Re: [PyMOL] list_hb.py

2021-04-08 Thread Robert Campbell
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

Re: [PyMOL] How to iterate commands in pymol

2020-11-01 Thread Robert Campbell
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,

Re: [PyMOL] Effect of different align method

2020-06-17 Thread Robert Campbell
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"

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

2020-06-17 Thread Robert Campbell
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 =

Re: [PyMOL] Extract all phi and psi angles

2020-05-11 Thread Robert Campbell
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

Re: [PyMOL] Drawing lines between residues

2019-10-17 Thread Robert Campbell
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

Re: [PyMOL] Pymol recolour B factors

2019-03-22 Thread Robert Campbell
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

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

2017-06-21 Thread Robert Campbell
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.

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

2017-06-21 Thread Robert Campbell
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

Re: [PyMOL] Scripting coloring method via own calculations

2017-02-14 Thread Robert Campbell
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

Re: [PyMOL] Fw: symmetry and pdb remark

2017-02-02 Thread Robert Campbell
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

Re: [PyMOL] Function signature

2016-04-17 Thread Robert Campbell
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] efficiency assigning b-factors

2015-06-16 Thread Robert Campbell
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

Re: [PyMOL] Backbone RMSD

2014-09-10 Thread Robert Campbell
Hello Amita, On Wed, 2014-09-10 09:41 EDT, Amita Rani Sahoo amita.r.sa...@gmail.com 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

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

2014-06-09 Thread Robert Campbell
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

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

2014-06-09 Thread Robert Campbell
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

Re: [PyMOL] ccp4 question

2014-02-04 Thread Robert Campbell
Dear Stefan, On Tue, 2014-02-04 14:44 EST, Stefan Ivanov stefan.iva...@postgrad.manchester.ac.uk 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

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

2014-01-16 Thread Robert Campbell
Hi Jed, On Thu, 2014-01-16 10:28 EST, Jed Goldstone jgoldst...@whoi.edu 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

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

2014-01-07 Thread Robert Campbell
On Tue, 2014-01-07 12:05 EST, Jed Goldstone jgoldst...@whoi.edu 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

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

2013-06-25 Thread Robert Campbell
Hi Stephen, On Tue, 2013-06-25 09:16 EDT, Stephen P. Molnar s.mol...@sbcglobal.net 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

Re: [PyMOL] PyMOL 1.6 pre-release announcement

2013-06-14 Thread Robert Campbell
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 li...@cowsandmilk.net

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

2013-05-10 Thread Robert Campbell
Hello Bachar, On Fri, 2013-05-10 14:29 EDT, Bachar Cheaib cheaib.bac...@gmail.com 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

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

2013-05-10 Thread Robert Campbell
Hello Bachar, On Fri, 2013-05-10 14:29 EDT, Bachar Cheaib cheaib.bac...@gmail.com 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

Re: [PyMOL] SS in a trajectory

2013-04-24 Thread Robert Campbell
Hi, On Wed, 2013-04-24 10:31 EDT, Jianghai Zhu j...@idi.harvard.edu 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

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

2013-04-04 Thread Robert Campbell
Hello Anasuya, On Thu, 2013-04-04 15:49 EDT, Anasuya Dighe anas...@mbu.iisc.ernet.in 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

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

2013-02-21 Thread Robert Campbell
Hi Anasuya, On Thu, 21 Feb 2013 17:10:40 +0530 Anasuya Dighe anas...@mbu.iisc.ernet.in 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.

