Re: [PyMOL] Installing in Linux

Hello Peter, Which Linux distribution are you using? If you are using one of the Debian-based versions like Ubuntu, then PyMOL is likely available in the distribution's repository. Then you could use the package management system to install it or simply type in a terminal window: sudo apt-

Re: [PyMOL] list_hb.py

Hi Evgeny and Chen, Unfortunately, if Chen wants the list of atoms that form H-bonds, "distance" only provides a displayed object and only returns the average distance between all atoms. Also unfortunately, that script list_hb.py (which I wrote) uses the find_pairs function which warns that it

Re: [PyMOL] How to iterate commands in pymol

Hi Zuben, You need to import the colorbyrmsd.py script within your script, then you can call it that way. For example your script could say: import colorbyrmsd as cbr for obj in seleobjs: cmd.enable(obj) cbr.colorbyrmsd(obj,target) Cheers, Rob On Sat, 2020-10-31 20:36 +, "Brown, Zu

Re: [PyMOL] Effect of different align method

Hello Sunyeping, I would first point out that if you align on chain A of each molecule, then chain B of ASFV aligns with chain C of MTUB and vice versa. In other words you don't have the same assignment of chain ids in your trimer. The alignment of just alpha carbons of chain A with "align" g

Re: [PyMOL] hydrogen bond list for a series of files

Hi, I would make one minor change to your script -- the command "run list_hb.py" needs to be run only once at the beginning of the script so: # multiple_hb.py from pymol import cmd from glob import glob cmd.do("run list_hb.py") for file in glob("model.000.*.pdb"): print(file) #file_list = [f'{m

Re: [PyMOL] Extract all phi and psi angles

Hi Neena, If you give a different selection, then phi_psi will give you a list of phi/psi angles for all residues in the selection. For example if your protein object is called "obj_1", then typing phi_psi obj_1 will provide a list of phi_psi values to the terminal: PyMOL>phi_psi obj_1 LYS-3

Re: [PyMOL] Drawing lines between residues

Hi Jorge, I have written a script that will draw lines between arbitrary pairs of atoms using CGO cylinders. The script is called "draw_links.py" and can be found on my script page: http://pldserver1.biochem.queensu.ca/~rlc/work/pymol/ Besides listing the pairs of atoms to connect you can con

Re: [PyMOL] Pymol recolour B factors

Hi Mark, In that data2bfactor.py script (which I wrote) you need to provide the molecular object name, not a file name. In other words in your example you should load the 1d3z.pdb file as an object (defaults to 1d3z as object name). Then after using the run command to load the script into you

Re: [PyMOL] ExecutivesSymexp-Error: No Symmetry loaded!

Hi Leila, You need the "CRYST1" line from the template pdb file. That is where PyMOL gets the symmetry information from. Cheers, Rob On Wed, 2017-06-21 09:29 +0200, leila karami wrote: > Dear PYMOL users, > > I have done a homology modelling using swiss model. Template pdb file > contain

Re: [PyMOL] ExecutivesSymexp-Error: No Symmetry loaded!

Hi Leila, I responded too quickly without reading carefully! Adding those lines should have worked (but only the CRYST1 line is needed). Your model.pdb file that you linked to on Dropbox does not have the CRYST1 line. Adding that line works for me. Cheers, Rob On Wed, 2017-06-21 09:29 +02

Re: [PyMOL] Scripting coloring method via own calculations

Hello Peleg, I think there are other possibilities, but my data2bfactor.py script will do that for you. You create a file with whitespace-separated columns (spaces and/or tabs) in which each line contains: chain resi resn name data (i.e. chain, residue number, residue name, atom name and val

Re: [PyMOL] Fw: symmetry and pdb remark

Hello Smith, I had a look at the two structures. In some crystallographic space groups there are alternate choices for the origin that are all equivalent. It appears that this is what you are seeing here. If you look carefully at the mates generated separately for 2zam and 2zan, they are equi

Re: [PyMOL] Function signature

Hi Martin, If you simply want to be able to have the function operate on any selection, simply do this: def zoom_custom(position): cmd.zoom(position) cmd.extend("zoom_custom", zoom_custom) This allows you to type: zoom_custom resi 117 or any other more complicated selection syntax without

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] 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] 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] 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] 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] 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] 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] 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] 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] 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] 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] 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] 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] 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] 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] 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] 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] 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] 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] 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] 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] 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] Selecting ASP and GLU

Hi Martin, On Tue, 01 Mar 2011 13:44:36 +0100 Martin Hediger wrote: > Dear all > What is the selection syntax to select all GLU and ASP residues within > an object? > > I'm trying it the way its written on the wiki: > > remove resn hoh# remove water > h_add # add hydrogens >

Re: [PyMOL] set sphere_scale question

On Wed, 26 Jan 2011 10:13:25 -0500 Bradley Hintze wrote: > Hi all, > > I have a question regarding the changing of sphere size in a PyMOL API. When > I use the command as presented on the PyMOLwiki, namely: > > cmd.set ("sphere_scale", size=1, selection='', state=0, updates=1, log=0, > quiet=1)

Re: [PyMOL] Loading multiple ligands into a single view

On Fri, 21 Jan 2011 10:10:02 -0500 Robert Campbell wrote: > Hello Tom, > > On Fri, 21 Jan 2011 15:28:26 +1100 Tom Dupree wrote: > > > Hello all, > > > > I have a *.sdf (it can be a *.mol2 if that makes it easier) that contains > > multiple ligands. I'

Re: [PyMOL] Loading multiple ligands into a single view

Hello Tom, On Fri, 21 Jan 2011 15:28:26 +1100 Tom Dupree wrote: > Hello all, > > I have a *.sdf (it can be a *.mol2 if that makes it easier) that contains > multiple ligands. I'd like to open this one file and see them all at once. > It currently loads each ligand into its own state. Is there a

