Re: [PyMOL] Source version?

The source of 1.9.0.0 is likely the subversion repository, which also has the history that shows the changes. https://sourceforge.net/p/pymol/code/4184/log/?path=/trunk As for pymol 2.0 coming to open source, the announcement for 2.0 said the improvements would be pushed to the open source reposi

Re: [PyMOL] Record and load coordinates

The transform matrix you’re using is the identity matrix, so it won’t have any effect. -David > On Jan 11, 2018, at 6:54 PM, Benjamin Bailly wrote: > > Hi Thomas, > > Thanks for your reply. > > So if I am correct, for my protein get_coords fetches a very large matrix of > thousands and thou

Re: [PyMOL] Combining views of different Pymol sessions in one single file ?

You can use the partial argument of the load command to get two sessions together. load session1.pse load session2.pse, partial=1 > On Dec 28, 2017, at 6:03 PM, david gae wrote: > > Dear Maria, > > I don’t think there is a direct way to connect two sessions together. One > thought I had is

Re: [PyMOL] Help- PyMOL 1.8.7 on Python 3.6- Plugin Manager Issue

See https://sourceforge.net/p/pmw/patches/7/ > On Aug 21, 2017, at 10:32 PM, Vijay Masand wrote: > > Dear Christoph > Thank you for the help. I followed your suggestion, but no success. > However, a new line is appearing now at the bottom of the error

Re: [PyMOL] (no subject)

For some reason, the people doing brew have decided to stop supporting compiling tcl-tk with X11 support. Not 100% sure, but I'm pretty certain pymol cannot use tcl-tk with aqua. If you already had pymol installed, this seems to eliminate the external gui. If you didn't, new installations of pymol

Re: [PyMOL] Why does Pymol display the chain as disconnected?

PyMol doesn’t display any atoms for a region of the protein for the same reason the rcsb doesn’t for that area. The crystallographer deposited a structure without coordinates for residues 25-38. http://www.rcsb.org/pdb/explore/remediatedSequence.do?structureId=1AX8

Re: [PyMOL] Error aroused when install pymol from source

I think if you install "msgpack-devel”, it will compile and install. Generally, header files (which is what is included in C++ files) are in *-devel packages. The regular msgpack package just contains the shared library for use by programs already compiled against msgpack. -David > On Jun 7, 2

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

PyMol does not use QM methods. It also does not "determine the structures of molecules". -David > On Jun 1, 2017, at 12:38 AM, Susmita/Rajib wrote: > > Thank you, Dr. Tyugashev, for replying to my query. > Doesn't PyMol also use those QM methods to determine the structures of > molecules? > Th

Re: [PyMOL] show surface on pymol

It sounds like you may need to change surface mode to include hets https://pymolwiki.org/index.php/Surface_mode -David > On May 24, 2017, at 4:45 AM, 刘艳超 wrote: > > > Dear Madem/Sir, > > I am a user of Pymol software. Pymol facilitates me a lot during my study. I > have a problem and maybe

[PyMOL] Packaging python3 version of pymol

Hi, I maintain the pymol package for openSUSE. I'm considering packaging a python3 version alongside the python2 version. Are there maintainers of other distributions that have done so? Do you rename /usr/bin/pymol to /usr/bin/pymol3 for your python3 version? I'm looking to see if there is a prece

Re: [PyMOL] Using API to select resi, and return some information within a certain distance

When debugging, it is good to stop running pymol as a command line app and just run your script in a pymol gui and see what it is going on. In this case, you would find your selections have zero atoms. Why? Because you are basing them on something like "resn 102" , which is using the residue name

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

6:30 AM, Ahmad Abdelzaher >> wrote: >> >>> Well I'm assuming the selection goes in the argument of cmd.centerofmass(), >>> however, does it have to be an atom? How should I calculate the center of >>> mass for an entire protein? >>> &g

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

It returns the x, y, and z coordinates of the center of mass as a list of 3 floats, presumably in that order? Is there another question? The page describes the arguments and their defaults so I am unsure what is lacking. -David > On Apr 5, 2017, at 10:29 PM, Ahmad Abdelzaher wrote: > > I fin

Re: [PyMOL] problems creating object using align method

The error is due to you not surrounding AlnAB in quotes, so python treats it as a variable which has not been defined. That said, align modifies the coordinates of the existing object, the object created just shows the correspondence of residues used for alignment. To save the superimposed coor