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

2012-12-13 Thread Robert Campbell
Hi Jon, On Thu, 2012-12-13 16:09 EST, Jonathan Grimes jonat...@strubi.ox.ac.uk 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

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

2012-12-13 Thread Robert Campbell
Hi, (replying to my own message) On Thu, 2012-12-13 15:52 EST, Robert Campbell robert.campb...@queensu.ca wrote: Hi Jon, On Thu, 2012-12-13 16:09 EST, Jonathan Grimes jonat...@strubi.ox.ac.uk wrote: Hi All, I have 2 different states of the same molecule..different

Re: [PyMOL] sequence file extraction

2012-07-24 Thread Robert Campbell
Hi Thomas, On Tue, 2012-07-24 12:57 EDT, Thomas Holder spel...@users.sourceforge.net 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:

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

2011-12-26 Thread Robert Campbell
Dear Pavan, On Tue, 27 Dec 2011 00:15:38 +0530, PAVAN PAYGHAN pavana...@gmail.com wrote: Dear PyMol Users, I am using PyMol +v0.97 version on Windows XP .I have downloded super_all.pyhttp://pldserver1.biochem.queensu.ca/~rlc/work/pymol/super_all.py and tried to install the plugin by using

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

2011-12-21 Thread Robert Campbell
Hi John, On Wed, 2011-12-21 11:12 EST, John Ladasky john_lada...@sbcglobal.net 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

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

2011-10-26 Thread Robert Campbell
Hi Alexander, On Wed, 2011-10-26 12:53 EDT, Alexander Schulz sch...@dwi.rwth-aachen.de 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

Re: [PyMOL] change transparency for only a selection

2011-05-18 Thread Robert Campbell
Hi Nick, On Wed, 2011-05-18 11:39 EDT, Nicolas Bock nicolasb...@gmail.com 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:

Re: [PyMOL] slab mode fine-tuning

2011-03-29 Thread Robert Campbell
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 the

Re: [PyMOL] Selecting ASP and GLU

2011-03-01 Thread Robert Campbell
Hi Martin, On Tue, 01 Mar 2011 13:44:36 +0100 Martin Hediger ma@bluewin.ch 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

Re: [PyMOL] set sphere_scale question

2011-01-26 Thread Robert Campbell
On Wed, 26 Jan 2011 10:13:25 -0500 Bradley Hintze bradle...@aggiemail.usu.edu 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,

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

2011-01-21 Thread Robert Campbell
Hello Tom, On Fri, 21 Jan 2011 15:28:26 +1100 Tom Dupree t.dup...@unsw.edu.au 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

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

2011-01-21 Thread Robert Campbell
On Fri, 21 Jan 2011 10:10:02 -0500 Robert Campbell robert.campb...@queensu.ca wrote: Hello Tom, On Fri, 21 Jan 2011 15:28:26 +1100 Tom Dupree t.dup...@unsw.edu.au wrote: Hello all, I have a *.sdf (it can be a *.mol2 if that makes it easier) that contains multiple ligands. I'd like

Re: [PyMOL] Rendering issues with education version 1.3

2011-01-18 Thread Robert Campbell
Hi Paul, On Mon, 17 Jan 2011 19:00:09 -0800 Paul Rigor paul.ri...@uci.edu 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.

Re: [PyMOL] Model pdb section support

2011-01-10 Thread Robert Campbell
Hello Sergey, On Mon, 10 Jan 2011 16:38:52 +0100 Sergey Ivanov icegood1...@gmail.com 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

Re: [PyMOL] Pseudoatom for Benzene Centre

2010-12-10 Thread Robert Campbell
Hello Imtiaz, On Fri, 10 Dec 2010 08:41:14 + imtiaz biobr...@gmail.com 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

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

2010-11-17 Thread Robert Campbell
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

Re: [PyMOL] Access viewport size

2010-09-23 Thread Robert Campbell
Hi, On Wed, 22 Sep 2010 23:29:14 -0400 Jason Vertrees jason.vertr...@schrodinger.com 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

Re: [PyMOL] coloring labels

2010-08-31 Thread Robert Campbell
Hi Craig, On Tue, 31 Aug 2010 09:29:44 -0500 Craig Smith boiler...@mac.com 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

Re: [PyMOL] PyMol Connectivity Data

2010-08-05 Thread Robert Campbell
Dear Martin, On Thu, 05 Aug 2010 10:44:45 +0200 Martin Hediger ma@bluewin.ch 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

