOL] APBS

eports "i686" or "x86_64" Rob > > Steve > > -Original Message- > From: pymol-users-boun...@lists.sourceforge.net > [mailto:pymol-users-boun...@lists.sourceforge.net] On Behalf Of > Oganesyan, Vaheh > Sent: Thursday, May 31, 200

Re: [PyMOL] low-end graphics cards/laptops

Hi David, * David A. Horita [2007-06-14 11:52] wrote: > Hi, > While I've seen a number of examples of good graphics cards to use with > Pymol, I'd like some feedback on what an acceptable low-end is for a > Windows laptop computer. Specifically, is the Intel GMA950 completely > useless or just

Re: [PyMOL] spectral coloring

Hi Martin, * Martin Höfling [2007-06-26 15:15] wrote: > Hi there, > > i am trying to map b factors on a surface representation. > > I am using spectrum b,blue_white_red,mymol and the colors are fine. Is there > a > way to fine tune the color spectrum, such as with the "Midpoint" and "Offset

Re: [PyMOL] coloring based on sequence identity

* Martin Höfling [2007-06-27 01:33] wrote: > Am Dienstag, 26. Juni 2007 schrieb Eva Vanamee: > > Hi, > > > > I'd like to color a molecule based on its sequence similarity to another > > molecule. > > Can this be done in Pymol? > > If you can quantify "similarity" in a number you can write it into

Re: [PyMOL] How to dislocate independently each structure when you have loaded two structures?

* Andreas Henschel [2007-06-27 15:49] wrote: > Hi Julio, > > If I understood you right, you can simply use translate, eg.: > translate [20,0,0], mol_to_dislocate > > The important thing is that "turn" and "move" modify the camera, while > translate and rotate modify the coordinates. > > Cheers

Re: [PyMOL] python for loop with pymol command usage

Hi Louis, * Clark, Louis [2007-07-04 12:01] wrote: > Dear user-group, > > I'm trying to learn how to use python commands inside pymol .pml > scripts. I seem to be missing some understanding about how the > interface works. Could somebody tell me how to fix this command below? > > > > PyM

[PyMOL] my color_b.py script

To all you colouring aficionados, I've updated the color_b.py script on my web page to include Mark Wall's addition of user-defined, 3-colour, gradients. Now you can type on the command line something like: color_b selection, gradient=user, user_rgb=(0.,.3,1.,.8,.8,.8,1.,.8,0.) to get colours

Re: [PyMOL] aligning multimodel pdb file

Hi Abhi, On Thu, 23 Aug 2007 12:51:10 -0700, Abhinav Verma wrote: > I want to align different models of a multimodel pdb file. > > How can I do that without extracting models as identical pdb. > > cheers, > Abhi Try the intra_fit command. Cheers, Rob -- Robert L. Campbell, Ph.D. Senior Rese

Re: [PyMOL] getting lists of resn, resi, and atom ID of a selection.

Dear Tomoko, On Tue, 18 Sep 2007 21:40:34 +0900 (JST), Tomoko Niwa wrote: > Dear all > > I am a beginner in Python programming. > I would like to get lists of resn (residue names), resi (residue > identifiers) and atom ID of a selection. > For example, in case of 1IEP_organic; > [

Re: [PyMOL] chain atom seq by cmd

On Wed, 03 Oct 2007 03:11:41 +0900, Hyunchul Kim wrote: > Hi, all > > How can I extract protein sequence from given pdb files by python API for > pymol ? > I want to get a sequence which is extracted from coordinates not the > annotated residue sequence in remarks. Assuming the protein has all

Re: [PyMOL] moving objects freely

Hi Tom, On Thu, 04 Oct 2007 11:20:35 -0700, Tom wrote: > From time to time, I have a need to manually move objects relative to > one another. For example, manual docking of a ligand requires that it the > translated and rotated relative to its binding pocket. It there a simple, > intuitive