Re: [PyMOL] Atom Order when Saving

https://pymolwiki.org/index.php/Retain_order > On Nov 14, 2016, at 3:04 PM, Subha K wrote: > > Hi There, > > Just wondering if there is a way to have the same order of atoms (with that > of the initial loaded file) while saving a pdb file with pymol? > > I came across an old post on this >

Re: [PyMOL] loading StringIO

https://pymolwiki.org/index.php/Read_Pdbstr -David > On Oct 26, 2016, at 3:55 AM, Albert Solernou wrote: > > Dear All, > I was wondering if there was a way to load a PDB file stored in memory > instead of disk, i. e., a memory file, defined through StringIO or > tempfile.SpooledTemporaryFile.

Re: [PyMOL] problem saving the transformed coordinate after alignment

I think the answer is to just use save, not that save_transformed function. -David > On Oct 19, 2016, at 1:47 PM, Subha K wrote: > > Hi there, > > I am trying to save the transformed coordinates of an object after performing > an alignment. I came across the save_transformed.py > [https://py

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

Every time you loop through the list of files, you set X=1 ; you do your X=X+1 in a loop that will only run once ( because glob.glob(“lig.pdb”) is only going to return a list of length 1 that has lig.pdb) , so you set X=1 , then X=2, then back to X=1 before you process the next entry. That is wh

Re: [PyMOL] Modeling protein-dna complex

Select the protein you want and the dna, then save the selection as a PDB. There are many ways to make a selection; visually, the easiest might be: You said you’ve removed the DNA from the protein-dna complex, so now you should have: (1) an object that has just your protein that you want in the

Re: [PyMOL] Video in Ubuntu Linux

Do you have the python code from freemol.org ? -David > On Jul 8, 2016, at 7:02 AM, Ioannis Michalopoulos > wrote: > >> On Friday 08 of July 2016 11:10:08 Folmer Fredslund wrote: >> Dear Ioannis, >> >>> On 2016-07-08 09:04, Ioannis Michalopoulos wrote: >>> Dear PyMOL users, >>> >>> I use Kub

Re: [PyMOL] ABPS Tools 2.1 plugin error

http://www.poissonboltzmann.org psize.py and pdb2pqr.py are part of pdb2pqr The others are part of apbs > On Jul 6, 2016, at 5:15 AM, Yanni wrote: > > Hello > > I'm using pymol 1.7 on OS X 10.11.5. > XQuartz version: 2.7.9 > python version: 2.7.12 > > When I launch the ABPS Tools 2.1, I get

Re: [PyMOL] High Resolution Ray Tracing

Feel free to send me the files off list. -David Hall > On May 6, 2016, at 1:54 PM, Stephen Kerry wrote: > > Dear All, > > I have a protein complex scene that I need to create a large, high resolution > (1200 dpi) ray traced image of, but am unable to do so as I always run o

Re: [PyMOL] Bash scripting and pymol

You need to add “,async=0” to your fetch calls. http://pymolwiki.org/index.php/Fetch > On Apr 28, 2016, at 4:51 AM, James Starlight wrote: > > Hi, > > My script is > > pdb_array=("1UBI" "1IGD" "1G33" "1CC7" "4LGJ" "5A2H") > pdb_array_store=$template/pymol > > > # A simple FETCHER via PYMO

Re: [PyMOL] pymolrc location

Make a file at ~/.pymolrc -David > On Apr 8, 2016, at 10:35 AM, harold steinberg > wrote: > > where in OS X is pymolrc located? > >> On Apr 7, 2016, at 2:39 PM, Thomas Holder >> wrote: >> >> pymolrc > > H. Adam Steinberg > 7904 Bowman Rd > Lodi, WI 53555 > 608/592-2366 > > > ---

Re: [PyMOL] running python scripts from within python loops in a pymol scripts

I think you can use cmd.do cmd.do("com /DARPin2//A/37-135/CA, object=com2”) -David > On Apr 1, 2016, at 8:48 AM, Honegger Annemarie wrote: > > Hi! > > I am trying to automate some model building tasks > > this loop in my pml script works just fine, it generates models in which two > protei

Re: [PyMOL] why lib/python folder is missing?

