Re: [PyMOL] Source version?

[David Hall]

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 repository in early 2018.

On Fri, Jan 12, 2018 at 4:48 PM, CAS IT Services  wrote:

> Disclaimer:  I am not a chemist, nor a PyMol user.  I am an IT guy trying
> to assist students and educators with installing PyMol.
>
> I am pretty sure I can figure out how to get PyMol working from the
> compiled source that Christoph Gohlke offers for download, but I thought I
> should try to compile it myself.
>
> Does anyone know why there is a discrepancy between the version of the
> downloadable source tarball found here (v1.8.6.0) and the version Christoph
> offers (v1.9.0.0)?
>
> Assuming that I trust Christoph's offering, what changed between 1.8.6.0
> and 1.9.0.0?
>
> Also, does anyone know if 1.9.0.0 is the end for open source PyMol?  Has
> Schrodinger completed a conversion to a fully commercial (and likely
> profitable) version with v2.0?
>
> Thanks.
>
> 
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Re: [PyMOL] Record and load coordinates

[David Hall]

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 thousands of rows. This could prove very impractical if I want 
> to stores those coordinates in a script.
> 
> To circumvent this issue I tried the following but it did not seem to work:
> 
> print cmd.get_object_matrix('%prot')   # to obtain my coordinates in a 4X4 
> format
> 
> PyMOL>cmd.transform_selection("su", [[1.0,0.0,0.0,0.0], [0.0,1.0,0.0,0.0], 
> [0.0,0.0,1.0,0.0], [0.0,0.0,0.0,1.0]], homogenous=1)
> CmdTransformSelection-DEBUG: bad matrix
> 
> PyMOL>cmd.transform_selection("su", 
> [1.0,0.0,0.0,0.0,0.0,1.0,0.0,0.0,0.0,0.0,1.0,0.0,0.0,0.0,0.0,1.0], 
> homogenous=1)  # In that case nothing happens
> 
> What do you think I am doing wrong?
> 
> Many thanks,
> 
> Ben
> 
> --
> 
> Dr Benjamin Bailly | Research Scientist – von Itzstein group
> 
> Institute for Glycomics
> Griffith University | Gold Coast campus | QLD 4222 | Institute for Glycomics 
> (G26) Room 4.30
> 
> 
> 
> ___
> 
> Benjamin Bailly 
> +61 479 17 66 34 (Australia)
> 
>> On 11 January 2018 at 17:26, Thomas Holder  
>> wrote:
>> Hi Ben,
>> 
>> The coordinates argument must have a Nx3 shape, that means:
>> len(coordinates) = number of atoms
>> len(coordinates[0]) = 3
>> 
>> You can use numpy's reshape() function:
>> 
>> import numpy
>> coordinates = numpy.asfarray(coordinates).reshape((-1,3))
>> cmd.load_coords(coordinates, '%prot')
>> 
>> I recommend to prefix the object name with "%" to unambiguously address a 
>> named object or selection. I mention this because I just ran into a common 
>> selection language ambiguity problem myself: I named my object "obj01" and 
>> then pasted your code without changing the object name. The error message 
>> was "atom count mismatch" instead of "invalid selection name". Why? Because 
>> "prot" was evaluated as the selection keyword "protected", so it was a valid 
>> (but empty) selection expression.
>> 
>> Cheers,
>>   Thomas
>> 
>> > On Jan 11, 2018, at 7:43 AM, Benjamin Bailly  wrote:
>> >
>> > Hi everyone,
>> >
>> > I have been scratching my head quite a bit on this one, I am sure there 
>> > must be a simple solution but I can't seem to figure it out.
>> >
>> > In short, I would like to record the spacial coordinates of a protein so 
>> > that when I run my script I can fetch it from the PDB and place it exactly 
>> > where I would like it to be.
>> >
>> > I used this command to obtain the coordinates, and here is the output I 
>> > get:
>> >
>> > PyMOL>print cmd.get_coords('prot')
>> > [[159.402 258.709 204.556]
>> >  [159.932 259.514 204.223]
>> >  [158.951 258.206 203.792]
>> >  ...
>> >  [117.662 263.108 309.314]
>> >  [115.591 265.038 307.88 ]
>> >  [116.386 259.713 306.195]]
>> >
>> > To load the position in my script I know that I should be able to use the 
>> > following command however I can not figure out the format required:
>> >
>> > cmd.load_coords(coordinates, 'prot')
>> >
>> > I tried to use all the floats the ones after the other like [1.1, 2.2, 
>> > 3.3,...] and I was close to making it work, but it said the numbers of 
>> > atoms did not match. I read that I should probably used a numpy array but 
>> > I am not sure of its format.
>> >
>> > Your help would be much appreciated,
>> >
>> > Many thanks
>> >
>> > Ben
>> 
>> --
>> Thomas Holder
>> PyMOL Principal Developer
>> Schrödinger, Inc.
>> 
> 
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Re: [PyMOL] Combining views of different Pymol sessions in one single file ?

[David Hall]

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 that you could save coordinates from one session and then 
> same coordinates from the other session.
> 
> lastly, open an another session and do the following:
> 
> load state1.pdb 
> load state2.pdb, state1
> 
> cheers,
> David 
> 
>  
>> On Dec 28, 2017, at 10:16 AM, COSTA Maria > > wrote:
>> 
>>  
>> Dear PyMOL users,
>>  
>> I would like to do a movie showing a conformational change of my molecule. I 
>> guess that for that purpose I need to store the views of the two states but 
>> the problem is that my two states are in two different pymol sessions. Is 
>> there a way to combine the two views in the same pymol file ? or I need to 
>> redo the views in the same pymol session from the beginning ?
>> I hope I’m being clear enough….
>>  
>> Thank you so much for any help !
>>  
>> Maria Costa
>>  
>> I2BC – UMR9198
>> 91198 Gif-sur-Yvette cedex
>> France  
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Re: [PyMOL] (no subject)

[David Hall]

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 will now crash randomly.

Here's how I got to the old version that worked

$ cd /usr/local/Homebrew/Library/Taps/homebrew/homebrew-core/Formula/
$ git checkout 46e1ef94247cd2fb9555b724c051e8907996 -- tcl-tk.rb
$ cd ../../homebrew-science/
Edit the pymol.rb file so that it depends on "tcl-tk" instead of
"homebrew/dupes/tcl-tk"

$ brew remove tcl-tk python pymol
$ brew install pymol
$ brew pin tcl-tk

Really, I uninstalled all my homebrew packages and then reinstalled
everything because some of their changes over the last 6 months had made
things oddly broken. If you want to do the same, you can try this:

$ brew list > installed
$  wrote:

> Hi,
> pymol external gui menus missing, I have compiled pymol in mac os by using
> brew.
>
> Anyone can provide some suggestions?
>
> Jacky
>
> --
> Lei Zhao, Ph.D. & M.D.
> Associate Professor
> National Clinical Research Center for Normal Aging and Geriatric
> National Engineering Research Center for Antibody Medicine
> The Key Lab of Normal Aging and Geriatric
> PLA General Hospital
> Beijing 100853
> P.R.China
> Tel:86-15210661966
>
>
> 
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Re: [PyMOL] Why does Pymol display the chain as disconnected?

[David Hall]

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 




> On Jun 20, 2017, at 6:09 AM, Ahmad Abdelzaher  wrote:
> 
> http://www.rcsb.org/pdb/explore.do?structureId=1ax8
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Re: [PyMOL] Error aroused when install pymol from source

[David Hall]

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, 2017, at 10:18 PM, sunyeping via PyMOL-users 
>  > wrote:
> 
> Dear pymol users,
> 
> I am trying to intall pymol on my centos 7 system from source using the 
> mothed discribed at pymolwiki (https://pymolwiki.org/index.php/Linux_Install 
> )
> Everything was ok until I run install script: 
> 
> #!/bin/bash -e
> 
> prefix=/opt/pymol-svn
> modules=$prefix/modules
> 
> # If you want to install as root, then split this line up in "build"
> # and "install" and run the "install" with "sudo"
> python2.7 setup.py build install \
> --home=$prefix \
> --install-lib=$modules \
> --install-scripts=$prefix
> 
> I got a error message and the installation process was terminated:
> 
> In file included from contrib/mmtf-c/mmtf_parser.cpp:31:0:
> contrib/mmtf-c/mmtf_parser_private.h:38:23: fatal error: msgpack.hpp: No such 
> file or directory
>  #include 
>^
> compilation terminated.
> 
> I then installed msgpack by yum command and tried to run the pymol install 
> script again, but the same error still occurred.
> 
> I googled this problem but cannot find a answer. Could anyone help me here?
> 
> Best regards.
> 
> Yeping Sun
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Re: [PyMOL] Is it possible in Pymol to determine Individual Bond, Dissociation Energy for any Bond in organic molecules?

[David Hall]

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?
> Then why not PyMol be capable of yielding such values for individual bonds?
> 
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Re: [PyMOL] show surface on pymol

[David Hall]

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 need your help. I want to show surface of a ligand 
> in which there is a methylated lysine. Other residues are OK except the 
> methylated lysine. Could you help me to deal with this problem? Should I 
> install any plugin that can recognize molecules like methylated lysine or 
> anything? Thanks a lot.
> 
> Yanchao Liu
> 
> Shanghai Institute of Biochemistry and Cell Biology.
> 
> Shanghai Institutes for Biological Sciences.
> 
> Chinese Academy of Sciences.
> 
> 320 Yueyang Road ,Shanghai 200031,China.
> 
> 
>  
> 
> 
> 
> 
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[PyMOL] Packaging python3 version of pymol

[David Hall]

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
precedent for how to name the python3 version so they can be installed
beside each other. Another option is to use the alternatvies system so that
a user can choose which they want to use.

Other maintainers, let me know if you've added a python3 version and if you
made any decisions along these lines,

David

(P.S. to be clear, there are no issues building pymol for python3, this is
just about naming the /usr/bin/pymol file when installing a python3 version
so that users can also have the python2 version installed alongside it)
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Re: [PyMOL] Using API to select resi, and return some information within a certain distance

[David Hall]

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 selector with a residue number.

If you replace resn with resi , you should get nice pictures.

> 2) I still have no idea what the command cmd.get_pdbstr do

It returns a string in PDB format of the set of atoms in the selection. So,
the same string as would be in a file if you said save('xxx.pdb', 'sele')



On Tue, May 2, 2017 at 3:47 AM, Ahmad Abdelzaher 
wrote:

> Thank you. I made a few mistakes in my code. I wasn't paying attention
> to the commented code because I was only trying stuff there. I still
> get:
>
> 1) a bunch of 3 kb black png's
> 2) I still have no idea what the command cmd.get_pdbstr do
> 3) can you give me a line using iterate to get the residue names and
> numbers?
>
>
> import __main__
> __main__.pymol_argv = ['pymol','-qc']
> import pymol
> from pymol import cmd, stored, util
>
> pymol.finish_launching()
>
> residues = {'3s4m.pdb': {'102': 'THR',
>   '143': 'TYR',
>   '158': 'SER',
>   '166': 'TYR',
>   '173': 'TRP',
>   '181': 'SER',
>   '183': 'HIS',
>   '206': 'SER',
>   '95': 'TYR'}}
>
> for name, data in residues.items():
> for resnumber, resname in data.items():
> cmd.delete('all')
> bare_name = name.split('.')[0]
> cmd.load(name, bare_name)
> cmd.select('%s_%s%s' % (bare_name, resname, resnumber), 'byres
> resn %s around 10' % resnumber)
> cmd.dist('mysele_polar_conts','%s_%s%s' % (bare_name, resname,
> resnumber),'all within 5 of %s_%s%s' % (bare_name, resname,
> resnumber), quiet=1,mode=2,label=0,reset=1)
> cmd.show_as('sticks', '%s_%s%s' % (bare_name, resname, resnumber))
> util.cnc('%s_%s%s' % (bare_name, resname, resnumber))
> cmd.hide('everything', 'all and not %s_%s%s' % (bare_name,
> resname, resnumber))
> cmd.zoom('%s_%s%s' % (bare_name, resname, resnumber), 5)
> cmd.png('%s_%s%s.png' % (bare_name, resname, resnumber), ray=1)
>
>
>
> On Tue, May 2, 2017 at 7:14 AM, Jared Sampson
>  wrote:
> > Hi Ahmad - Please see below for some suggestions on getting your script
> to
> > do what I understand you would like to do.
> >
> > Cheers,
> > Jared
> >
> >
> > On May 1, 2017, at 4:54 PM, Ahmad Abdelzaher 
> wrote:
> >
> > OK I finally tried some of Jared suggestions, I'm not sure why
> > util.cnc doesn't work I get "NameError: name 'util' is not defined",
> >
> >
> > You will need to import the `util` namespace.  Try changing the pymol
> > submodule import line to:
> >
> > from pymol import cmd, stored, util
> >
> > Again, I want to color by element, second option from the gui. Also
> > the script outputs black screenshots, nothing is there, so there is a
> > bug somewhere! I attached the script and pdb below. I would appreciate
> > your help.
> >
> > import __main__
> > __main__.pymol_argv = ['pymol','-qc']
> > import pymol
> > from pymol import cmd, stored
> >
> > pymol.finish_launching()
> >
> > residues = {'3s4m.pdb': {'102': 'THR',
> >  '143': 'TYR',
> >  '158': 'SER',
> >  '166': 'TYR',
> >  '173': 'TRP',
> >  '181': 'SER',
> >  '183': 'HIS',
> >  '206': 'SER',
> >  '95': 'TYR'}}
> >
> > for name, data in residues.items():
> >for resnumber, resname in data.items():
> >cmd.delete('all')
> >cmd.load(name, name)
> >
> >
> > The load command here gives you an object called "3s4m.pdb" but you later
> > try to use a selection called only "3s4m" (`bare_name`).  If you leave
> the
> > second argument off from cmd.load(), the .pdb extension will be stripped
> > automatically.  Alternatively, you could assign `bare_name` first and
> give
> > that as the 2nd argument:
> >
> > bare_name = name.split('.')[0]
> > cmd.load(name, bare_name)
> >
> >
> >bare_name = name.split('.')[0]
> >cmd.select('%s_%s%s' % (bare_name, resname, resnumber), 'byres
> > resn %s around 3' % resnumber)
> >#selee = cmd.get_pdbstr('%s' % name.split('.')[0])
> >
> >
> > Since you've already assigned a variable for this, you can (and should!)
> use
> > `bare_name` instead of `name.split('.')[0]` wherever it occurs.  Also,
> you
> > don't need to do "%"-style string formatting if your variable is a string
> > and comprises the entire argument string.  Simply
> > `cmd.get_pdbstr(bare_name)`, for example, will work just fine.
> >
> >#print(selee)
> >cmd.dist('mysele_polar_conts','%s_%s%s' % (bare_name, resname,
> > resnumber),'all within 5 of %s_%s%s' % (name.split('.')[0], resname,
> > resnumber), quiet=1,mode=2,label=0,reset=1)
> >cmd.show_as('sticks', '%s_%s%s' % (bare_name, resname, resnumber))
> >#util.cnc('%s' % name.split('.')[0])
> >cmd.hide('everything', 

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

[David Hall]

> how to calculate the center of mass of an entire structure

Let's say I want the center of mas of the structure from the PDB 1vdd

cmd.fetch('1vdd', async=0)

cmd.centerofmass('1vdd')

Now, I see 1vdd has a bunch of water molecules that I don't want in in my
calculation

cmd.centerofmass('1vdd and not solvent')

Now maybe I only care about chain A.

cmd.centerofmass('1vdd and not solvent and chain A')

I suggest reading more about selections in the pymolwiki. That is actually
a topic where I feel the wiki could be better organized, but almost every
command in pymol operates on selections, so it is a fundamental concept you
should spend time to understand if you are planning to use pymol.

https://pymolwiki.org/index.php/Category:Selecting


On Thu, Apr 6, 2017 at 1:13 AM, Ahmad Abdelzaher <underoath...@gmail.com>
wrote:

> Hi Tsjerk,
>
> What you said makes perfect sense. Since an atom could be considered as a
> point with uniform density, it's center of mass is indeed its position.
>
> Which, begs the question, what is the purpose of cmd.centerofmass() and
> how to calculate the center of mass of an entire structure (the only
> calculation that would make sense with regards to the center of mass).
>
> Cheers.
>
>
> On Thu, Apr 6, 2017 at 6:49 AM, Tsjerk Wassenaar <tsje...@gmail.com>
> wrote:
>
>> Hi Ahmad,
>>
>> The center of mass of an atom is its position. A function like
>> cmd.centerofmass in the context of pymol only makes sense with a selection.
>> E.g.:
>>
>> x,y,z = cmd.centerofmass('byres n. ca')
>> print "COM of protein:", x, y, z
>>
>> Hope it helps,
>>
>> Tsjerk
>>
>> On Thu, Apr 6, 2017 at 6:30 AM, Ahmad Abdelzaher <underoath...@gmail.com>
>> 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?
>>>
>>> On Thu, Apr 6, 2017 at 4:48 AM, David Hall <li...@cowsandmilk.net>
>>> wrote:
>>>
>>>> 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 <underoath...@gmail.com>
>>>> wrote:
>>>>
>>>> I find the documentation about the python api here to be a bit lacking.
>>>>
>>>> https://pymolwiki.org/index.php/Centerofmass
>>>>
>>>> I would appreciate more info on how to use this: cmd.centerofmass()
>>>> returns a list of 3 floats.
>>>>
>>>> 
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>>>>
>>>
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>>
>>
>>
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>>
>>
>
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Re: [PyMOL] Calculating center of mass for the entire protein

[David Hall]

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 find the documentation about the python api here to be a bit lacking. 
> 
> https://pymolwiki.org/index.php/Centerofmass
> 
> I would appreciate more info on how to use this: cmd.centerofmass() returns a 
> list of 3 floats.
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Re: [PyMOL] problems creating object using align method

[David Hall]

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 coordinates, you use the existing objects.

-David

> On Mar 13, 2017, at 1:31 AM, Sanaa Syed  wrote:
> 
> Hello,
> Can somebody please help me with creating aligned object using pymol API? i 
> want   to split chains from my protein and superimpose first chain on the 
> rest. the chains get loaded. and superimposed as well but i am unable to save 
> superimposed coordinates in a new file because no object is created.  this is 
> my script:
> list1=["chain_A","chain_B","chain_C","chain_D"]
> for every in list1:
> cmd.load("/home/sanaa/pymol/"+every+".pdb")
> object_list=cmd.get_object_list()
> aligned=[ ]
> list2=[ ]
> #object=string(alignedA_B)
> for j in range(len(object_list)):
>try:
> 
> aligned=cmd.align(object_list[0],object_list[j+1],object=AlnAB)
> list2.append(aligned)
> except IndexError:
> pass
> 
> this is giving me name error like:
> NameError: name 'AlnAB' is not defined
> 
> the object is not being created after calling the align command. it creates 
> an object if i give the command directly on  pymol command line but not 
> through the script. i have tried everything. please help!
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Re: [PyMOL] Atom Order when Saving

[David Hall]

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 
> [https://sourceforge.net/p/pymol/mailman/message/7561093/ 
> ] and not sure if 
> there is a direct way now to do this.
> 
> Thanks and Best Regards,
> Subha
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Re: [PyMOL] loading StringIO

[David Hall]

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. Is there a variant of cmd.load that could 
> handle an open file instead of a file?
> 
> Thanks,
> Albert
> 
> 
> -- 
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>   EPSRC Research Fellow,
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>   University of Leeds
>   Tel: +44 (0)1133 431451
> 
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Re: [PyMOL] Placing pseudo atom on COM and saving it as pdb

[David Hall]

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 why you are only 
processing the first file, probably doing so 100 times.

you probably want something like

with open(“out") as f:
for line in f:
  in_pdb_file = line.strip()
  // code for processing in_pdb_file here

or

for X in range(1,101):
in_pdb_file = “dockout/F"+ str(X).zfill(2)
   // code for processing in_pdb_file here


Generally, I would recommend strongly against using os.system for performing 
file operations. You should look into shutil.copy , shutil.move , and os.remove 


> On Oct 12, 2016, at 2:16 PM, Subha K  wrote:
> 
> Hi There,
> 
> I am looking to automate the calculation of centre of mass and placing a 
> pseudo atom on the COM and save it as a pdb file . Going through the forum 
> [https://sourceforge.net/p/pymol/mailman/message/34458943/ 
> ] , I found some 
> useful scripts for this, but, I am having trouble getting it done for all 
> files in a directory. My script does what I need for the first file alone. 
> Some looping or other is not correct. Or there could be an easy and better 
> way to do it. I couldn't figure that out.  So, could some one please help me 
> solve this?
> 
> I have 100 files F01, F02, F100 ... in the directory dockout. I would like to 
> calculate the COM and place a pseudo atom on the COM and save it as a pdb for 
> all the 100 files. 
> 'out' in the script corresponds to the list of all the 100 files.
> 
> import pymol
> from pymol import cmd
> pymol.finish_launching()
> import numpy as np
> import glob
> import fileinput
> def center(selection, com=True):
> model = cmd.get_model(selection)
> xyz = np.array(model.get_coord_list())
> mass = [i.get_mass() for i in model.atom]
> xyz_m = xyz * np.array([mass]).T
> if com:
> return tuple(np.sum(xyz_m, 0)/model.get_mass())
> else:
> return tuple(np.average(xyz, 0))
> 
> def GetListOfFiles (filename):
> l = []
> for line in fileinput.input( filename ):
> tokens = line.split( )
> l.append(tokens)
> return l
> 
> def Calculate_COM (list):
> for i in range (len(list)):
> print list[i][0]
> X=1
> if (X<101):
> os.system("cp ./dockout/F"+ str(X).zfill(2)+ " ./lig.pdb")
> for pdb in glob.glob("lig.pdb"):
> cmd.load(pdb)
> COM = center('resn UNK')
> cmd.pseudoatom('ligCOM', pos=COM)
> cmd.save("complex_dummy.pdb", "all")
> os.system("mv complex_dummy.pdb complex_" + str(X).zfill(2) + 
> "_dummy.pdb")
> os.system("rm lig.pdb")
> X=X+1
> else:
> break
> listofFiles = GetListOfFiles ("./out")
> print listofFiles
> Calculate_COM(listofFiles)
> 
> 
> Thanks,
> Subha 
> 
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Re: [PyMOL] Modeling protein-dna complex

[David Hall]

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 complex
(2) an object that has just your DNA that you want in the complex

In the bottom right, where it typically says “Selecting Residues”, click where 
it says Residues until that it says “Objects”

Click on your protein

Click on your dna

Click on File->Save Molecule and save “sele” as a PDB file.