Re: [PyMOL] obtaining coordinates of solvent-surface points

Hello John, On Thu, 22 Nov 2007 12:36:32 -0800 (PST), JJ wrote: > Hello: > Im new at pymol and would like to obtain the > coordinates of the dots that make up the > solvent-accessible surface. I can obtain the vertices > using cmd.get_povray()[1], but that will give me a > list of coordinates o

Re: [PyMOL] obtaining coordinates of solvent-surface points

On Thu, 22 Nov 2007 22:43:27 -0800 (PST), JJ wrote: > > >> > From: Robert Campbell - > 2007-11-22 21:56 > > Rather than use PyMOL's surface, I've used the > triangulated surface output > by Michel Sanner's msms program. << > > Thanks m

Re: [PyMOL] Calculation of Domain Volume in Pymol

Dear Buz, On Fri, 04 Jan 2008 15:43:41 -0500, Buz Barstow wrote: > Dear all, > > I'd like to very accurately calculate the volume of a selection in > pymol, or with tools that are callable by pymol? Could anyone suggest > a program or algorithm? MSMS will calculate areas and volumes. I ha

Re: [PyMOL] Changing Bfactors

On Sat, 12 Jan 2008 20:21:37 +0530, rama krishna wrote: > Dear User, > I need to color the Molecule based on generalized order parameter > after running the script "data2bfactor" > i used the command data2b_res 'mol','datafile' > > after that it shows that > IOError: [Errno 2] No such file or di

Re: [PyMOL] MSMS Cavity Visualization in Pymol

Hi Buz, On Wed, 30 Jan 2008 14:41:00 -0500, Buz Barstow wrote: > Does anyone know of a script that is capable of displaying the > surfaces identified by msms in pymol? I have a script called msms_cgo.py that you can download from: http://pldserver1.biochem.queensu.ca/~rlc/work/pymol/ Downlo

Re: [PyMOL] MSMS Cavity Visualization in Pymol

A little oops! On Wed, 30 Jan 2008 16:33:00 -0500, I wrote: > Hi Buz, > > On Wed, 30 Jan 2008 14:41:00 -0500, Buz Barstow wrote: > > > Does anyone know of a script that is capable of displaying the > > surfaces identified by msms in pymol? > > I have a script called msms_cgo.py that you can

Re: [PyMOL] merging many frames to one

Hello Dimitry, On Tue, 12 Feb 2008 16:43:28 +0300, DimitryASuplatov wrote: > Hello, > I have a .pdb1 file with biological unit. It consists of two frames > representing two chains (one per frame) together forming biologicaly > significant molecule. I could apply crystallographic symmetry, instea

Re: [PyMOL] merging many frames to one

Hi again, Dimitry, On Tue, 12 Feb 2008 09:10:23 -0500, Robert Campbell wrote: > Hello Dimitry, > > On Tue, 12 Feb 2008 16:43:28 +0300, DimitryASuplatov > wrote: > > > Hello, > > I have a .pdb1 file with biological unit. It consists of two frames > > repre

Re: [PyMOL] Fwd: Apply a transformation matrix to a selection

Hi Toni, On Tue, 04 Mar 2008 13:01:58 +0100, Toni Pizà wrote: > > create a, resi > > > > cmd.transform_selection("a", [[x,x,x,x],[x,x,x,x],[x,x,x,x],[x,x,x,x]], > > homogenous=1) > > > Thanks (is better late than never)! > > But I want to apply a set of selective transformations with a

Re: [PyMOL] getting a list of main-chain hydrogen bonds

Hi Tomoko, On Mon, 05 May 2008 18:26:17 +0900, Tomoko Niwa wrote: > Thanks for kind advices. > > Whatif and PISA worked excellently, but I want to get the list within Pymol. > > > By parsing the pymol modules, I found > > hb = cmd.find_pairs("((byres "+sss1+") and n;n)", >

Re: [PyMOL] Spheres for metal ions

Hi Gary, On Tue, 20 May 2008 12:12:43 +0200, Gary Hunter wrote: > I am displaying pdb files of metalloenzymes, and like to show the metal ions > as spheres. > I select the metal and use show>spheres > Fine > Somehow recently I must have done something to reset the vdw radius of > manganese (MN i