Doesn’t using --install-lib mean you are explicitly telling it to put the files in your modules directory instead of creating any lib/python type directories? > On Mar 5, 2016, at 2:50 PM, Albert wrote: > > Hello: > > I am using the following command line to compile PYmol: > > setenv prefix

Re: [PyMOL] Filled rings on stick mode

would something like these work for you? fetch 1rna, async=0 as cartoon set cartoon_ring_mode, 1 cartoon skip show sticks set cartoon_ladder_mode, 0 > On Jan 28, 2016, at 6:28 PM, COSTA Maria > wrote: > > Hi, > > I would like to know if it is possible to have the rings filled for the > nucle

Re: [PyMOL] pdb edition

Well, yes, programs do use the CONECT records, including pymol http://pymolwiki.org/index.php/Connect_mode Removing bonds is http://pymolwiki.org/index.php/Unbond Atoms can be translated using the command line http://pymolwiki.org/index.php/Editing_atoms#Get_coordinates_from_Python Or in edit

Re: [PyMOL] optimize and open babel troubles

Ubuntu’s universe repository has a 32-bit version of pymol? http://packages.ubuntu.com/precise/pymol Obviously, being a 4-year old distro, it is an older release, but it may still work with the plugin. -David > On Jan 6, 2016, at 2:39 PM, Joe Gauthier wrote: > > Hello all, > > I am trying t

Re: [PyMOL] Pymol issues for coloring ball and stick representation

set_bond stick_color, color, selection For more info on what is used to create the ball and stick preset, see: http://sourceforge.net/p/pymol/code/HEAD/tree/trunk/pymol/modules/pymol/preset.py#l144 -David > On Dec 17, 2015, at 2:35 AM, ANURAG SANKHYAN wrote: > > Dear all > > I am a user of

Re: [PyMOL] Pymol under El Capitan

Try the last comment on: https://github.com/Homebrew/homebrew-science/issues/2273 -David On Fri, Dec 11, 2015 at 3:39 AM, Chris Swain wrote: > Hi, > > I maintain a list of science applications that work under El Capitan ( > http://www.macinchem.org/blog/files/c92b0faf48c1bb7dee5eeba1260cff43-1

Re: [PyMOL] on PDB

http://pymolwiki.org/index.php/Save ?? -David > On Nov 24, 2015, at 9:45 PM, Smith Liu wrote: > > Dear All, > > Suppose the original PDB was not oriented. Once we have it oriented by pymol, > is any way we can save the new PDB oriented? > > Smith > > > > > --

Re: [PyMOL] on coloring residues based on y values in the x y z coordinates

another file? Can you introduce to me a server of software which can delete the original b-factors in the original PDB and have the ys pasted on the b-factors positions in the PDB file? Smith At 2015-11-18 21:13:05, "David Hall" wrote: I forgot: spectrum b at the end. On W

Re: [PyMOL] on coloring residues based on y values in the x y z coordinates

I forgot: spectrum b at the end. On Wed, Nov 18, 2015 at 8:11 AM, David Hall wrote: > Assuming you are ok with overwriting the B-factors > > > stored.y=[] > iterate_state 1, prot, stored.y.append(y) % prot here should be replaced > with your pymol object name > alter p

Re: [PyMOL] on coloring residues based on y values in the x y z coordinates

Assuming you are ok with overwriting the B-factors stored.y=[] iterate_state 1, prot, stored.y.append(y) % prot here should be replaced with your pymol object name alter prot, b=stored.y.pop(0) % again, replace prot with your pymol object name On Wed, Nov 18, 2015 at 7:49 AM, Smith Liu wrote

Re: [PyMOL] placing protein into lipid bilayer

I would disagree with your assertion that they use pymol to "insert" the protein into the membrane. They use the program they wrote, g_membed, to insert the protein. They used pymol to overlap them for the beginning of the simulation. That is, they use pymol to place the atoms of the protein on top

Re: [PyMOL] Pymol Morph movie error

org <http://freemol.org/> > > Hans, what Windows version do you use? I can't reproduce this problem on > Windows 7 or 8. > > Cheers, > Thomas > > -Original Message- > > David Hall mailto:li...@cowsandmilk.net>> wrote: > > > there is no m

Re: [PyMOL] Pymol Morph movie error

there is no mpeg_encode.exe binary. mpeg_encode, as far as I am aware, has long been abandoned. You can find what I believe is the last version of the source code (1.5c) at https://build.opensuse.org/package/show/home:cowsandmilk/mpeg_encode , you can download by clicking the files with the up arr

Re: [PyMOL] pymol to webGL?