> On Aug 13, 2016, at 8:22 AM, soumi  wrote:
> 
> Hi,
> I carry on my research work on protein-dna complex system.I have one dna 
> pdb and one protein-dna complex pdb.I want to make new protein-dna complex 
> pdb taking  dna from single pdb and protein from protein-dna complex.Protein 
> possess similar DNA-binding specificities.I superimpose two pdb file and 
> remove dna from protein-dna complex pdb .But I can not save new protein-dna 
> complex.Please let me know by pymol how I would be able to model of the 
> referred paper was done.
> Thanks
> soumi
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Re: [PyMOL] Video in Ubuntu Linux

[David Hall]

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 Kubuntu 14.04. I compiled PyMOL, following some instructions on the
>>> web. This produced the directory:
>>> 
>>> /opt/pymol-svn/
>>> 
>>> and a symbolic link to pymol executable:
>>> 
>>> /usr/bin/pymol -> /opt/pymol-svn/pymol*
>>> 
>>> PyMOL works fine. Nevertheless, when I try:
>>> 
>>> File > Save Movie As > MPEG...
>>> 
>>> I get the following error message:
>>> 
>>> MPEG encoder missing.
>>> The FreeMOL add-ons may not be installed
>>> 
>>> I downloaded the source code for mpeg_encode (freemol-mpeg_encode.tar.gz)
>>> from:
>>> 
>>> http://www.bioinformatics.org/cgi-bin/viewvc.cgi/freemol/trunk/src/mpeg_en
>>> code/?view=tar
>>> 
>>> and I did the following:
>>> 
>>> tar zxvf freemol-mpeg_encode.tar.gz
>>> cd mpeg_encode
>>> ./configure
>>> make
>>> sudo make install
>>> 
>>> This created the following file:
>>> 
>>> /bin/mpeg_encode.exe
>>> 
>>> That means that mpeg_encode.exe is in the PATH (it runs from any
>>> directory). mpeg_encode.exe seems to work. Unfortunately, when I try to
>>> produce a movie in pymol, I get the same error message. What have I done
>>> wrong?
>> 
>> I hope it is very simple.
>> You need to include an environment variable $FREEEMOL pointing at the
>> directory where
>> freemol is installed
>> 
>> If you are using bash that would be
>> export FREEMOL=/your/bath/to/freemol/
>> where the mpeg_encode.exe file is in
>> /your/bath/to/freemol/bin/mpeg_encode.exe
>> 
>> Hope this helps!
> 
> I created a directory:
> 
> /opt/freemol
> 
> with two subdirectories:
> 
> /opt/freemol/bin
> /opt/freemol/licenses
> 
> which contain the files:
> 
> /opt/freemol/bin/mpeg_encode.exe
> /opt/freemol/licenses/mpeg_encode.txt
> 
> I created the file:
> 
> pymol.sh
> 
> with this content:
> 
> #!/bin/bash
> FREEMOL=/opt/freemol
> export FREEMOL
> pymol
> 
> I ran pymol.sh, but the problem remained the same. Any idea?
> 
> Ioannis
> 
>> Folmer
>> 
>>> Thank you in advance.
>>> 
>>> Best Regards,
>>> 
>>> Ioannis
> 
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Re: [PyMOL] ABPS Tools 2.1 plugin error

[David Hall]

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 these errors:
> 
> Could not find default location for file: psize.py
> Could not find default location for file: apbs.exe
> Could not find default location for file: apbs-mpi.exe
> Could not find default location for file: apbs-mpi-openmpi.exe
> Could not find default location for file: apbs-mpi-lammpi.exe
> Could not find default location for file: pdb2pqr.py
> 
> I run a "find / -name psize.py " command but it can not locate the file.
> 
> Can somebody please help me? Where can I get 'psize.py' and the APBS 
> binary so I can
> specify them in the APBS plugin under "Program locations"?
> 
> Many thanks
> 
> 
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Re: [PyMOL] High Resolution Ray Tracing

[David Hall]

Feel free to send me the files off list.

-David Hall

> On May 6, 2016, at 1:54 PM, Stephen Kerry <stephen.kerr...@outlook.com> 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 out of 
> memory at the end of the ray tracing process, with the following error:
> 
> python2.7(972,0x7fff7397f300) malloc: *** 
> mach_vm_map(size=18446744068907188224) failed (error code=3)
> *** error: can't allocate region
> *** set a breakpoint in malloc_error_break to debug
> 
> This is with PyMOL 1.81 from Fink on OSX 10.10 with an i7-4790K processor and 
> 32 GB of DDR3. Python2.7 expands up to 15 GB of RAM, with more than twice 
> this reserved for virtual memory, but no swap is actually used.
> 
> Decreasing hash_max just increases the ray tracing time until the error at 
> the end. Sometimes PyMOL will be terminated with this error, whilst at other 
> times a transparent PNG is all that is produced.
> 
> Is there a way to force PyMOL to use virtual memory to avoid these 
> errors/crashes at the expense of processing time?
> 
> If not, is there anyone who has PyMOL 1.8x installed on a system with 64 GB 
> or more RAM, who would be able to render this ray traced image if I send the, 
> the .pse file and .pml script off list? Takes about 10 mins to process.
> 
> Cheers,
> 
> Stephen
> 
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Re: [PyMOL] Bash scripting and pymol

[David Hall]

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 PYMOL: download pdbs to the folder and pre-process 
> them!
> mkdir ${pdb_array_store}
> for i in ${pdb_array[@]}; do
> pdb_tit=$(basename "$i")
> pymol -d "fetch $i; save ${pdb_array_store}/${pdb_tit}_proc.pdb,
> ${pdb_tit}" -c ;
> rm ${pdb_array_store}/*.log
> done
> 
> 
> while executing it sends error
> 
> PyMOL>fetch 5A2H; save
> /projects/clouddyn/md_bench/script_amber/inputs/pymol/5A2H_proc.pdb,
> 5A2H
> please wait ...
> Selector-Error: Invalid selection name "5A2H".
> ( 5A2H )<--
> Save: wrote 
> "/projects/clouddyn/md_bench/script_amber/inputs/pymol/5A2H_proc.pdb".
> PyMOL: normal program termination.
> 
> if I change save selection just to 'polymer' it saved empty pdbs-
> where might be an error here?
> 
> Thanks!
> 
> 2016-04-27 16:53 GMT+02:00 Tsjerk Wassenaar :
>> Hi,
>> 
>> You need
>> 
>> for i in ${pdb_array[@]}
>> do
>> ...
>> done
>> 
>> Cheers,
>> 
>> Tsjerk
>> 
>> On Apr 27, 2016 4:44 PM, "James Starlight"  wrote:
>>> 
>>> so As I tried to do it but it was not worked :-O)
>>> 
>>> #pdbs list
>>> pdb_array=("1UBI" "1IGD" "1G33" "1CC7" "4LGJ" "5A2H")
>>> #where to save
>>> pdb_array_store=$template/pymol/
>>> 
>>> 
>>> # A simple FETCHER: download pdbs to the folder and pre-process them!
>>> #mkdir ${pdb_array_store}
>>> for i in `cat ${pdb_array}` ; do wget
>>> http://www.rcsb.org/pdb/files/${i}.pdb ${pdb_array_store}/${i}.pdb ;
>>> done
>>> 
>>> result
>>> cat: 1UBI: No such file or directory
>>> 
>>> 2016-04-27 12:29 GMT+02:00 James Starlight :
 Please give me an example of the list of 3 pdbs instead of just cat $1
 :)
 as well as proper syntax of how to save each pdb after fetching in
 pymol using same command line
 Forgot to mention important points:
 1) that list should be physically in my script like in python
 2) I use pymol because I will need to process each of the pdb- e,g to
 remove from them ligands or water etc
 
 Thanks!
 
 2016-04-27 12:18 GMT+02:00 James Starlight :
> Please give me an example of the list of 3 pdbs instead of cat $1  as
> well as how to save syntax of how to save each pdb
> 
> 
> Thanks!
> 
> J
> 
> 2016-04-27 12:09 GMT+02:00 Jordan Willis :
>> If you really want to use pymol, this works
>> 
>> #!/bin/bash
>> #myscript.bash
>> for i in `cat $1` ; do pymol -d "fetch $i" -c ; done
>> 
>> 
>> Then on the command line
>>> chmod +x myscript.bash; ./myscript.bash mylist.txt
>> 
>> 
>> On Apr 27, 2016, at 2:55 AM, Jordan Willis 
>> wrote:
>> 
>> Must you use pymol?
>> 
>> 
>> Try directly from the PDB
>> 
>> #!/bin/bash
>> #myscript.bash
>> 
>> for i in `cat $1` ; do wget http://www.rcsb.org/pdb/files/${i}.pdb ;
>> done
>> 
>> 
>> 
>> 
>> Then on the command line
>>> chmod +x myscript.bash; ./myscript.bash mylist.txt
>> 
>> 
>> J
>> 
>> On Apr 27, 2016, at 2:41 AM, James Starlight 
>> wrote:
>> 
>> Dear Pymol users!
>> 
>> I need to add a few strings to my simple bash script which will creat
>> a list of pdb files and than will call pymol without GUI from the
>> terminal to fetch all the pdbs and save it to the desired location.
>> For one pdb it should be smth like
>> 
>> pdbs="1f88"
>> 
>> pymol -c -q -d "fetch ${pdbs}; save $template/pymol/*.pdb " >
>> ${tmp}/pymol_${pdbs}.log
>> 
>> will be thankful for the correction of this string as well as example
>> how it can be adapted for a list of pdbs in bash.
>> 
>> Thanks!
>> 
>> J
>> 
>> 
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>> Manager
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>> 
>> 
>> 
>>> 
>>> 
>>> 

Re: [PyMOL] pymolrc location

[David Hall]

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

[David Hall]

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 
> protein domains are joined by a shared helix
> and highlights backbone steric clashes
> 
> python 
> for i in range(1, 25):
> cmd.fit('/DARPin2//C/15-22/CA','/helix1//B/%d-%d/CA'%(i, i+7),matchmaker 
> = -1) 
> cmd.save('model_%d.pdb'%i,'/DARPin1//A/1-160 or /helix1//B/1-%d or 
> /DARPin2//C/23-169'%(i+7))
> cmd.color('white','DARPin1')
> cmd.color('paleyellow','/DARPin1//A/37-135')
> cmd.hide('spheres')
> cmd.select('clash','/DARPin1//A/1-157/N+CA+C+A within 2.5 of 
> /DARPin2//C/26-169/N+CA+C+N')
> cmd.show('spheres','clash')
> cmd.color('red','clash')
> cmd.ray(2048, 1536)
> cmd.png('model_%dA.png'%i)
> cmd.turn('x', -90)
> cmd.ray(2048, 1536)
> cmd.png('model_%dB.png'%i)
> cmd.turn('x', 90)
> cmd.hide('spheres','clash')   
> python end 
> 
> 
> Now, to visualize and quantitate the relative domain orientations in the 
> models by a pseudo-torsion angle 
> between the centers of gravity of the two domains around the axis of the 
> shared helix.
> 
> #this needs to be done only once: 
> 
> run py_scripts/center_of_mass.py
> run py_scripts/anglebetweenhelices.py
> 
> ...
> 
> com /DARPin1//A/37-135/CA, object=com1
> color black, name PS1
> helix_orientation_hbond /helix1//B/159-193
> 
> ...
> 
> # this would define the center of gravity of the mobile domain and should be 
> within the loop:
> 
> com /DARPin2//A/37-135/CA, object=com2
> 
> however, since “com” is not a standard pymol command, but added by script 
> center_of_mass.py,
> I do not know how to use it from within the loop. If I try to use it 
> analogous to normal commands, I get the error message:
> 
> Traceback (most recent call last):
>   File 
> "/Users/ahonegger/Desktop/MacPyMOL1.8.0.2.app/Contents/pymol/modules/pymol/parser.py",
>  line 157, in parse
> exec(py_block,self.pymol_names,self.pymol_names)
>   File "", line 4, in 
> AttributeError: 'module' object has no attribute 'com'
> 
> Can somebody please help me?
> 
>   Thanks
>   Annemarie
> ___
> 
> Dr. Annemarie Honegger PhD
> Department 
> of Biochemistry
> Zürich University
> Winterthurerstrasse 190
> CH-8057 Zürich
> Switzerland
> 
> e-Mail: honeg...@bioc.uzh.ch 
> 
> websites
> http://www.bioc.uzh.ch/plueckthun 
> http://www.bioc.uzh.ch/plueckthun/antibody 
> 
> http://www.bioc.uzh.ch/plueckthun/nanowelt 
> 
> 
> 
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Re: [PyMOL] why lib/python folder is missing?

[David Hall]

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 /home/albert/install/pymol/open-1.8
> setenv modules $prefix/modules
> python setup.py build install --home=$prefix --install-lib=$modules 
> --install-scripts=$prefix
> 
> However, I noticed that there is no the "lib/python2.7" folder in the 
> installation directory..
> 
> normally this should be placed in :
> 
> /home/albert/install/pymol/open-1.8/ext/lib/python2.7
> 
> I am just wondering how can we fix this problem?
> 
> thanks a lot
> 
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Re: [PyMOL] Filled rings on stick mode

[David Hall]

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 
> nucleobases (or nucleobases + riboses) while being simply in the mode "stick" 
> and not in the "cartoon" mode.
> 
> Many thanks for your answers,
> 
> 
> Maria,
> 
> I2BC - CNRS
> France
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Re: [PyMOL] pdb edition

[David Hall]

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 mode 
http://www-cryst.bioc.cam.ac.uk/members/zbyszek/figures_pymol#move

And then save http://pymolwiki.org/index.php/Save


But honestly, the description sounds like something that would be infinitely 
easier to do using some plain python code rather than in pymol.