Re: [PyMOL] No module Error in running pymol

2010-07-12 Thread Robert Campbell
Hi Rituraj, On Mon, 12 Jul 2010 17:43:02 +0530 rituraj purohit riturajpuro...@gmail.com 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

Re: [PyMOL] Ray Trace Triangles

2010-07-09 Thread Robert Campbell
Hi Sean, On Fri, 09 Jul 2010 11:05:09 -0400 Sean Law magic...@hotmail.com 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:

Re: [PyMOL] crankshaft flip

2010-06-28 Thread Robert Campbell
Dear Jakob, On Mon, 28 Jun 2010 15:32:59 +0200 Jakob Nielsen jtoudahl.niel...@gmail.com 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

Re: [PyMOL] msms_pymol.py

2010-05-18 Thread Robert Campbell
Hi Sujuan, On Tue, 18 May 2010 15:58:59 +0800 sujuan wang wsjpy...@gmail.com 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

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

2010-05-14 Thread Robert Campbell
Hello Abhi, On Fri, 14 May 2010 12:19:34 +0200 Abhinav Verma abhinav1...@gmail.com 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

Re: [PyMOL] msms_pymol.py

2010-05-12 Thread Robert Campbell
Hi Hongbo, On Wed, 12 May 2010 15:59:36 +0200 Hongbo Zhu hongbo@biotec.tu-dresden.de 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

Re: [PyMOL] How draw the line in images

2010-05-12 Thread Robert Campbell
Hi Peter, On Wed, 12 May 2010 10:42:36 -0400 Jason Vertrees jason.vertr...@schrodinger.com 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:

Re: [PyMOL] PyMOL Plugin Architecture

2010-04-22 Thread Robert Campbell
Hi Maia, Just to add to what Jason said: On Thu, 22 Apr 2010 17:16:41 -0400, Jason Vertrees jason.vertr...@schrodinger.com 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

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

2010-04-06 Thread Robert Campbell
Hello Jenna, On Tue, 06 Apr 2010 00:36:38 -0400 JiangJiang Liu jli...@uwo.ca 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

Re: [PyMOL] coordinates

2010-03-22 Thread Robert Campbell
Hi Jed, On Mon, 22 Mar 2010 10:23:34 -0400 Jed Goldstone jgoldst...@whoi.edu 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

Re: [PyMOL] frustrating rms command

2010-03-16 Thread Robert Campbell
Hello Alan, On Tue, 16 Mar 2010 11:33:41 + Alan alanwil...@gmail.com wrote: Hello there, I am very frustrated with a very simple command, let me show: PyMOLrms (out and not hydrogen), (018.none_neutral.pdb_NEW and not hydrogen) ExecutiveRMS-Error: No atoms selected. PyMOLsele r,

Re: [PyMOL] frustrating rms command

2010-03-16 Thread Robert Campbell
Hi, On Tue, 16 Mar 2010 09:23:50 -0400 David Hall li...@cowsandmilk.net 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

Re: [PyMOL] B-factor replacing problem

2010-03-09 Thread Robert Campbell
Hi Thomas, On Tue, 09 Mar 2010 10:29:17 +0100 Thomas Holder spel...@users.sourceforge.net 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

Re: [PyMOL] B-factor replacing problem

2010-03-08 Thread Robert Campbell
Hi Simon, On Mon, 08 Mar 2010 18:09:31 +0100 Simon Lindhoud simon.lindh...@wur.nl 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:

Re: [PyMOL] Whitespacing?