You can set: pse_export_version to the 3-part version of pymol you would like to use as an export version. -David > On Oct 18, 2015, at 3:48 AM, Takanori Nakane > wrote: > > Hi, > > It looks like the structure of PyMOL session (what > we got from cmd.get_session) has changed in recent upgra

Re: [PyMOL] Using cartoon putty-like command

presumably: http://sourceforge.net/p/pymol/code/HEAD/tree/trunk/pymol/modules/pymol/preset.py#l164 On Mon, Oct 5, 2015 at 5:42 AM, Clavel wrote: > Hello everyone, > > I would like to create my own command within the pymol environement. > > I have currently a set of points in a pdb files with

Re: [PyMOL] creation of a sphere

What version of PyMol are you using? > On Aug 27, 2015, at 7:50 AM, Christian Trindler > wrote: > > Hello, > > I’ve been trying to make a pseudoatom/sphere simply by typing: > pseudoatom name > into the command line of Pymol, but it only gives me the following error > message instead of the

Re: [PyMOL] Python from PyMOL or PyMOL from Python?

I vastly prefer calling the python program from pymol You can call any python program using pymol as: pymol -r program.py — arg1 arg2 arg3 Or, my full preferred method is: pymol -qrck program.py — arg1 arg2 arg3 These make it quieter, stay on the command line, and not read the .pymolrc file

Re: [PyMOL] How to find RMSD values using fitting.py using Shell script

ormation. > Symmetry: Found 1 symmetry operators. > CmdLoad: "4OE9.txt" loaded as "4OE9.txt". > > 2. > pymol -cqr fitting.py --1A6M.pdb 4OE9.txt > PyMOL>run fitting.py,main > > Do I need to import Pymol module in the shell script to use the

Re: [PyMOL] How to find RMSD values using fitting.py using Shell script

http://www.pymolwiki.org/index.php/Command_Line_Options see the -c and -r options. I also use -q pymol -qcr script.py — arg1 arg2 arg3 > On Jul 10, 2015, at 8:44 AM, Gazal wrote: > > Hi, > > I'm trying to find the RMSD values for bat

Re: [PyMOL] Problem with loadBfact.py on windows

This is the problem. Pymol’s working directory is not where you have this file. So, the script never loads. > On Jul 10, 2015, at 12:20 PM, ABEL Stephane 175950 > wrote: > > No such file or directory: './loadB2Fact.py'

Re: [PyMOL] how can we rotate torsion angle of a molecule?

> On Jul 6, 2015, at 10:44 AM, Albert wrote: > > Hello: > > I am just wondering is it possible to rotate the torsion angle of a > molecule in Pymol? I search in pymolwiki, and I only find how to > translate a molecule or move the atom positions, but I didn't find > anything about how to rota

Re: [PyMOL] opensource for commercial use?

PyMol's License can be found at: http://sourceforge.net/p/pymol/code/HEAD/tree/trunk/pymol/LICENSE Generally, this is considered a "permissive" license ( https://en.wikipedia.org/wiki/Permissive_free_software_licence ). If you plan to use it in a commercial tool, you should pay for a couple hour

Re: [PyMOL] SCWRL version with educational-use PyMOL?

I believe all versions of Pymol use the 2002 version of the library. -David > On Jun 1, 2015, at 1:32 PM, Emilia C. Arturo (Emily) wrote: > > Hello. > > Does anyone know which version of SCWRL (backbone-dependent rotamer library) > is used in the educational-use-only version of PyMOL? > > R

Re: [PyMOL] PyMOL ball & stick representation of imatinib in 2HYY

preset.ball_and_stick('r. STI’) > On Apr 23, 2015, at 12:52 PM, Brenton Horne wrote: > > Hi, > > I recently read this reply > (http://www.mail-archive.com/pymol-users@lists.sourceforge.net/msg13248.html > ) > to