-David


> On Jan 19, 2016, at 4:59 PM, Edward A. Berry  wrote:
> 
> 
> 
> On 01/19/2016 03:11 PM, Tsjerk Wassenaar wrote:
>> Hi Pascual,
>> 
>> The PDB file does not really have information on bonds. If atoms are closer 
>> than some cutoff a bond is drawn. Unbonding and saving will not change the 
>> distance, so the bond will be drawn again when loaded again. What is your 
>> aim?
>> 
>> Cheers,
> 
> (Actually of course the PDB file format does (or did) have a way to specify
> bonds, but i guess no programs ever used it)
> But the poster did specify moving atoms (to) break bonds and separate atoms,
> so maybe that is where the help is needed- how do you move atoms in Pymol?
> Or since this is probably a RTFM-type question, perhaps a pointer
> to chapter and verse in the wiki would be more appropriate?
> And then to save the modified pdb: I suppose file:save:molecule, and
> it will be obvious which molecule to save?
>> 
>> Tsjerk
>> 
>> On Tue, Jan 19, 2016 at 12:15 PM, Pascual Lahuerta >  > >> wrote:
>> 
>>I am new user of Pymol and I would like to use this program for a very 
>> simple task that I describe here in three steps:
>> 
>>1. Start with a simple structure (structure 1.pdb1) either loaded or 
>> created with the editor.
>>2. The second task will be to change the position of the atoms in 
>> structure 1, breaking bonds and separating atoms.
>>3. The third step will be to save the resulting structure as 
>> structure2.pdb file.
>> 
>>I wonder if  pymol allows me to perform this task.  iI hope someone can 
>> guide me in this task.
>> 
>>Thanks in advance
>> 
>>Pascual
>>=
>> 
>> 
>>Pascual Lahuerta
>>Universitat de Valencia
>>Dep. Q. Inorganica
>>Edificio Investigación 3.36
>>Dr. Moliner 50
>>46100 Burjassot-Valencia
>>Despacho 96 354 3147
>>Movil 617 188 331
>>lahue...@uv.es  > >
>> 
>> 
>> 
>>
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>> 
>> 
>> 
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>> 
>> 
>> 
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Re: [PyMOL] optimize and open babel troubles

[David Hall]

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 to utilize the optimize plugin within pymol. I have installed 
> open babel per their instructions on their website. All of the "test to see 
> if it is working" tests seem to work (eg,using import openbabel in the cmd 
> window).
> 
> For what it is worth, I am running 64 bit windows, but am using the 32 bit 
> windows pymol since there doesn't seem to be a 64 bit version of open babel 
> for windows.
> 
> When I load pymol, I still get the following:
> "Optimize plug-in needs openbabel to be installed in your system, please 
> follow the instructions at
> http://openbabel.org/wiki/Get_Open_Babel 
> "
> 
> Several other plugins also fail to load properly, due to the inability to 
> import scimath.
> 
> I have also tried this on ubuntu 12.04, but that is a 32 bit operating system 
> and it seems there is no 32 bit linux version of pymol readily available.
> 
> Thanks for your time,
> Joe
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Re: [PyMOL] Pymol issues for coloring ball and stick representation

[David Hall]

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 PyMol using an academic version (free). 
> I am trying to develop a 3D model for my protein-protein interactions. I have 
> chosen a ball and stick preset representations.
> The problem is that I cannot get a single color for the stick and the ball 
> for representing my molecule. While the ball color is easily changed, the 
> stick color remains grey. I have tried most of the options for color change 
> but am not getting the desired results. Any suggestions for this?
> 
> Anurag
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Re: [PyMOL] Pymol under El Capitan

[David Hall]

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/c92b0faf48c1bb7dee5eeba1260cff43-1657.php)
> and I tried a pre installed version of Pymol and it worked without issue.
> However I have had a few readers email me saying they are having problems
> so I took a new machine running El Capitan and tried to instal a variety of
> cheminformatics tools including Pymol using Homebrew and PIP as described
> here (http://www.macinchem.org/reviews/cheminfo/cheminfoMac.php). All
> worked fine except Pymol which opened but crashed with the following error.
>
> Username:~ prompt$ pymol
>  PyMOL(TM) Molecular Graphics System, Version 1.7.6.0.
>  Copyright (c) Schrodinger, LLC.
>  All Rights Reserved.
>
>
> Created by Warren L. DeLano, Ph.D.
>
>
> PyMOL is user-supported open-source software.  Although some versions
> are freely available, PyMOL is not in the public domain.
>
>
> If PyMOL is helpful in your work or study, then please volunteer
> support for our ongoing efforts to create open and affordable
> scientific
> software by purchasing a PyMOL Maintenance and/or Support subscription.
>
> More information can be found at "http://www.pymol.org;.
>
>
> Enter "help" for a list of commands.
> Enter "help " for information on a specific command.
>
>  Hit ESC anytime to toggle between text and graphics.
>
>  Detected OpenGL version 2.0 or greater. Shaders available.
>  Detected GLSL version 1.20.
>  OpenGL graphics engine:
>   GL_VENDOR:   NVIDIA Corporation
>   GL_RENDERER: NVIDIA GeForce 8600M GT OpenGL Engine
>   GL_VERSION:  2.1 NVIDIA-10.0.40 310.90.10.05b12
>  Detected 2 CPU cores.  Enabled multithreaded rendering.
> libpng warning: Application built with libpng-1.6.19 but running with
> 1.5.23
> /usr/local/bin/pymol: line 4:  3628 Segmentation fault: 11
> "/usr/local/opt/python/bin/python2.7" "/usr/local/Cellar/pymol/
> 1.7.6.0/libexec/lib/python2.7/site-packages/pymol/__init__.py" "$@“
>
> Any suggestions?
>
> Cheers
> Chris
>
>
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Re: [PyMOL] on PDB

[David Hall]

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

[David Hall]

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:

> Dear All,
>
> Is any way we can colour the molecule by pymol based on the y values in
> the z y z coordinates, so that we can view easily the residues (or atoms)
> with equivalent position in the primary sequence but has a y-axis shift in
> the 3-D structure?
>
> Smith
>
>
>
>
>
> --
>
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Re: [PyMOL] on coloring residues based on y values in the x y z coordinates

[David Hall]

I forgot:

spectrum b


at the end.



On Wed, Nov 18, 2015 at 8:11 AM, David Hall <li...@cowsandmilk.net> 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 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 <smith_liu...@163.com> wrote:
>
>> Dear All,
>>
>> Is any way we can colour the molecule by pymol based on the y values in
>> the z y z coordinates, so that we can view easily the residues (or atoms)
>> with equivalent position in the primary sequence but has a y-axis shift in
>> the 3-D structure?
>>
>> Smith
>>
>>
>>
>>
>>
>> --
>>
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Re: [PyMOL] on coloring residues based on y values in the x y z coordinates

[David Hall]

clearly shouldn’t write e-mails before having my morning coffee. Those %
symbols should have been pounds, I was aiming to make comments


As an example:

fetch 1acb, prot,  async=0
stored.y=[]
iterate_state 1, prot, stored.y.append(y)
alter prot, b=stored.y.pop(0)
spectrum b



On Nov 18, 2015, at 9:12 AM, Smith Liu <smith_liu...@163.com> wrote:

Dear David,

I am unfamiliar with the pymol scripts so I do not understands where your
scripts end at each line. Can we write this way,

stored.y=[]
iterate_state 1, prot, stored.y.append(y)
alter prot, b=stored.y.pop(0)

which means those from % in your scripts will be not used in each line for
pymol reading?

Can you introduce a website to introduce the pymol scripts? For stored.y=，
following y= is it the file name of file stores y for each coordinates? Can
you introduce to me a server or software which can extract y coordinates
from the PDB and save it as 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" <li...@cowsandmilk.net> wrote:

I forgot:

spectrum b


at the end.



On Wed, Nov 18, 2015 at 8:11 AM, David Hall <li...@cowsandmilk.net> 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 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 <smith_liu...@163.com> wrote:
>
>> Dear All,
>>
>> Is any way we can colour the molecule by pymol based on the y values in
>> the z y z coordinates, so that we can view easily the residues (or atoms)
>> with equivalent position in the primary sequence but has a y-axis shift in
>> the 3-D structure?
>>
>> Smith
>>
>>
>>
>>
>>
>> --
>>
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Re: [PyMOL] placing protein into lipid bilayer

[David Hall]

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 of the atoms of the membrane.

For this, they likely:
1) Open protein and equilibrated membrane in pymol
2) From the menu: Choose Mouse-> 3 button editing
3) Shift+Middle click to move the protein on top of the membrane
4) Shift+Left click to rotate the protein into the desired orientation.
5) save the protein in its new location

Then, they run the program they wrote, which uses grimaces to insert the
protein into the membrane at roughly the position and orientation where
they have dragged it.

If you don't have any experimental evidence for how the protein sits in the
membrane, http://opm.phar.umich.edu/server.php can give you a start.




On Sat, Nov 14, 2015 at 11:35 AM, samira poulakchi 
wrote:

> there is an article''g membed: Efficient insertion of a membrane protein
> into an equilibrated lipid bilayer with minimal perturbation.'' which use
> pymol to insert protein into bilayer membrane. How can they do it?
>
>
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Re: [PyMOL] Pymol Morph movie error

[David Hall]

Are you using “Incentive Pymol” (that based on a license from Schrodinger) or 
“Open Source Pymol” (that built from source code)?

For anyone looking for mpeg_encode source code on freemol.org , there is source 
code in the svn repository

http://www.bioinformatics.org/cgi-bin/viewvc.cgi/freemol/trunk/src/mpeg_encode/

-David

> On Oct 20, 2015, at 4:46 AM, <h.c.van_leeu...@lumc.nl> 
> <h.c.van_leeu...@lumc.nl> wrote:
> 
> Dear Thomas, David,
>  
> I appreciate your help.
> First I'm using windows 7.
>  
> The link from:
> http://freemol.org <http://freemol.org/>
> leading to 
> http://bmrc.berkeley.edu/frame/research/mpeg/mpeg_encode.html 
> <http://bmrc.berkeley.edu/frame/research/mpeg/mpeg_encode.html>
>  
> is empty.(?)
>  
> David your link is for Linux correct?
> http://software.opensuse.org/download.html?project=home%3Acowsandmilk=mpeg_encode
>  
> <http://software.opensuse.org/download.html?project=home%3Acowsandmilk=mpeg_encode>
>  
> I attached my Pymol file maybe you can see whether you get the same error. 
> (The movie is mout)
>  
> Thanks again,
>  
> Hans
>  
>  
>  
> -Original Message-
> From: Thomas Holder [mailto:thomas.hol...@schrodinger.com 
> <mailto:thomas.hol...@schrodinger.com>] 
> 
>  
> David, Incentive PyMOL does bundle mpeg_encode.exe and uses it for movie 
> export. It is also available from http://freemol.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 <li...@cowsandmilk.net <mailto:li...@cowsandmilk.net>> wrote:
>  
> > 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) 
> > athttps://build.opensuse.org/package/show/home:cowsandmilk/mpeg_encode 
> > <https://build.opensuse.org/package/show/home:cowsandmilk/mpeg_encode> , 
> > you can download by clicking the files with the up arrow (I know, those 
> > symbols make no sense).
> > 
> > It uses an old version of libjpeg with apis that have been long abandoned.
> > 
> > Basically, you don't have a binary for what I think is a long abandoned 
> > program that depends on old versions of libraries.
> > 
> > Hopefully someone else will tell me there's some magical updated version 
> > floating around out there, but I doubt it. Otherwise, no new features in 20 
> > years and no bug/compatibility fixes in 13.
> > 
> > -David
> > 
> -Original Message-
>  
> > On Mon, Oct 19, 2015 at 8:36 AM, <h.c.van_leeu...@lumc.nl 
> > <mailto:h.c.van_leeu...@lumc.nl>> wrote:
> > Dear Pymol community,
> > 
> >  
> > 
> > Im using Pymol 1.7.6 and created a morph movie. Looks nice on screen!
> > 
> > However when I tried to save the movie, I get an error:
> > 
> > --
> > 
> > produce: creating 'C:/Users/hcvanleeuwen/Desktop/test2.mpg' (in 
> > background)...
> > 
> > please wait ...
> > 
> > Error: mpeg_encode did not run
> > 
> > Traceback (most recent call last):
> > 
> >   File "C:\Program Files\PyMOL\\PyMOL/modules\freemol\mpeg_encode.py", line 
> > 35, in run
> > 
> > mpeg_encode_in, mpeg_encode_out, mpeg_encode_err = 
> > os.popen3(_mpeg_encode_exe)
> > 
> > WindowsError: [Error 2] The system cannot find the file specified: 'Ex: 
> > C\\Temp /c "C:\\Program  
> > Files\\PyMOLPyMOL\\ext\\bin\\mpeg_encode.exe"'
> > 
> > produce: compression failed
> > 
> > -
> > 
> > Anyone suggestions how to solve this?
> > 
> > Thanks in advance,
> > 
> > Hans van Leeuwen
>  
> 

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Re: [PyMOL] Pymol Morph movie error

[David Hall]

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 arrow (I know, those symbols
make no sense).