Re: [PyMOL] Rendering issues with education version 1.3

Hi Paul, On Mon, 17 Jan 2011 19:00:09 -0800 Paul Rigor wrote: > Hi gang, > Just wondering if anyone has experienced some weird rendering issues, ie, > aberrant bonds between atoms. I've attached a sample pdbqt file which > contains 4 molecules which are outputs of autodock vina. Can someone try

Re: [PyMOL] "Model" pdb section support

Hello Sergey, On Mon, 10 Jan 2011 16:38:52 +0100 Sergey Ivanov wrote: > Have pdb file with pseudobeads: > MODEL 2 > HETATM1 O24.000 46.000 39.000 > HETATM2 O24.000 47.000 39.000 etc. I displayed this file using Nathan's suggestion to set all_

Re: [PyMOL] Pseudoatom for Benzene Centre

Hello Imtiaz, On Fri, 10 Dec 2010 08:41:14 + imtiaz wrote: > I want to create a Pseudoatom in the center of a benzene ring for a ligand. > > I can easily create a Pseudoatom in the center of aromatic ring of > amino acids in a protein by following the instructions give at > > http://www.py

Re: [PyMOL] small molecule geometry gets whacked in creating multi-state object

Hi Seth and Jason, I just tried out Jason's commands and while that works for this case I can't verify that it fails in Seth's case. While checking the command line options for create, I did notice that, like the load command, the create command also has a discrete flag. It is not described in t

Re: [PyMOL] small molecule geometry gets whacked in creating multi-state object. rebuild?

Hi Seth, On Tue, 09 Nov 2010 22:54:59 -0500 Jason Vertrees wrote: > Hi Seth, > > I haven't seen that (in this scenario). Can you send me a few PDB examples? > > Cheers, > > -- Jason > > On Mon, Nov 8, 2010 at 10:13 PM, Seth Harris wrote: > > Hi all, > > I feel I should know this one. I hav

Re: [PyMOL] Access viewport size

Hi, On Wed, 22 Sep 2010 23:29:14 -0400 Jason Vertrees wrote: > Hi Mark, > > We used to be able to call this to get the viewport size. But, > somewhere along the line Warren removed this. I'll see if I can add > it back in, or find out why he removed it. As mentioned in this email: http://ww

Re: [PyMOL] coloring labels

Hi Craig, On Tue, 31 Aug 2010 09:29:44 -0500 Craig Smith wrote: > Hello, > > Thanks for the prompt responses I received so far. That really helped. > But, set_color black changes the color globally. Can I do this locally? > For example, I'm highlighting two polypeptide chains one blue and one

Re: [PyMOL] list of hydrogen bonds

Hi Martin, On Wed, 11 Aug 2010 12:02:32 +0200 Martin Hediger wrote: > I was thinking about this as well, I saw an older post on this topic > http://www.mail-archive.com/pymol-users@lists.sourceforge.net/msg06211.html > but it seems that the script mentioned there starts to see 'hydrogen > bonds

Re: [PyMOL] PyMol Connectivity Data

Dear Martin, On Thu, 05 Aug 2010 10:44:45 +0200 Martin Hediger wrote: > I am confused about the requirement of providing connectivity data in a > pdb file to properly render a protein with PyMol. > Right now, I am displaying a pdb file not containing any connectivity > data but still the prote

Re: [PyMOL] need more info

Hi Vivek, On Tue, 13 Jul 2010 13:18:07 -0400 Vivek Ranjan wrote: > Thank you once again. I have been trying to change the color of the cell. > > cell = [] > cell.append(CYLINDER) > cell = cell + vert_000 + vert_100 + [radius] + [0,0,0] + [1,0,0] > cell.append(CYLINDER) > cell = cell +

Re: [PyMOL] need more info

Hello Vivek, On Tue, 13 Jul 2010 11:21:03 -0400 Vivek Ranjan wrote: > Hello, > > First, thanks a lot for your help. Pymol with cctbx works now for me. > I changed the script "pymol" and replaced "/usr/binpython" to "python" > and thats it. Few more questions: > > (i) draw_cell.py uses lavv.pdb

Re: [PyMOL] python

On Mon, 12 Jul 2010 10:37:07 -0400 Vivek Ranjan wrote: > Hello, > > How can I find out what version of python my current installation of > pymol is using ? One way is simply to type "python" in a terminal window and you should see something like: Python 2.6.5+ (release26-maint, Jul 1 2010, 00

Re: [PyMOL] No module Error in running pymol

Hi Rituraj, On Mon, 12 Jul 2010 17:43:02 +0530 rituraj purohit wrote: > Dear friends > > I am having Ubuntu 10.04 and want to use pymol. > There is no error in installation but it is giving following error > during running pymol > > "r...@ritu-laptop:~$ pymol > Traceback (most recent call last

Re: [PyMOL] cctbx

On Fri, 09 Jul 2010 16:11:47 -0400 Vivek Ranjan wrote: > Hello, > > I downloaded a pymol script from > http://pldserver1.biochem.queensu.ca/~rlc/work/pymol/ called > draw_cell.py. I have "Python 2.6.5", numpy version: 1.3.0, I > downloaded cctbx for unix (self extracting files) and installed cct

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"

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] 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] 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] 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] 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] 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] 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 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] 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] 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] 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] 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] 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] 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] 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] 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] 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] 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] 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] 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] 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] 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] 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] 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] 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] 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] 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] 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] 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] 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] 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] 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] 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] 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] 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] 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] 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] 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] 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] 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] 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] 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] 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] 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

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