Re: [PyMOL] APBS plugin not working on both Ubuntu & Windows 7

There is an "INSTALL" file that provides instructions. The first step, calling ./configure , generates pdb2pqr.py from pdb2pqr.py.in If you want to manually do it, it just changes the first line in the file to point to your python installation. But, since there's a whole bunch of other things ./co

Re: [PyMOL] green rings

you can set cartoon_ring_color ? > On Mar 9, 2015, at 11:20 AM, Quentin Vicens wrote: > > Hi folks, > > I'm wondering how to get rid of the default green shine that's present in the > middle of every ring (see attached snapshot) following commands such as: > spectrum count,blue_white_red >

Re: [PyMOL] Ball and stick model

http://pymolwiki.org/index.php/Ball_and_Stick ? You used the "handmade" method on that page. Generally, I like using the preset better. On Sun, Feb 1, 2015 at 11:42 PM, Seera Suryanarayana wrote: > Dear Pymol Users > I would like to represent the protein what I have in ball and stick model. > I

Re: [PyMOL] The problem of save molecule to PDB after mutagenesis wizard

This occurs when retain_order is set before loading a protein. You have to: unset retain_order Then load your protein again. You might say: "I didn't set retain_order". This is likely true. Some very popular pymol plugins set it when loaded, most famously the autodock plugin. -David On Tue, Ja

Re: [PyMOL] Compilation problem with Pymol v1.7.4.0

> On Jan 23, 2015, at 7:32 PM, McCully, Dwayne (NIH/NIAMS) [C] > wrote: > > When running "python setup.py build" in the pymol directory of version > 1.7.4.0, > I get an error that stops pymol from compiling (see below). Does anyone know > how > to fix this problem. > > Dwayne > > > layer3/

Re: [PyMOL] MacPyMOL fink download

(2) assuming you didn't change it when installing fink, fink will install pymol in the /sw/bin directory. (4) this is fink setting environment variables such as PATH. You can add a line to your .bashrc to source it so it will be sourced every time you open a terminal. On Mon, Jan 19, 2015 at

Re: [PyMOL] Scripting attempts

(a) I'll let someone else say whether you can use range in pml files, not completely sure on that one and the formatting rules. personally, I would write this in python, and you would need a : after the range (b) you are missing any indication of what %4d refers to. See example 3.23 on http://www.

Re: [PyMOL] sulfated tyrosine's losing connection

my experience shows that when you have two HETATM residues one after another, pymol never shows this bond because the crystallographer never put a CONECT record for it, which pymol wants. eg for 1674, there is not CONECT showing 1676 as being bonded and since they are HETATM , pymol decides to

Re: [PyMOL] CGOs

where are you getting this from? I don’t see a LINE command in pymol/modules/cgo.py -David > On Dec 22, 2014, at 11:40 AM, Robert Hanson wrote: > > OK. I will look at the PyMOL code if I need to. For instance: > > LINE has eight parameters. I don't know what the first two are. > > LINE ?

Re: [PyMOL] DNA representation

colored by chain set cartoon_ladder_radius, 2 set cartoon_tube_radius, 2 set ray_trace_mode, 1 -David > On Dec 13, 2014, at 1:22 AM, Jacob Lewis wrote: > > Hi, > > Does anyone know how to show DNA like this in pymol? > > > Cheers, > > Jacob >

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

also http://www.pymolwiki.org/index.php/Transform_selection and PyMOL>help rotate DESCRIPTION "rotate" rotates the atomic coordinates of atoms in a selection about an axis. Alternatively, it modifies the matrix associated with a particular object or object state. USAGE rotate

Re: [PyMOL] select state not working

I'm a little confused by what PDB assemblies you are talking about that are distributed as multi-state structures, but assuming they are similar to NMR models... you can use intra_fit ( http://www.pymolwiki.org/index.php/Intra_fit ) For example, with 2kgx, we start out with chain a in state 1 and

Re: [PyMOL] CONECT table

http://www.pymolwiki.org/index.php/Connect_mode -David > On Oct 6, 2014, at 6:35 PM, Markus Heller wrote: > > Hello, > > How can I get PYMOL to use the CONECT table from a PDB file? My protein is > glycosylated, and I'd like to properly and automatically display the > glycosides including t