It uses an old version of libjpeg with apis that have been long abandoned.

Basically, you don't have a binary for what I think is a long abandoned
program that depends on old versions of libraries.

Hopefully someone else will tell me there's some magical updated version
floating around out there, but I doubt it. Otherwise, no new features in 20
years and no bug/compatibility fixes in 13.

-David


On Mon, Oct 19, 2015 at 8:36 AM,  wrote:

> Dear Pymol community,
>
>
>
> Im using Pymol 1.7.6 and created a morph movie. Looks nice on screen!
>
> However when I tried to save the movie, I get an *error*:
>
> --
>
> *produce**: creating 'C:/Users/hcvanleeuwen/Desktop/test2.mpg' (in
> background)...*
>
> *please wait ...*
>
> *Error**: mpeg_encode did not run*
>
> *Traceback (most recent call last):*
>
> *  File "C:\Program Files\PyMOL\\PyMOL/modules\freemol\mpeg_encode.py",
> line 35, in run*
>
> *mpeg_encode_in, mpeg_encode_out, mpeg_encode_err =
> os.popen3(_mpeg_encode_exe)*
>
> *WindowsError**: [Error 2] The system cannot find the file specified:
> 'Ex: C\\Temp /c "C:\\Program
> Files\\PyMOLPyMOL\\ext\\bin\\mpeg_encode.exe"'*
>
> *produce: compression failed*
>
> -
>
>
>
> Anyone suggestions how to solve this?
>
>
>
> Thanks in advance,
>
>
>
> Hans van Leeuwen
>
>
>
>
>
>
>
>
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Re: [PyMOL] pymol to webGL?

[David Hall]

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 upgrades.
> I have to rewrite the program.
> 
> Does anyone know if there is a setting to export in the 'old' format?
> 
> Best regards,
> 
> Takanori Nakane
> 
> On 2015/10/18 1:47, Osvaldo Martin wrote:
>> That really weird! the script is expecting a list but is getting an
>> integer. Could you send me the "my" molecule or a pse file with that
>> molecule? or at least other molecule that give you the same error?
>> 
>> Cheers,
>> Osvaldo.
>> 
>> 
>> 
>> On Sat, Oct 17, 2015 at 5:49 PM, Albert  wrote:
>> 
>>> Thanks a lot for further advice.
>>> 
>>> Here is what I got:
>>> 
>>> PyMOL> run exportToWeb.py
>>> PyMOL>exportToWeb my
>>> Traceback (most recent call last):
>>>   File "/home/albert/install/pymol-1.7.6/modules/pymol/parser.py", line
>>> 256, in parse
>>> self.result=apply(layer.kw[0],layer.args,layer.kw_args)
>>>   File "exportToWeb.py", line 118, in dump_rep
>>> ret += parseObjMol(obj)
>>>   File "exportToWeb.py", line 50, in parseObjMol
>>> if (rep[5] == 1):
>>> TypeError: 'int' object has no attribute '__getitem__'
>>> 
>>> 
>>> If possible, would you please give me some suggestions?
>>> 
>>> Thanks a lot
>>> 
>>> Albert
>>> 
>>> 
>>> 
>>> 
>>> On 10/17/2015 04:36 PM, Osvaldo Martin wrote:
>>> 
>>> Hi Albert,
>>> 
>>> I do the following steps and I get a .html file as expected.
>>> 
>>>1. I download and unpack this
>>>
>>> 
>>>file. The script there seems to be similar to the one you attached.
>>>2. Lauch PyMOL and do some stuff
>>>3. cd to the folder creating during unpacking
>>>4. run the script by doing
>>> 
>>> run exportToWeb.py
>>> 
>>>5. then run the commnand
>>> 
>>> exportToWeb PymolObjectName
>>> 
>>>where PymolObjectName is the name of the pymol object you want to
>>>export
>>>6. check the unpacked folder for a file with the name
>>>PymolObjectName.html
>>> 
>>> Could you try to follow these steps and tell us what you get?
>>> 
>>> Cheers,
>>> 
>>> Osvaldo.
>>> 
>>> 
>>> 
>> 
>> 
>> 
>> --
>> 
>> 
>> 
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Re: [PyMOL] Using cartoon putty-like command

[David Hall]

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 b-factors that i
> would like to represent as the *cartoon putty* command is doing.(ie pdb
> file)
> The main problem is that I don't precisely know what *cartoon putty* is
> doing.
>
> So I would like to know where the code of cartoon putty is hidden in pymol
> and how the code could be modify in order to work on all atoms rather than
> CA.
>
> Many thanks,
>
>
> --
> *Damien CLAVEL*
> Cellphone +33 7 81 66 61 70
> Landline   +33 4 57 42 87 35
> PhD student at Laboratoire Chimie Physique (UP Sud)
> and Institut de Biologie Structurale (EPN Campus)
> --
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> Institut de
> Biologie Structurale 
> Bul. 350 Campus Orsay EPN Campus
> 15, Av. Jean Perrin 6, rue Jules Horowitz
> F-91405 ORSAY Cedex F-38000 GRENOBLE
>
>[image: Image and video hosting by TinyPic]
> 
>
>
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Re: [PyMOL] creation of a sphere

[David Hall]

What version of PyMol are you using?

 On Aug 27, 2015, at 7:50 AM, Christian Trindler 
 christian.trind...@unibas.ch 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 pseudoatom:
  
 Traceback (most recent call last):
   File C:\Program Files (x86)\DeLano 
 Scientific\PyMOL/modules\pymol\parser.py, line 370, in parse
 exec(com2[nest]+\n,pymol_names,pymol_names)
   File string, line 1
  pseudoatom name
   ^
 SyntaxError: invalid syntax
  
 What is the error? What do I have to change?
  
 Thanks for your help,
 Christian
  
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Re: [PyMOL] Python from PyMOL or PyMOL from Python?

[David Hall]

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

Other options at: http://www.pymolwiki.org/index.php/Command_Line_Options 
http://www.pymolwiki.org/index.php/Command_Line_Options


Why is this my preferred method?
Running python from pymol doesn’t require you to do any of these arcane things 
like call “finish_launching”, etc. You just write a python script and run it.



 On Aug 14, 2015, at 5:27 AM, Dirk Kostrewa kostr...@genzentrum.lmu.de wrote:
 
 Dear PyMOLers,
 
 I want to modify atomic coordinates in a python program and make 
 pictures with PyMOL for making a movie.
 
 In your experience, is it better to call the python program from PyMOL 
 or to call PyMOL from the python program?
 
 And could you please give me any good pointer for your preferred method 
 (other than the simple scripting tutorial)?
 
 Best regards,
 
 Dirk.
 
 -- 
 
 ***
 Dirk Kostrewa
 Gene Center Munich, A5.07
 Department of Biochemistry
 Ludwig-Maximilians-Universität München
 Feodor-Lynen-Str. 25
 D-81377 Munich
 Germany
 Phone:  +49-89-2180-76845
 Fax:+49-89-2180-76999
 E-mail: kostr...@genzentrum.lmu.de
 WWW:www.genzentrum.lmu.de
 ***
 
 
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Re: [PyMOL] How to find RMSD values using fitting.py using Shell script

[David Hall]

I assume you are referring to 
http://pldserver1.biochem.queensu.ca/~rlc/work/pymol/fitting.py 
http://pldserver1.biochem.queensu.ca/~rlc/work/pymol/fitting.py

That is a script that creates a function. To turn it into a program, you need 
to set up what you read in and what you output.

In python, this is often done by command line arguments that can read from 
sys.argv 

import sys

arg1 = sys.argv[1]
arg2 = sys.argv[2]

cmd.load(arg1, “protein1”)
cmd.load(arg2, “protein2”)

You can have the definition of fitting in your script, then call

fitting(“protein1”, , “protein2”, )

I left in questions for the select1 and select2 arguments of the function since 
it is not at all clear what you would like to put in as arguments there.

Beyond that, I would recommend reading up on python assuming you are not 
familiar with the language.

-David


 On Jul 11, 2015, at 10:00 AM, Gazal gazal...@gmail.com wrote:
 
 Thank you for your help, Osvaldo and David.
 
 I tried using the command but did not get the RMS as expected.. Following are 
 the results:
 
 1.
 pymol -cqr fitting.py 1A6M.pdb 4OE9.txt
 PyMOLrun fitting.py,main
 HEADEROXYGEN TRANSPORT26-FEB-98   1A6M
 TITLE OXY-MYOGLOBIN, ATOMIC RESOLUTION
 COMPNDMOL_ID: 1;
 COMPND   2 MOLECULE: MYOGLOBIN;
 COMPND   3 CHAIN: A
  ObjectMolecule: Read secondary structure assignments.
  ObjectMolecule: Read crystal symmetry information.
  Symmetry: Found 2 symmetry operators.
  CmdLoad: 1A6M.pdb loaded as 1A6M.
 HEADERPROTEIN BINDING 12-JAN-14   4OE9
 TITLE THE CRYSTAL STRUCTURE OF THE N-TERMINAL DOMAIN OF COMMD9
 COMPNDMOL_ID: 1;
 COMPND   2 MOLECULE: COMM DOMAIN-CONTAINING PROTEIN 9;
 COMPND   3 CHAIN: A, B;
 COMPND   4 FRAGMENT: COMMD9, UNP RESIDUES  1-117;
 COMPND   5 ENGINEERED: YES;
 COMPND   6 MUTATION: YES
  ObjectMolecule: Read secondary structure assignments.
  ObjectMolecule: Read crystal symmetry information.
  Symmetry: Found 1 symmetry operators.
  CmdLoad: 4OE9.txt loaded as 4OE9.txt.
 
 2.
 pymol -cqr fitting.py --1A6M.pdb 4OE9.txt
 PyMOLrun fitting.py,main
 
 Do I need to import Pymol module in the shell script to use the pymol scripts 
 like you did in python? 
 Am I missing something? 
 
 ​Thanks​
 
 --
 ​Gazal​
 
 On Fri, Jul 10, 2015 at 11:36 PM, David Hall li...@cowsandmilk.net 
 mailto:li...@cowsandmilk.net wrote:
 http://www.pymolwiki.org/index.php/Command_Line_Options 
 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 gazal...@gmail.com 
 mailto:gazal...@gmail.com wrote:
 
 Hi,
 
 I'm trying to find the RMSD values for batch purposes. The command which I 
 found works for the Pymol-command line. 
 I was hoping if I could get an idea about using the python script fitting.py 
 in my shell script without triggering the Pymol GUI.
 
 Thanks in advance.
 