Re: [PyMOL] How to view electron densities from the PDB

Hi, On Fri, 27 Jun 2008 13:25:02 -0400, Michael Lerner wrote: > This is probably a fairly basic question, but I'm stumped. I want to > visualize electron densities along with my PDB file. So, say I'm interested > in 2DJX. I go to the PDB and download 2DJX.pdb and 2djx-sf.cif. PyMOL > doesn't see

Re: [PyMOL] coloring based on sequence identity

Dear Morri, On Fri, 22 Aug 2008 13:35:32 -0700, Morri Feldman wrote: > Dear Rob, > > I'm interested in using your variability script with a substitution matrix. > Would you please send me an example of a substitution matrix file? Thanks > for writing such a useful script. Sure. Attached are

Re: [PyMOL] I want to represent a domain of my molecule as a low resolution solid shape

Dear Pietro, On Thu, 11 Sep 2008 13:18:20 +0100, Pietro Roversi wrote: > Dear everyone, > I want to represent a domain of my molecule as a low > resolution solid shape. > > I have chosen surface representation but the surface is clipped, > exposing the inner part, which mak

Re: [PyMOL] Showing conserved residues

Hi Abhinav, On Thu, 29 Jan 2009 13:10:25 -0800, Abhinav Kumar wrote: > Is there someway to select and show conserved residues when a bunch of > superimposed structures are loaded into Pymol? > And if so, can identical and similar residues be selected separately? I don't believe that there is a

Re: [PyMOL] trouble with symexp command

Hi Dave, On Tue, 03 Feb 2009 16:33:28 -0500, David Garboczi wrote: > I am examining packing in several space groups by issuing the command > > symexp foo, foo.pdb, sele, 10 > > If I select the whole reference molecule, I think that I should get > all the symmates within 10 A displayed. But f

Re: [PyMOL] fitting problem

Hi Sébastien, On Mon, 02 Mar 2009 18:21:15 +0100, sconill...@chimie.u-strasbg.fr wrote: > Hi all (for the second time today ...), > > I have a problem using the "fit" function. When I try to do this : > > > fit (fittest1 and resn P and !h.), (2VT4 and resn P and !h.) > > I have this message er

Re: [PyMOL] problem in showing the electron density map

Hi Peter, On Fri, 03 Apr 2009 02:38:03 +0530, peter hudson wrote: > Hello all > > I am trying to upload the ED map on pymol. but, it is not visible on the > screen. Although i checked at pymol wiki and i did as it is given on the > wiki. > For example. > > I took ccp4 format map and coverted i

Re: [PyMOL] POVRAY Usage

Hi Tom On Fri, 15 May 2009 14:57:36 -0700, Thomas Stout wrote: > What version of PyMOL does this work with? I've been trying your commands > with versions 1.1 and 1.2b and while PyMOL reports that the primitives have > been processed, nothing is written to the file "protein.pov" other than the

Re: [PyMOL] surface for oligosaccharide chains

On Fri, 03 Jul 2009 16:18:10 +0200, Raluca Mihaela ANDREI wrote: > Hi! > Can somebody tell me why I can't create surfaces for the > oligosaccharide chains? By default, the surface and mesh commands ignore all atoms in HETATM records in a PDB file. You can change that with: set surface_mode,

Re: [PyMOL] Pymol build from source

Dear Joseph, On Tue, 07 Jul 2009 11:00:10 +0200, Andre Joseph wrote: > Dear Delano Scientific support > > I've been fetching source code from the sourceforge repositories yesterday. > I've no error or warning during "./configure", "make" or "make install" > steps. > However, when I launch pymol

Re: [PyMOL] Measure surface area

Hi Mirek, On Mon, 10 Aug 2009 11:21:39 -0700 Warren DeLano wrote: > PyMOL isn't the optimal tool for measuring surface area -- perhaps > others on the list can suggest good alternatives. I like MSMS for this. I have a script that will calculate the area (both solvent exposed and solvent acce