2010-01-26 Thread Robert Campbell
Hi, On Tue, 26 Jan 2010 10:48:58 -0600 Michael Zimmermann micha...@iastate.edu 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

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

2009-12-08 Thread Robert Campbell
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 micha...@iastate.edu wrote: I have no experience with fuse, but my guess would be Mariana might want to just use 'bond' and translate one

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

2009-11-29 Thread Robert Campbell
Hi Jason, On Sun, 29 Nov 2009 12:29:08 -0500, Jason Vertrees jason.vertr...@gmail.com 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

Re: [PyMOL] spectrum

2009-11-09 Thread Robert Campbell
Hi Mark and Sean, On Sat, 07 Nov 2009 10:05:59 -0500 Sean Law magic...@hotmail.com wrote: Sorry for the earlier confusion. I think I found a hackish way of getting a gray spectrum: snip Sean's extensive explanation I know I'm biased, since I wrote the color_b.py script, but I fail to see

Re: [PyMOL] Spectrum

2009-11-09 Thread Robert Campbell
Hi Sean, On Mon, 09 Nov 2009 10:58:53 -0500 Sean Law magic...@hotmail.com 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

Re: [PyMOL] Alignment Objects

2009-09-11 Thread Robert Campbell
Hi David On Thu, 10 Sep 2009 14:47:43 -0700 (PDT) David Hall dwash59_2...@yahoo.com 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

Re: [PyMOL] Measure surface area

2009-08-10 Thread Robert Campbell
Hi Mirek, On Mon, 10 Aug 2009 11:21:39 -0700 Warren DeLano war...@delsci.com 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

Re: [PyMOL] Pymol build from source

2009-07-07 Thread Robert Campbell
Dear Joseph, On Tue, 07 Jul 2009 11:00:10 +0200, Andre Joseph andrejos...@gmail.com 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

Re: [PyMOL] surface for oligosaccharide chains

2009-07-03 Thread Robert Campbell
On Fri, 03 Jul 2009 16:18:10 +0200, Raluca Mihaela ANDREI r.and...@sns.it 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

Re: [PyMOL] POVRAY Usage

2009-05-15 Thread Robert Campbell
Hi Tom On Fri, 15 May 2009 14:57:36 -0700, Thomas Stout tst...@exelixis.com 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

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

2009-04-03 Thread Robert Campbell
Hi Peter, On Fri, 03 Apr 2009 02:38:03 +0530, peter hudson peter.hudson.pe...@gmail.com 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

Re: [PyMOL] fitting problem

2009-03-02 Thread Robert Campbell
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 error :

Re: [PyMOL] trouble with symexp command

2009-02-04 Thread Robert Campbell
Hi Dave, On Tue, 03 Feb 2009 16:33:28 -0500, David Garboczi dgarbo...@niaid.nih.gov 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

Re: [PyMOL] Showing conserved residues

2009-01-29 Thread Robert Campbell
Hi Abhinav, On Thu, 29 Jan 2009 13:10:25 -0800, Abhinav Kumar abhin...@slac.stanford.edu 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

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

2008-09-11 Thread Robert Campbell
Dear Pietro, On Thu, 11 Sep 2008 13:18:20 +0100, Pietro Roversi pietro.rove...@path.ox.ac.uk 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

Re: [PyMOL] coloring based on sequence identity

2008-08-25 Thread Robert Campbell
Dear Morri, On Fri, 22 Aug 2008 13:35:32 -0700, Morri Feldman morrifeld...@gmail.com 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.

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

2008-06-27 Thread Robert Campbell
Hi, On Fri, 27 Jun 2008 13:25:02 -0400, Michael Lerner mgler...@gmail.com 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.

Re: [PyMOL] Spheres for metal ions

2008-05-20 Thread Robert Campbell
Hi Gary, On Tue, 20 May 2008 12:12:43 +0200, Gary Hunter gary.hun...@um.edu.mt wrote: I am displaying pdb files of metalloenzymes, and like to show the metal ions as spheres. I select the metal and use showspheres Fine Somehow recently I must have done something to reset the vdw radius of

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

2008-05-05 Thread Robert Campbell
Hi Tomoko, On Mon, 05 May 2008 18:26:17 +0900, Tomoko Niwa tmk.n...@gmail.com 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] merging many frames to one