Re: [PyMOL] Help with rms_cur command

almost definitely is http://www.mail-archive.com/pymol-users@lists.sourceforge.net/msg1.html -David On Mon, Oct 6, 2014 at 12:17 PM, Soisson, Stephen M < stephen_sois...@merck.com> wrote: > Hi everyone- > > > > I’m having a few issues with the rms_cur command that I am hoping someone > can h

Re: [PyMOL] need help

I am very unsure of your question, but I believe you're asking if you have a PDB id, how to load that into pymol. For that, you can use the fetch command ( http://www.pymolwiki.org/index.php/Fetch ) You type: fetch 1acb into the pymol interface and it will download pdb id 1acb and load it into the

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

(sed '1d' protein.pdb; sed '1d' lipid.pdb) > merged.pdb --or-- tail -q -n '+2' protein.pdb lipid.pdb > merged.pdb -David On Thu, Sep 4, 2014 at 6:19 AM, James Starlight wrote: > Hi Tsjerk, > > Thanks alot! > Also I have the task to merge protein.pdb and lipids.pdb with some 1 line > shell

Re: [PyMOL] Pymol wrl output

hen "Show Suface" and Shapeways liked it! > > So I now have a working solution! > > Thanks EVERYONE! > > This is a great support mailing list! > > Ciao, > Bob > > > On Sun, May 4, 2014 at 2:08 PM, David Hall wrote: > >> Have you tried doing show &

Re: [PyMOL] Pymol wrl output

Have you tried doing show > as > surface It appears the wrl file has a bunch of extra information from the cartoon representation, which could confuse shapeways? -David On Sun, May 4, 2014 at 4:49 AM, Grateful Frog wrote: > Hi Jared & everyone, > > First, thanks for all your help. I really ap

Re: [PyMOL] noInvalidateMMStereoAndTextType flag

Not sure if the git svn stopping at rev 3938 was a question, but maybe you are using the old svn URL? svn://svn.code.sf.net/p/pymol/code/ Should get you up to date -David > On Mar 23, 2014, at 10:18 PM, David Osguthorpe > wrote: > >> On Sun, Mar 23, 2014 at 06:02:32PM -0400, Thomas Holder w

Re: [PyMOL] Color starting midway between adjacent chains

set_bond line_color, color_name, n. CA+CB will color all bonds between CA and CB whatever color you put in as color_name If you're doing sticks instead of lines, you should use set_bond stick_color, color_name, n. CA+CB -David On Mon, Mar 3, 2014 at 10:01 PM, I-Ji Jung wrote: > Hi everyo

Re: [PyMOL] Still need help with fetch and pymol 1.7

I think there's a bug in python's code, not pymol's In the file that it describes at the end ( C:\Python27\lib\mimetypes.py ) , you should change line 250 from: except UnicodeEncodeError: to except (UnicodeEncodeError,UnicodeDecodeError): keeping the indentation in the file and so on. Then the c

Re: [PyMOL] Trouble with saving mol2 format

One feature request, it would be nice if I open a mol2 and then save that molecule as mol2, it would remember the atom types and charges. No need for assignment, just remember what the user read in. -David On Thu, Sep 19, 2013 at 1:03 PM, Thomas Holder < thomas.hol...@schrodinger.com> wrote: >

Re: [PyMOL] using pymol commands in a script

I couldn't reproduce the exact error message you received, but I will note: (1) your splitting of lines leaves out the chain, so chain is never defined (2) line 9 of your python is missing an opening quotation mark before (resi matching the closing quotation mark right before the % sign (3) line 9

Re: [PyMOL] How to move/turn CGO

For a definition of TTT , see http://pymolwiki.org/index.php/Object_Matrix You'll notice that set_object_ttt takes a 16-member list that corresponds to this matrix. -David On Aug 12, 2013, at 11:48 AM, Павел Томашевский wrote: > Thank you Thomas, translate and rotate works great, but I'm not

Re: [PyMOL] Leap motion control

Jason can fill you in if there's an update, but the latest status update I'm aware of was: http://www.mail-archive.com/pymol-users@lists.sourceforge.net/msg11572.html -David -David On Monday, July 29, 2013 at 11:04 AM, H. Adam Steinberg wrote: > It would be great if we could control PyMOL wi

Re: [PyMOL] Pymol Library Script: findSurfaceResidues

your file has a weird non-ASCII character on line 5, causing the syntax error it mentions on line 5. Actually, your file has such characters on a whole bunch of lines (5, 37, 40, 45, 53, 54, 59, 61, 63, 64). Not sure how they were added, but if you delete them, then your file runs. If you provid