 Gazal 
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Re: [PyMOL] How to find RMSD values using fitting.py using Shell script

[David Hall]

http://www.pymolwiki.org/index.php/Command_Line_Options 
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 gazal...@gmail.com wrote:
 
 Hi,
 
 I'm trying to find the RMSD values for batch purposes. The command which I 
 found works for the Pymol-command line. 
 I was hoping if I could get an idea about using the python script fitting.py 
 in my shell script without triggering the Pymol GUI.
 
 Thanks in advance.
 
 Gazal 
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Re: [PyMOL] Problem with loadBfact.py on windows

[David Hall]

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 stephane.a...@cea.fr 
 wrote:
 
 No such file or directory: './loadB2Fact.py'

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

[David Hall]

 On Jul 6, 2015, at 10:44 AM, Albert mailmd2...@gmail.com 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 rotate a torsion angle of a molecule.

http://www.pymolwiki.org/index.php/Set_dihedral 
http://www.pymolwiki.org/index.php/Set_dihedral
http://stackoverflow.com/questions/19958043/change-dihedral-angles-using-the-mouse-in-pymol/25355318#25355318
 
http://stackoverflow.com/questions/19958043/change-dihedral-angles-using-the-mouse-in-pymol/25355318#25355318

 Meanwhile, I am just wondering is it possible for pymol give alternative 
 rotamer conformation of a protein residue?

http://pymolwiki.org/index.php/Mutagenesis 
http://pymolwiki.org/index.php/Mutagenesis (using without mutating gives you 
rotamers for a residue)
http://www.pymolwiki.org/index.php/Rotamer_Toggle 
http://www.pymolwiki.org/index.php/Rotamer_Toggle

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Re: [PyMOL] opensource for commercial use?

[David Hall]

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
hours of a lawyer's time to understand what you should do to comply with
the license.

-David


On Fri, Jul 3, 2015 at 10:39 AM, Albert mailmd2...@gmail.com wrote:

 Hello:

 I just got a question: can we use the open source version of pymol for
 commercial usage? Or can we develop some commercial tool based on Pymol?

 thank you very much.

 Albert


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

[David Hall]

preset.ball_and_stick('r. STI’)



 On Apr 23, 2015, at 12:52 PM, Brenton Horne brentonho...@ymail.com wrote:
 
 Hi, 
 
 I recently read this reply 
 (http://www.mail-archive.com/pymol-users@lists.sourceforge.net/msg13248.html 
 http://www.mail-archive.com/pymol-users@lists.sourceforge.net/msg13248.html)
  to another users' query on this list so I went to the PyMOL Wiki page 
 hyperlinked in the answer and found this piece of code:
 
 preset.ball_and_stick(selection='all', mode=1)
 set_bond stick_color, white, selection, selection
 set_bond stick_radius, 0.14, selection, selection
 set sphere_scale, 0.25, selection
 show sticks, selection
 show spheres, selection
 
 I want to customize it such that the selection that is changed in 
 representation from the cartoon style (which is the present style for the 
 macromolecule  I'd like it to stay the representation style for the 
 macromolecule) to ball-and-stick style, is just het ID STI (i.e., the 
 imatinib ligand) in 2HYY. Any ideas of how I might achieve this? 
 
 Thanks for your time,
 Brenton
 
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Re: [PyMOL] APBS plugin not working on both Ubuntu Windows 7

[David Hall]

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 ./configure appears to do, I suggest following the steps in
the INSTALL file.

-David


On Tue, Apr 14, 2015 at 2:39 AM, Brenton Horne brentonho...@ymail.com
wrote:

 Hi,

 pdb2pqr.py doesn't exist in the pdb2pqr tar.gz file (for either 2.0.0 or
 1.8 versions; in a previous question I was advised to use the 1.8
 version) and consequently APBS tools doesn't work. I have tried turning
 the pdb2pqr.py.in into pdb2pqr.py by removing the in extension, but
 the APBS failed to set up the grid after I did this. Is there any way
 around this?

 Thanks for your time,
 Brenton


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Re: [PyMOL] green rings

[David Hall]

you can set cartoon_ring_color ?




 On Mar 9, 2015, at 11:20 AM, Quentin Vicens qvic...@unistra.fr 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
 set cartoon_ladder_mode,4
 set cartoon_ring_mode,3
 set cartoon_ring_finder,2
 
 Thanks in advance for any help!
 Quentin
 
 Quentin Vicens
 Tél : +33 (0)3 88 41 70 42
 Tél 2 : +33 (0)7 61 37 83 10
 Fax : +33 (0)3 88 60 22 18
 qvic...@unistra.fr mailto:qvic...@unistra.fr
  http://www.unistra.fr/
 UPR9002-CNRS-University of Strasbourg
 Institut de Biologie Moléculaire et Cellulaire
 15 rue René Descartes
 F - 67084 Strasbourg 
 http://www-ibmc.u-strasbg.fr/arn/Eriani/equi_Eriani_fr.php 
 http://www-ibmc.u-strasbg.fr/arn/Eriani/equi_Eriani_fr.php
 
 spectrum.tiff
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Re: [PyMOL] Ball and stick model

[David Hall]

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 paluso...@gmail.com
wrote:

 Dear Pymol Users
 I would like to represent the protein what I have in ball and stick model.
 I have done it by executing the command lines as following

 hide all
 show spheres
 show sticks
 set sphere_scale, 0.3
 set stick_radius, 0.1

 My question is can I do it by any other method? Means from pymol
 interface..!!

 Surya
 Graduate student
 India.


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

[David Hall]

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, Jan 27, 2015 at 2:58 AM, Biao Ma jackyma1...@gmail.com wrote:

 Hi, pymol users.

 I want to change same residues to another one.

 I try to do it refer to following site, I changed TRY128 to PHE128,
 http://www.pymolwiki.org/index.php/Mutagenesis

 But when I save the modified molecular to PDB file, the sequence of
 residue is out of turn.

 Who can tell me how to fix this problem?

 Thank a lot.

 Jacky

 The following is a part of PDB.(the original pdb file is start from 124)

 ATOM  1  N   GLY A 124  -9.861  12.581   5.804  1.00  1.00
   N
 TER   2  GLY A 124
 ATOM  3  N   PHE A 128 -12.196  10.147   0.017  1.00  0.00
   N
 TER   4  PHE A 128
 ATOM  5  CA  GLY A 124 -10.625  12.191   4.609  1.00  1.00
   C
 TER   6  GLY A 124
 ATOM  7  CA  PHE A 128 -11.765   8.834   0.485  1.00  0.00
   C
 TER   8  PHE A 128
 ATOM  9  C   GLY A 124  -9.855  12.324   3.299  1.00  1.00
   C
 TER  10  GLY A 124

 [image: Inline image 1]


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

[David Hall]

 On Jan 23, 2015, at 7:32 PM, McCully, Dwayne (NIH/NIAMS) [C] 
 dmccu...@mail.nih.gov 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/Executive.cpp:13998: error: ‘glutLeaveFullScreen’ was not declared in 
 this scope


This was fixed in the svn commit following 1.7.4.0 (commit 4105)

http://sourceforge.net/p/pymol/code/4107/log/?path=/trunk 
http://sourceforge.net/p/pymol/code/4107/log/?path=/trunk

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Re: [PyMOL] MacPyMOL fink download

[David Hall]

(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 2:29 AM, Lau Sze Yi (SIgN) 
lau_sze...@immunol.a-star.edu.sg wrote:

 Hi,
 Since my edu copy failed after I upgrade to yosemite. I have downloaded
 pymol on my iMac 10.10.1 following the fink for 10.10 instructions on
 scottslab web:
 http://scottlab.ucsc.edu/~wgscott/xtal/wiki/index.php/Fink_for_10.10
 After setting up fink, I ran sudo apt-get install pymol-py27. I am still
 quite new to unix,  and have a few questions that I need clarified:

1. I did not uninstall my old copy of MacPyMOL. I assume there is no
interference between different versions?
2. Where exactly is the newly installed pymol stored?
3. I did not notice this before, but I have two copies of MacPyMOL
buried in one of the folders of my PHENIX versions 1.8.3-1479 and 1.9-1692
respectively. I wasn’t sure if the pymol was already present when I
downloaded my phenix or these are the ones I installed. I can open pymol
using command line but not double clicking the icons in my finder window.
Both these versions were shown to be last opened corresponding to the time
I  used command line pymol on two separate time. I am confused now as
to when I type pymol in my terminal, which MacPyMOL is supposed to be
opened.
4. I need to do source /sw/bin/init.sh before I can start pymol. Is
init.sh same as starting up fink to do its job? Is there a direct way to
open pymol.

 Appreciate your advice.

 Regards,
 Sze Yi




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Re: [PyMOL] sulfated tyrosine's losing connection

[David Hall]

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 use the CONECT records.

-David

 On Dec 23, 2014, at 12:20 AM, Jordan Willis jwillis0...@gmail.com wrote:
 
 Does anyone know why PyMoL renders the PDBs 3U2S and 3U4E without connecting 
 backbone atoms at residue 100G and 100H? Are the bond distances for these two 
 residue types not within the right parameters? SimpleViewer and JalView both 
 bridge this connection.
 
 Thanks,
 Jordan
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Re: [PyMOL] CGOs

[David Hall]

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 hans...@stolaf.edu 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 ? ? x1 y1 z1  x2 y2 z2
 
 
 
 
 On Sun, Dec 21, 2014 at 3:17 PM, Tsjerk Wassenaar tsje...@gmail.com 
 mailto:tsje...@gmail.com wrote:
 Hi Bob,
 
 Unfortunately, there is little documentation on CGO objects. You can have a 
 look in modules/cgo.py and in the example scripts in examples/devel/ in the 
 pymol directory to get some more information. If there is something specific 
 you want to do, please let us know.
 
 Cheers,
 
 Tsjerk
 
 
 On Sun, Dec 21, 2014 at 9:57 PM, Robert Hanson hans...@stolaf.edu 
 mailto:hans...@stolaf.edu wrote:
 I'm looking for something that is relatively comprehensive. There are far 
 more commands than VERTEX, CYLINDER, CONE, and SPHERE, I think. 
 
 
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Re: [PyMOL] DNA representation

[David Hall]

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 jl...@uowmail.edu.au wrote:
 
 Hi, 
 
 Does anyone know how to show DNA like this in pymol? 
 PastedGraphic-1.tiff
 
 Cheers, 
 
 Jacob
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Re: [PyMOL] select state not working

[David Hall]

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 2 and
having an rms of 0.927 and chain b having an rms of 1.143

intra_fit 2kgx and chain a

now, chain a has an rms of 0.923 and chain b has an rms of 1.155

intra_fit 2kgx and chain b

now, chain a has an rms of 0.952 and chain b has an rms of 1.130

Note, it can take a target state, that all other states are aligned to, etc.


On Wed, Nov 5, 2014 at 5:23 AM, Spencer Bliven sbli...@ucsd.edu wrote:

 Hey, I've been doing a lot of work with PDB assemblies, which are
 distributed as multi-state structures. I would like to be able to align
 them based on individual chains from individual states. However, I haven't
 been able to figure out any way to uniquely identify atoms by state.

 The select statement contains a `state` parameter, but as noted in this
 2010 thread
 https://www.mail-archive.com/pymol-users@lists.sourceforge.net/msg08224.html
 it doesn't seem to do anything. The thread also suggests using
 cmd.get_model(), but I'm not sure how to get a selection based on a
 chempy.models.Indexed instance.

 My current workaround is to split_states, use alter to make all the chains
 unique, then merge the structures again. This is incredibly tedious. Does
 anyone know a better way?

 It would be nice if (1) the select command were fixed, and/or (2) add a
 property selector for states.

 Cheers,
 Spencer


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Re: [PyMOL] CONECT table

[David Hall]

http://www.pymolwiki.org/index.php/Connect_mode

-David

 On Oct 6, 2014, at 6:35 PM, Markus Heller mhel...@cdrd.ca 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 their linkage to the protein.
 
 Thanks and Cheers
 Markus
 
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Re: [PyMOL] need help

[David Hall]

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 interface.

Alternatively, you can go to Plugin - PDB Loader Service , which will
allow you to specify a PDB file.