2008-02-12 Thread Robert Campbell
Hi again, Dimitry, On Tue, 12 Feb 2008 09:10:23 -0500, Robert Campbell robert.campb...@queensu.ca wrote: Hello Dimitry, On Tue, 12 Feb 2008 16:43:28 +0300, DimitryASuplatov gene...@gmail.com wrote: Hello, I have a .pdb1 file with biological unit. It consists of two frames

Re: [PyMOL] MSMS Cavity Visualization in Pymol

2008-01-31 Thread Robert Campbell
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 b...@mac.com 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

Re: [PyMOL] MSMS Cavity Visualization in Pymol

2008-01-30 Thread Robert Campbell
Hi Buz, On Wed, 30 Jan 2008 14:41:00 -0500, Buz Barstow b...@mac.com 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:

Re: [PyMOL] Changing Bfactors

2008-01-14 Thread Robert Campbell
On Sat, 12 Jan 2008 20:21:37 +0530, rama krishna ram...@gmail.com 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

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

2007-11-22 Thread Robert Campbell
Hello John, On Thu, 22 Nov 2007 12:36:32 -0800 (PST), JJ josh8...@yahoo.com 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

Re: [PyMOL] moving objects freely

2007-10-04 Thread Robert Campbell
Hi Tom, On Thu, 04 Oct 2007 11:20:35 -0700, Tom tl...@optonline.net 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

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

2007-09-18 Thread Robert Campbell
Dear Tomoko, On Tue, 18 Sep 2007 21:40:34 +0900 (JST), Tomoko Niwa outp...@yahoo.co.jp 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

Re: [PyMOL] aligning multimodel pdb file

2007-08-23 Thread Robert Campbell
Hi Abhi, On Thu, 23 Aug 2007 12:51:10 -0700, Abhinav Verma abhinav1...@gmail.com 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,

[PyMOL] my color_b.py script

2007-07-30 Thread Robert Campbell
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

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

2007-07-04 Thread Robert Campbell
Hi Louis, * Clark, Louis louis.cl...@codexis.com [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

Re: [PyMOL] spectral coloring

2007-06-27 Thread Robert Campbell
Hi Martin, * Martin Höfling martin.hoefl...@physik.uni-muenchen.de [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

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

2007-06-27 Thread Robert Campbell
* Andreas Henschel a...@biotec.tu-dresden.de [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

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

2007-06-14 Thread Robert Campbell
Hi David, * David A. Horita dhor...@wfubmc.edu [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

Re: [PyMOL] APBS

2007-05-30 Thread Robert Campbell
Hi Vaheh, * Oganesyan, Vaheh oganesy...@medimmune.com [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.

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

2007-05-11 Thread Robert Campbell
Hi Adiphol * adi di adipho...@yahoo.com [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

Re: [PyMOL] simple cgo question

2007-02-19 Thread Robert Campbell
Hi Richard, * Richard Gillilan r...@cornell.edu [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

Re: [PyMOL] mesure line width

2007-02-02 Thread Robert Campbell
Hi Andrea, * andrea carotti and...@chimfarm.unipg.it [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

Re: [PyMOL] Paths to loaded objects

2006-08-23 Thread Robert Campbell
Hi folks, * Michael Lerner mgler...@gmail.com [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()

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

2006-08-16 Thread Robert Campbell
Hi Jonathan, * Jonathan Stuckey sblood@yahoo.com [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

Re: [PyMOL] align states

2006-07-19 Thread Robert Campbell
Hi, * Joel Tyndall joel.tynd...@otago.ac.nz [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

Re: [PyMOL] debian: error in opening pymol

2006-06-08 Thread Robert Campbell
Hi Arvind, * Arvind Marathe arv...@mbu.iisc.ernet.in [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] Problem loading chempy objects to pymol

2006-06-07 Thread Robert Campbell
Hello Raúl, * Raúl Mera butil_li...@yahoo.com [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

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