Re: [PyMOL] PyMOL 1.6 pre-release announcement

sion > >> 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: > >

Re: [PyMOL] Pymol error

without +quartz? Are these issues happening because > OSX 10.8.2 comes with preinstalled tcl and tk ? > > Thanks > Rhitankar > > > > > > On Tue, May 7, 2013 at 12:30 PM, David Hall wrote: > >> by default, macports installs tcl with the +corefoundation variant (

Re: [PyMOL] Pymol error

by default, macports installs tcl with the +corefoundation variant (see http://guide.macports.org/#using.variants ) if you do: sudo port install tcl -corefoundation that will solve the problem. -David On Mon, May 6, 2013 at 8:26 PM, Rhitankar Pal wrote: > Dear Thomas, > > One more questio

Re: [PyMOL] Pymol error in Mac OS X 10.8.2

what method did you use for installation? -- David Hall On Wednesday, May 1, 2013 at 11:53 AM, Rhitankar Pal wrote: > I am having some issues after installing pymol in Mac OS 10.8.2. It seems > the program is installed but when I try to open in using command line > "pymol&qu

Re: [PyMOL] PyMOL 1.6 pre-release announcement

Hi Thomas, I'm running into issues with color compatibility between 1.6 and earlier versions when opening pses (a) when I open any 1.5 pse in 1.6, I see a bunch of errors like: Setting-Error: type read mismatch (color) 6 Setting-Error: type read mismatch (color) 663 Setting-Error: type read mismat

Re: [PyMOL] How to hide the object control panel

http://pymolwiki.org/index.php/Internal_gui -David On Sunday, March 24, 2013 at 7:54 PM, Matthias Haffke wrote: > Dear all, > > this might be a simple question, but I would like to know how to hide the > object control panel on the right side in the PyMol window. > I would like to give a full

Re: [PyMOL] iPad pymol questions

Hi Steve, I'll suggest a workaround to having pymol cache the files: (1) Install the DropBox app (2) Favorite your PDB files in that app, this will cache those files locally within the DropBox app for offline access (3) From the dropbox app, you can open PDB files in Pymol using the button in the

Re: [PyMOL] Custom menus and shortcuts?

http://pymolwiki.org/index.php/Set_Key http://pymolwiki.org/index.php/Extend is also useful. -David On Tuesday, October 23, 2012 at 6:02 AM, Boris Kheyfets wrote: > Hello PyMOL users, > > Menus > = > > Is there a way I can add custom menu in PyMOL? > > Ideally I'd like to be able to c

Re: [PyMOL] How to rotate entire section of structure relative to rest

If you are comfortable with the command line interface, you can use http://pymolwiki.org/index.php/Set_Dihedral -- David Hall On Monday, October 22, 2012 at 4:27 PM, Alex Truong wrote: > Hi All, > > I'm relatively new to this software, and even though I've been using it

Re: [PyMOL] I just built pymol, comes up but hangs on any attempt to view a "test" pdb.

You don't need a license for the open source version. If you provided details on what OS/distribution you are building on, people may try to replicate and understand why the python version hung. In my experience, using setup.py generally worked out of the box. -David On Oct 4, 2012, at 9:22 PM

[PyMOL] Pymol Rotated Screen

, the same thing happens. Interestingly, while the desktop background and any app on the screens are impacted, the mouse cursor is not. Note, the incentive build PyMolX11Hybrid does not have this problem. Thanks for any help, David Hall

Re: [PyMOL] Is there or should there be a pymol annotation server?