If you have a PDB formatted file on your hard drive, you can go to File -
Open and find the file on your hard drive. Alternatively, you can use the
load command ( http://www.pymolwiki.org/index.php/Load )

-David




On Tue, Sep 9, 2014 at 9:52 AM, Vic Pinas victorine1...@gmail.com wrote:

 Dear all,

 I need help.

 I just start using Pymol in Ubuntu, this was advised to me since windows
 give a lot of trouble.

 I install pymol already on ubuntu, but I need an manual how to transport
 the data from the pdb to ubuntu pymol.

 I can enter pdb nicely but after I dowload the files I cannot transport it
 into the pymol chart.

 Please can anyone help me?

 For the record I am a nearly digibite so please be very throughout in your
 explanation.


 Thank you in advance


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Re: [PyMOL] Pymol wrl output

[David Hall]

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 gratefulf...@gmail.comwrote:

 Hi Jared   everyone,

 First, thanks for all your help. I really appreciate it and am sorry to be
 such a noobie here...

 I am using the Pymol GUI (1.7).

 I've created a shared 
 folderhttps://drive.google.com/folderview?id=0B122hIUVdAXaWHN1X3dkS2VrQ1kusp=sharingwith
  all my files so you can test with them if you like.

 The important files are:

- TMD11.pdb : the source model
- *TMD11Ultracmyk.wrl.zip* : the output file from Pymol which fails to
3D print at Shapeways. *THIS IS THE FILE THAT I WANT TO PRINT!*
- TMD11UltracmykMesh.wrl.zip : the wrl output from MeshLab starting
from the wrl from Pymol, which does print at Shapeways.

 My process is:

1. File / Open TMD11.pdb
2. show surface
3. Display / Quality / Maximum Quality
4. Display / Color Space / CMYK (For Publications)
5. File / Save Image As / VRML 2
6. end

 I do not know what is wrong with this file since Shapeways does not
 provide any useful error message.

 If I save the model as a single color wrl file, it can print fine.

 Thanks again for any help!

 Ciao, Bob.





 On Sun, May 4, 2014 at 1:29 AM, Sampson, Jared jared.samp...@nyumc.orgwrote:

  Hi Bob - I've tried exporting several different types of models to .wrl
 in both RGB and CMYK color spaces, and haven't seen any colors output with
 negative values.  For example, this works fine for me:

  fab AAA, polyala
 python
 for rep in [lines, spheres, sticks, surface, cartoon]:
 cmd.show_as(rep)
 cmd.save(rgb_%s.wrl % rep)
 cmd.space(cmyk)
 cmd.save(cmyk_%s.wrl % rep)
 python end

   and it results in no instances of diffuseColor on the same line as a
 negative number in any of the output wrl files (as determined by: `grep
 -e diffuseColor.*- *.wrl` ).

  Could you be more specific with how you're generating the colors in
 your PyMOL session (perhaps with a minimal script that reproduces the
 problem), and/or post a bit of the output .wrl file, showing in particular
 anywhere you see a negative color value?

  Thanks,
 Jared

 --
 Jared Sampson
 Xiangpeng Kong Lab
 NYU School of Medicine
 kong.med.nyu.edu
   --
 *From:* Grateful Frog [gratefulf...@gmail.com]
 *Sent:* Saturday, May 03, 2014 1:53 PM
 *To:* Sampson, Jared
 *Cc:* Marcelo Marcet; pymol-users@lists.sourceforge.net

 *Subject:* Re: [PyMOL] Pymol wrl output

Hi,

  I tried it in white WRL as you suggested and that loaded into Shapeways
 ok.  Green would also load...

  The same file, then set to CMYK colors (menu DISPLAY / COLOR SPACE /
 CMYK )  would not load...

  Any help would be great!

 Thanks for all this!

 Ciao,
 Bob


 On Sat, May 3, 2014 at 6:44 PM, Sampson, Jared 
 jared.samp...@nyumc.orgwrote:

  Hi Bob -

  The reason you're getting these errors is because having negative
 values in a color tuple is not meaningful (you can't have a negative amount
 of color), and results in undefined behavior.  RGB colors use a number in
 the range 0.0-1.0 (inclusive) for each value in the tuple.  What color are
 you using for your model before exporting VRML?  Try setting everything to
 white (`color white` on the command line) and see what that does.

  Cheers,
 Jared

 --
 Jared Sampson
 Xiangpeng Kong Lab
 NYU School of Medicine
 kong.med.nyu.edu
   --
 *From:* Grateful Frog [gratefulf...@gmail.com]
 *Sent:* Friday, May 02, 2014 7:07 PM
 *To:* Marcelo Marcet
 *Cc:* pymol-users@lists.sourceforge.net
 *Subject:* Re: [PyMOL] Pymol wrl output

these are the errors that Shapeways sent back:
 
 Unfortunately, the model you recently uploaded TMD11Ultra.wrl did not
 pass our initial printability checks, so it's not yet ready for 3D
 printing. Printability Error:

- Model failed during repair. This is likely due to problems merging
shells.

 Please visit your 3D model page to update your file:
 http://www.shapeways.com/model/upload-and-buy/1932482http://www.shapeways.com/model/upload-and-buy/1932482?etId=14290783utm_source=automated-contactutm_medium=emailutm_campaign=model-processing-failed

 Our tutorials and 
 FAQhttp://www.shapeways.com/support?etId=14290783utm_source=automated-contactutm_medium=emailutm_campaign=model-processing-failedcan
  be super helpful for more detailed information, or you can always ask
 the community a specific question on our 
 forumhttp://www.shapeways.com/forum?etId=14290783utm_source=automated-contactutm_medium=emailutm_campaign=model-processing-failed

 If you're stuck or have any questions, don't hesitate to reach out at
 serv...@shapeways.com. Please include the file as an attachment to the
 email, as well as any notes on your design, so we can help you solve your
 problem as quickly as possible.

 Additional non-critical 

Re: [PyMOL] Color starting midway between adjacent chains

[David Hall]

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 u5205...@anu.edu.au wrote:

  Hi everyone,

  I have just started learning Pymol and PyMol seems to use a different
 colour convention than Molmol, i.e. the colour of a side chain starts half
 way between the CA and CB atoms (instead of starting at the CA). Do you
 know whether there would there be a way to start the side chain colour at
 the CA without changing the colour of the backbone?

  Any help will be greatly appreciated!

  Thank you.

  I-Ji


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

[David Hall]

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 code will skip the
entries in the windows registry that are causing issues.

-David



On Mon, Jan 20, 2014 at 8:40 AM, Lapolla, Suzanne M (HSC) 
suzanne-lapo...@ouhsc.edu wrote:

 I am posting this again as I have still not figured out why I am unable to
 fetch or use the pdb plugin loader with pymol 1.7 I have cut/copied/pasted
 the error msg I get below. I have tried uninstalling and reinstalling
 python 2.7.6 as well as python 1.7 (I have windows 64 bit --so I tried the
 64 bit version 1st, and when that did not work I unindtalled adn then
 re-installed using the windows 32 bit version. (I prev had pymol 1.3 but
 uninstalled that as well).  This forum has been a great source of help for
 my before so hope yoiu guys can help again! Thank you.

 PyMOLfetch 4bd2
  please wait ...
 Exception in thread Thread-4:
 Traceback (most recent call last):
   File C:\Python27\lib\threading.py, line 810, in __bootstrap_inner
 self.run()
   File C:\Python27\lib\threading.py, line 763, in run
 self.__target(*self.__args, **self.__kwargs)
   File C:\Python27\lib\site-packages\pymol\commanding.py, line 561, in
 wrapper
 func(*args, **kwargs)
   File C:\Python27\lib\site-packages\pymol\importing.py, line 1348, in
 _multifetch
 discrete, multiplex, zoom, type, path, file, quiet, _self)
   File C:\Python27\lib\site-packages\pymol\importing.py, line 1292, in
 _fetch
 contents = internal.file_read(url)
   File C:\Python27\lib\site-packages\pymol\internal.py, line 308, in
 file_read
 handle = urllib.urlopen(finfo)
   File C:\Python27\lib\urllib2.py, line 127, in urlopen
 return _opener.open(url, data, timeout)
   File C:\Python27\lib\urllib2.py, line 404, in open
 response = self._open(req, data)
   File C:\Python27\lib\urllib2.py, line 422, in _open
 '_open', req)
   File C:\Python27\lib\urllib2.py, line 382, in _call_chain
 result = func(*args)
   File C:\Python27\lib\urllib2.py, line 1403, in ftp_open
 mtype = mimetypes.guess_type(req.get_full_url())[0]
   File C:\Python27\lib\mimetypes.py, line 297, in guess_type
 init()
   File C:\Python27\lib\mimetypes.py, line 358, in init
 db.read_windows_registry()
   File C:\Python27\lib\mimetypes.py, line 258, in read_windows_registry
 for subkeyname in enum_types(hkcr):
   File C:\Python27\lib\mimetypes.py, line 249, in enum_types
 ctype = ctype.encode(default_encoding) # omit in 3.x!
 UnicodeDecodeError: 'ascii' codec can't decode byte 0xd7 in position 2:
 ordinal not in range(128)


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Re: [PyMOL] using pymol commands in a script

[David Hall]

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 has an error in that chain is the first argument in your tuple,
but should be the last argument based on the string format you are
substituting into.
(4) line 10 above cmd.distance(d,sele and n. CA, sele and n. CA)
 you need to have the second and third arguments as part of one string.
These should be two separate arguments in python:
 cmd.distance(d,sele and n. CA, sele and n. CA)
(5) cmd.color(sele, red)
 (a) you switched the order of the arguments for some reason from what
you showed in your pymol commands
 (b) red needs to be in quotation marks
(6) cmd.save(%s_%s.pse)%(pdbid,chain) ; you need to have .pse inside the
quotation marks, it is part of the string. Also, your parentheses matching
places the string substitution tuple outside the arguments of the function.
(7) cmd.png(%s_%s)%(pdbid,chain) again, the string substitution tuple is
outside the function
 as an example, you want cmd.png( %s_%s%(pdbid,chain) )
 so you produce your string inside the parentheses corresponding to the
command.
(8) cmd.delete(pdbid.split(',')[0]) ; you probably want to split on the
period, not a comma.

The line numbers in the error messages don't match the python you have
pasted. It seems the python you pasted is not what actually produced the
error message given.

Your off to a good start. Generally, you should look at the last few lines
of the error message, this will tell you what line number your error is on
and give you a clue what is happening. You can then start reading backwards
through the message to see if it gives more information. Since line numbers
are so important, you should use something to write your script that has
line numbers. There are many text editors that do so. One with syntax
highlighting for python would also be useful as it will make many of the
issues much more apparent.

-David






On Wed, Sep 4, 2013 at 3:30 AM, Anasuya Dighe anas...@mbu.iisc.ernet.inwrote:

 Hi everyone,

 How to write PyMol commands in Python script, save a session and then save
 a
 .png file of the same ?
 I have an input file which has the protein information i.e name, chain,
 and a
 list of residues.
 I want to plot the C-alpha atoms of these residues for each protein 
 calculate
 distances between this set of atoms, save these operations in a .pse file
 and
 also a .png file of the same.
 Below, I am writing all the commands which I use in PyMol.

 However,  I am having trouble automating this procedure for a large number
 of
 proteins.

 ***Input file [testpy.txt](Fields: PDB ID, chain, residue1, residue2,
 residue3***
 2YYI.pdb A 13 28 30
 2YYG.pdb A 45 42 67
 .
 .
 .
 .

 ***PyMol Commands***
 1) load 2YYI.pdb
 2) hide everything
 3) show cartoon
 4) set cartoon_transparency, 0.8
 5) set dash_gap, 0
 6) set sphere_scale, 0.45
 7) set sphere_mode, 4
 8) bg_color white
 9) select resi 13+28+30 and chain A and n. CA
 10) distance d, sele and n. CA , sele and n. CA
 11) hide labels, d*
 12) show spheres, sele
 13) color red, sele
 14) save session_2YYI.pse
 15) ray 1000,1000
 16) png ~/Desktop/temp/2YYI_A.png

 In the above set of commands, I am opening each PDB file as mentioned in
 the 1st
 column of the input file, selecting chain as in the 2nd column, and
 selecting
 residues as mentioned in the next 3 columns.
 Also when i save the sessions and the png file, I am taking them from the
 input
 file.
 How can i automate this procedure such that I have a total of 2 png files
 and 2
 sessions for each of the pdb that I am listing in the input file. I have
 tried
 doing this but, cant get ahead due to errors.
 I am not much of a coder in Python. PLease help.
 This is how far i have got.