Re: [PyMOL] Alignment Objects

Hi David On Thu, 10 Sep 2009 14:47:43 -0700 (PDT) David Hall wrote: > Is there any documentation on getting information out of alignment objects > into scripts? I tried looking around the wiki, but I didn't see anything. > > I'm just wondering things like if I have a residue in one object, find

Re: [PyMOL] spectrum

Hi Mark and Sean, On Sat, 07 Nov 2009 10:05:59 -0500 Sean Law wrote: > Sorry for the earlier confusion. I think I found a hackish way of getting > a gray spectrum: I know I'm biased, since I wrote the color_b.py script, but I fail to see what is difficult about typing: color_b "selectionna

Re: [PyMOL] Spectrum

Hi Sean, On Mon, 09 Nov 2009 10:58:53 -0500 Sean Law wrote: > > Robert, > > I would have to agree with you. I've used many of your scripts and have > also learned a lot from them and think that the color B script is pretty > robust and helpful. Thanks. > I could be wrong but I remember the

Re: [PyMOL] Show hydrogen bonds in current object only

Hi Jason, On Sun, 29 Nov 2009 12:29:08 -0500, Jason Vertrees wrote: > You can automate the task. Load your 100 proteins. Use a wildcard > from the command line or a script like loadDir > (http://pymolwiki.org/index.php/LoadDir). Align them. Then, run: > > python > for n in cmd.get_names("ob

Re: [PyMOL] difficulties with pymol’s fuse command .

Hi, I posted an answer on the blog, but I'll copy it here. Someone can correct me if I'm wrong! On Tue, 08 Dec 2009 10:02:59 -0600 Michael Zimmermann wrote: > I have no experience with fuse, but my guess would be Mariana might > want to just use 'bond' and translate one termini as needed. If

Re: [PyMOL] Whitespacing?

Hi, On Tue, 26 Jan 2010 10:48:58 -0600 Michael Zimmermann wrote: > If you have a lot of files to do this to, I would suggest learning at > least a little bit of perl. It might not be as nice an option as a > python tab manager (depending on your point of view), though. Or even better, try sed

Re: [PyMOL] B-factor replacing problem

Hi Simon, On Mon, 08 Mar 2010 18:09:31 +0100 Simon Lindhoud wrote: > Dear all, > > Unfortunately I'm not really familiar with programming in Python (yet) but > I've encountered a problem with MacPyMol in running the script that can be > found here: > http://cavanagh-lab.bch.ncsu.edu/bobay/intr

Re: [PyMOL] B-factor replacing problem

Hi Thomas, On Tue, 09 Mar 2010 10:29:17 +0100 Thomas Holder wrote: > Hi Simon and Robert, > > > It sounds like the file as it is read by the script is completely on one > > line. I wonder if this is the old UNIX vs MSDOS line ending problem. > > yes, sounds like a linefeed problem. But actuall

Re: [PyMOL] frustrating rms command

Hello Alan, On Tue, 16 Mar 2010 11:33:41 + Alan wrote: > Hello there, > > I am very frustrated with a very simple command, let me show: > > PyMOL>rms (out and not hydrogen), (018.none_neutral.pdb_NEW and not > hydrogen) > ExecutiveRMS-Error: No atoms selected. > PyMOL>sele r, (018.none_neu

Re: [PyMOL] frustrating rms command

Hi, On Tue, 16 Mar 2010 09:23:50 -0400 David Hall wrote: > See http://www.pymolwiki.org/index.php/Intra_Rms#USER_EXAMPLES.2FCOMMENTS > comments that start with "Fit, Rms, Rms_Cur are finicky and only > work..." as that likely explains your problem and a possible solution. > > But I agree that p

Re: [PyMOL] coordinates

Hi Jed, On Mon, 22 Mar 2010 10:23:34 -0400 Jed Goldstone wrote: > Of course, you could just use the .pdb file as a text file: > > grep CA .pdb | cut -f 2,4,7,8,9 > > will get you the amino acid number, the amino acid identity, and x,y,z > coordinates for the CA. Often this will work, but