The main technology I've seen used for interactive publications is ActiveICM (see http://www.molsoft.com/activeicm.html#aipub ). In my lab, we regularly include pymol sessions as supplementary material to help people understand our results. -David On Friday, July 13, 2012 at 6:41 AM, Troels E

Re: [PyMOL] GUI to improve interaction between user and PyMOL

Hi Suhaila, Correct me if I'm wrong but you want create *new* GUI elements for pymol to enhance your application, right? To my knowledge, there is not a great tutorial on this, but I can give you some pointers to plugins that do this currently and hopefully you can backfill some knowledge. The f

Re: [PyMOL] Editing of the pdb structure

On Tue, Mar 20, 2012 at 8:44 AM, Tsjerk Wassenaar wrote: > Hi Thomas, > > 'Wrong', certainly in the context it was given in, is a statement of > judgment. It suggest that there is a failure in the functioning, and > is a criticism to the developer, becoming a wrongdoer. My argument is, > that the

Re: [PyMOL] Little coordinate cross in Pymol?

http://pymolwiki.org/index.php/Axes -David On Feb 27, 2012, at 5:38 AM, Gudrun Lotze wrote: > Dear all, > > is it possible to show in Pymol a little coordinate cross with axes x,y,z, > for example like in VMD, please? > I have a protein made from dummy atoms and there is no unit cell. > I jus

Re: [PyMOL] Open Source PyMOL v1.5.0.1

On Mon, Feb 13, 2012 at 2:27 PM, Jason Vertrees wrote: > Greetings, > > It is my pleasure to announce the release of open source PyMOL > v1.5.0.1. The source code has been committed to the open-source > repository. It is revision 3976. An svn tag and downloadable bz2 > source file were also create

Re: [PyMOL] Using super correctly

n complains to you about "invalid selections" because it thinks the selections are empty. -David On Fri, Jan 13, 2012 at 8:37 AM, David Hall wrote: > I think super does not handle nucleic acid sequences well. > > super ec-5s, hm-5s, seq=-1 > > works. > > I'll l

Re: [PyMOL] cmd.do(png filename) error

On Fri, Jan 13, 2012 at 4:34 AM, tusi wrote: > Dear All, > > After updating to Ubuntu natty (11.04), cmd.do('png filename') does not > work. When I execute the following commands in pymol I get the wanted > png picture: > > load tmp.pdb tmp > png tmp.png > > > but, if I execute the following scrip

Re: [PyMOL] Using super correctly

I think super does not handle nucleic acid sequences well. super ec-5s, hm-5s, seq=-1 works. I'll leave it to someone else to say what that does. I just noted that align works, super doesn't, guessed it had to do with sequence and noted that for align, the default value of seq was -1 and for su

Re: [PyMOL] Installation PyMOL failure in Linux (CentOS)

the builds on https://build.opensuse.org/package/show?package=pymol&project=devel%3Alanguages%3Apython for opensuse 11.3 and 11.4 use gcc4.5 successfully. I blame ubuntu or linux mint. -David On Dec 2, 2011, at 10:21 AM, Marius Retegan wrote: > Could you please specified what exactly did the

Re: [PyMOL] Show Sticks - Turns Molecule Blue

Assuming you're using a recent version of openSUSE (11.3, 11.4, or Factory), feel free to grab the svn compiled version from http://software.opensuse.org/download.html?project=devel:languages:python&package=pymol -David 2011/9/11 Troels Emtekær Linnet : > This should get you on the way on compili

Re: [PyMOL] Pymol no longer fetches from pdb

Resolves fine for me. -David On Mar 22, 2011, at 12:30 PM, Jason Vertrees wrote: > Hi Roger, > > On Tue, Mar 22, 2011 at 9:20 AM, Roger Rowlett wrote: >> Hmm. At the RCSB site, I can see that the ftp server is ftp.wwpdb.org and it >> is currently generating a "cannot be found" error". I'll i

Re: [PyMOL] using pymol from python script

No idea if this will fix your problem, but what I've found is portable across binaries from Delano Scientific/Schroedinger and OS/self-compiled versions of pymol is to instead run: pymol -r examply.py -- mymolecule.xyz (or if I'm making pngs, usually pymol -qrck examply.py -- mymolecule.xyz ) Th

Re: [PyMOL] Start PyMOL session in web browser

Jmol certainly is not the only thing able to do that. In the applet world, you have at least OpenAstexViewer http://openastexviewer.net/web/ , but I also imagine it is possible to build a (jogl-accellerated) applet using jymol http://www.pymol.org/jymol , but I'm fairly certain it is not open s

[PyMOL] label_size in pymol 1.3 on Mac

Has anyone else run into a problem with label_size in pymol 1.3 on Mac? For both my fink and macports build, it doesn't work. The baseline of the text moves, but the size doesn't change. It does work when I compile from pymol trunk on my linux box. I don't see anything in the changelog or svn l

  1   2   >