Re: [PyMOL] please help-how to generate dimer file from monomer file in pymol

Hello Jenna, On Tue, 06 Apr 2010 00:36:38 -0400 JiangJiang Liu wrote: > When I open the pdb file 1B8E (a homodimer protein) through > pymol I can only see a monomer shown in the screen. Now I know the > biological dimer is produced through crystallographic symmetry operations > in

Re: [PyMOL] PyMOL Plugin Architecture

Hi Maia, Just to add to what Jason said: On Thu, 22 Apr 2010 17:16:41 -0400, Jason Vertrees wrote: > > 2. Which plugin allows me to move one structure relative to another. (I > > want to do manual docking of one structure into another). > > You don't need a plugin to move objects. Just use SH

Re: [PyMOL] msms_pymol.py

Hi Sujuan, Given that this is my script, I'll answer. :) On Tue, 11 May 2010 14:38:52 +0800 sujuan wang wrote: > Hi All, > When i run the script download from > http://pldserver1.biochem.queensu.ca/~rlc/work/pymol/, I issue the commond: > calc_msms_area 2mlt-melittin, there are always something

Re: [PyMOL] msms_pymol.py

Hi Sujuan, On Tue, 11 May 2010 14:38:52 +0800 sujuan wang wrote: > Hi All, > When i run the script download from > http://pldserver1.biochem.queensu.ca/~rlc/work/pymol/, I issue the commond: > calc_msms_area 2mlt-melittin, there are always something wrong as follows: In addition to my previous

Re: [PyMOL] msms_pymol.py

Hi Hongbo, On Wed, 12 May 2010 15:59:36 +0200 Hongbo Zhu wrote: > You can solve it by adding the following line in the msms_pymol.py you > downloaded from Robert's page to line 133, right before msms_cmd is defined. > > if msms_path.startswith('C:/'): msms_path = '\"%s\"' % (msms_path,) >

Re: [PyMOL] How draw the line in images

Hi Peter, On Wed, 12 May 2010 10:42:36 -0400 Jason Vertrees wrote: > Peter, > > If you knew the positions of the end points of the lines you could > make CGO lines, or you could just use a distance measure between two > pseudoatoms and modify some label/dash settings: As Jason says, if you hav

Re: [PyMOL] Helices as cylinder and ribbon - both in a single representation

Hello Abhi, On Fri, 14 May 2010 12:19:34 +0200 Abhinav Verma wrote: > I wish to show one chain in cylindrical helices, while the other one in > ribbon representation. How can I achieve this with pymol. If the two chains are in one object, then you need to split them into two objects. So if I'

Re: [PyMOL] msms_pymol.py

Hi Sujuan, On Tue, 18 May 2010 15:58:59 +0800 sujuan wang wrote: > thank you for you reply and modification of the script. now Ican calculate > the surface area. but when I calculate the surface of part protein, it seem > that the surface area including the surface adjacent with other residues,

Re: [PyMOL] crankshaft flip

Dear Jakob, On Mon, 28 Jun 2010 15:32:59 +0200 Jakob Nielsen wrote: > I would like to modify a protein pdb file with a "crankshaft" flip, which > is the anti-correlated double change: psi(i-1) += delta and phi(i) -= delta. > Such a change should leave the protein coordinates unchanged effecting

Re: [PyMOL] Ray Trace Triangles

Hi Sean, On Fri, 09 Jul 2010 11:05:09 -0400 Sean Law wrote: > I have been tackling this problem (on and off) for quite some time now but > without any luck. I have been trying to create CGO triangles using the > following simple sample script: > > > ### > > fr

Re: [PyMOL] how to run a python script

On Fri, 09 Jul 2010 13:46:57 -0400 Vivek Ranjan wrote: > Hello, > > I am trying to run a simple python script from Pymol and cannot run it: > I saved the above in a file named "axes.py" and put it in the same > directory from where I type "pymol" (on ubuntu linux). Then I type > "run axes.py"

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