 *
 from pymol import cmd

 def process_line(x):
  pdbid,res1,res2,res3 = x.split()
  cmd.load(pdbid)
  cmd.bg_color(white)
  cmd.hide(everything)
  cmd.show(cartoon)
  cmd.select((resi %s + resi %s + resi %s and chain %s name
 CA)%(chain,res1,res2,res3))
  cmd.distance(d,sele and n. CA, sele and n. CA)
  cmd.hide(labels,d*)
  cmd.color(sele, red)
  cmd.show(spheres,sele)
  cmd.ray(1000,1000)
  cmd.save(%s_%s.pse)%(pdbid,chain)
  cmd.png(%s_%s)%(pdbid,chain)
  cmd.delete(pdbid.split(',')[0])

 def process_all(filename):
  for line in open(filename):
process_line(line)

 process_all(testpy.txt)

 *
 What is going wrong? how can this be automated for all the pdbid's listed
 in
 input file ?

 errors I get:
 File /usr/lib/pymodules/python2.6/pymol/parser.py, line 338, in parse
 parsing.run_file(path,self.pymol_names,self.pymol_names)
   File /usr/lib/pymodules/python2.6/pymol/parsing.py, line 455, in
 run_file
 execfile(file,global_ns,local_ns)
   File anu.py, line 19, in module
 

Re: [PyMOL] How to move/turn CGO

[David Hall]

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 croov...@gmail.com wrote:

 Thank you Thomas, translate and rotate works great, but I'm not sure what 
 set_object_ttt function does. 
 
 I'm also looking for a function that can set absolute coordinates of my cgo 
 cone, not relative to current position like translate/rotate. Is there such a 
 function?
 
 
 2013/8/12 Thomas Holder thomas.hol...@schrodinger.com
 Hi Pawel,
 
  Currently I'm working on some plugin for PyMOL and I need your help.
  I need to draw an object (CGO) and create some function that will move
  this object or simply change its coordinates.
  I've done my job with the first part, that is drawing a sphere on a
  screen using
  cmd.load_cgo(data, 'name')
  function, but how can I change its coordinates?
 
 You can use translate and rotate with the object argument.
 
 PyMOL translate [10,0,0], object=yourcgo
 PyMOL rotate x, 20, object=yourcgo
 
 You can also use cmd.set_object_ttt, see the third example here:
 http://pymolwiki.org/index.php/Axes
 
  My second question is about the meaning of a parameters for CONE CGO, in
  some examples (http://www.pymolwiki.org/index.php/Axes) CONE gets about
  16 params, but I didn't found any description of those.
 
 There is no proper documentation for those. Did you have a look at
 pymol/examples/devel/cgo_axes.py, which has comments for all the CONE
 parameters?
 
 https://sourceforge.net/p/pymol/code/4038/tree/trunk/pymol/examples/devel/cgo_axes.py
 
 Cheers,
   Thomas
 
 --
 Thomas Holder
 PyMOL Developer
 Schrödinger Contractor
 
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Re: [PyMOL] Leap motion control

[David Hall]

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 with a Leap Motion control 
 https://www.leapmotion.com.
 
 I see it supports molecules.
 
 H. Adam Steinberg
 7904 Bowman Rd
 Lodi, WI 53555
 608/592-2366
 
 
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Re: [PyMOL] PyMOL 1.6 pre-release announcement

[David Hall]

I still have this problem:
session saved in 1.6 with a black background; opens in 1.5 (and earlier)
with a red background

Many of my collaborators use old versions of pymol, frequently installed
onto their machines when they were bought X years ago, and this essentially
makes it so I cannot use pymol 1.6 as I cannot share sessions with them (at
least not without getting weird e-mails asking why I have a sudden affinity
for the color red).

-David




On Tue, Jun 18, 2013 at 7:37 AM, Thomas Holder 
thomas.hol...@schrodinger.com wrote:

 This is fixed in SVN rev 4032.

 Cheers,
   Thomas

 Thomas Holder wrote, On 06/15/13 10:45:
  Hi Rob,
 
  this has not been fixed yet, I'm really sorry. We'll look into this
  ASAP. It only affects the open-source code, apparently we missed
  something when syncing with the incentive codebase.
 
  Cheers,
Thomas
 
  On Jun 14, 2013, at 9:23 PM, Robert Campbell robert.campb...@queensu.ca
 wrote:
  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
  wrote:
 
  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 mismatch (color) 664
  (b) background color disparity:
  saved in 1.5 with black background; opens in 1.6 with a white
 background
  saved in 1.6 with a blackground; opens in 1.5 (and earlier) with a red
  background
 
  These are run on openSUSE 12.3 with SVN rev 4028 . On a side note,
  others who would like to beta test can use devel:languages:python repo
  in openSUSE:
 
 https://build.opensuse.org/package/show?package=pymolproject=devel%3Alanguages%3Apython
 
  -David

 --
 Thomas Holder
 PyMOL Developer
 Schrödinger Contractor


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Re: [PyMOL] Pymol error

[David Hall]

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 rhitan...@gmail.com wrote:

 Dear Thomas,

 One more question. When I tried to install pymol using port [ sudo port
 install pymol ] I get the following error message:

 Error: org.macports.archivefetch for port pymol returned: tcl must be
 installed without +corefoundation.

 Do you have any idea why there is this error message?

 Eventually I downloaded the tar.gz and installed it using the setup.py
 inside. Which is apparently not compatible with the Pmw2 and therefore gave
 the error I mentioned in my previous email. Any help would be appreciated

 Thanks
 Rhitankar





 On Mon, May 6, 2013 at 8:20 PM, Rhitankar Pal rhitan...@gmail.com wrote:

 Dear Thomas,

 Now I have installed Pmw.1.3 which should be the one compatible with
 python2.7 I guess. However I am still getting the same error. I think pymol
 is trying to use Pmw2 by default. Is there any way we can ask it to use 1.3
 instead?

 Thanks for your help

 Rhitankar



 On Sat, May 4, 2013 at 6:21 AM, Thomas Holder 
 thomas.hol...@schrodinger.com wrote:

 Hi Rhitankar,

 looks like you installed the python3 version of Pmw which is not
 compatible with python 2.7.

 Cheers,
   Thomas

 Rhitankar Pal wrote, On 05/03/13 21:16:
  Dear Pymol developers,
 
  I have recently installed pymol 1.6.x in MAC OS X 10.8.2 and have the
  following error while opening the GUI
 
  Traceback (most recent call last):
File /Library/Python/2.7/site-packages/pmg_tk/__init__.py, line 35,
  in run
  PMGApp(pymol_instance,skin).run(poll)
File /Library/Python/2.7/site-packages/pmg_tk/PMGApp.py, line 325,
  in __init__
  self.runSkin()
File /Library/Python/2.7/site-packages/pmg_tk/PMGApp.py, line 251,
  in runSkin
  self.skin.setup()
File
  /Library/Python/2.7/site-packages/pmg_tk/skins/normal/__init__.py,
  line 3661, in setup
  self.createInterface()
File
  /Library/Python/2.7/site-packages/pmg_tk/skins/normal/__init__.py,
  line 3634, in createInterface
  self.balloon = Pmw.Balloon(self.root)
File
  /Library/Python/2.7/site-packages/Pmw/Pmw_2_0_0/lib/PmwBalloon.py,
  line 28, in __init__
  Pmw.MegaToplevel.__init__(self, parent)
File
 /Library/Python/2.7/site-packages/Pmw/Pmw_2_0_0/lib/PmwBase.py,
  line 982, in __init__
  super().__init__(parent, tkinter.Toplevel)
  TypeError: super() takes at least 1 argument (0 given)
 
  As a result it never opens the The Pymol Molecular Graphics System
  window. Can anyone help to find out what might be wrong.
 
  Thanks
  Rhitankar
 
  --
  Rhitankar Pal
  Postdoctoral Researcher,
  Dept of Chemistry, Yale University
  New Haven, CT 06511

 --
 Thomas Holder
 PyMOL Developer
 Schrödinger Contractor


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 --
 Rhitankar Pal
 Postdoctoral Researcher,
 Dept of Chemistry, Yale University
 New Haven, CT 06511




 --
 Rhitankar Pal
 Postdoctoral Researcher,
 Dept of Chemistry, Yale University
 New Haven, CT 06511


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Re: [PyMOL] Pymol error

[David Hall]

sudo port install tk -quartz

It has nothing to do with what OS X ships with, it has to do with current
macports defaults, which changed around 18 months ago. You can dig around
the macports bug reports to see discussion of the change.

-David


On Tue, May 7, 2013 at 1:32 PM, Rhitankar Pal rhitan...@gmail.com wrote:

 Hi David,

 I installed tcl without the corefoundation and now while trying to install
 pymol I am getting the following error message:

 Error: org.macports.archivefetch for port pymol returned: tk must be
 installed without +quartz.

 How can I install tk 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 li...@cowsandmilk.net wrote:

 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 rhitan...@gmail.comwrote:

  Dear Thomas,

 One more question. When I tried to install pymol using port [ sudo port
 install pymol ] I get the following error message:

 Error: org.macports.archivefetch for port pymol returned: tcl must be
 installed without +corefoundation.

 Do you have any idea why there is this error message?

 Eventually I downloaded the tar.gz and installed it using the setup.py
 inside. Which is apparently not compatible with the Pmw2 and therefore gave
 the error I mentioned in my previous email. Any help would be appreciated

 Thanks
 Rhitankar





 On Mon, May 6, 2013 at 8:20 PM, Rhitankar Pal rhitan...@gmail.comwrote:

 Dear Thomas,

 Now I have installed Pmw.1.3 which should be the one compatible with
 python2.7 I guess. However I am still getting the same error. I think pymol
 is trying to use Pmw2 by default. Is there any way we can ask it to use 1.3
 instead?

 Thanks for your help

 Rhitankar



 On Sat, May 4, 2013 at 6:21 AM, Thomas Holder 
 thomas.hol...@schrodinger.com wrote:

 Hi Rhitankar,

 looks like you installed the python3 version of Pmw which is not
 compatible with python 2.7.

 Cheers,
   Thomas

 Rhitankar Pal wrote, On 05/03/13 21:16:
  Dear Pymol developers,
 
  I have recently installed pymol 1.6.x in MAC OS X 10.8.2 and have the
  following error while opening the GUI
 
  Traceback (most recent call last):
File /Library/Python/2.7/site-packages/pmg_tk/__init__.py, line
 35,
  in run
  PMGApp(pymol_instance,skin).run(poll)
File /Library/Python/2.7/site-packages/pmg_tk/PMGApp.py, line
 325,
  in __init__
  self.runSkin()
File /Library/Python/2.7/site-packages/pmg_tk/PMGApp.py, line
 251,
  in runSkin
  self.skin.setup()
File
  /Library/Python/2.7/site-packages/pmg_tk/skins/normal/__init__.py,
  line 3661, in setup
  self.createInterface()
File
  /Library/Python/2.7/site-packages/pmg_tk/skins/normal/__init__.py,
  line 3634, in createInterface
  self.balloon = Pmw.Balloon(self.root)
File
  /Library/Python/2.7/site-packages/Pmw/Pmw_2_0_0/lib/PmwBalloon.py,
  line 28, in __init__
  Pmw.MegaToplevel.__init__(self, parent)
File
 /Library/Python/2.7/site-packages/Pmw/Pmw_2_0_0/lib/PmwBase.py,
  line 982, in __init__
  super().__init__(parent, tkinter.Toplevel)
  TypeError: super() takes at least 1 argument (0 given)
 
  As a result it never opens the The Pymol Molecular Graphics System
  window. Can anyone help to find out what might be wrong.
 
  Thanks
  Rhitankar
 
  --
  Rhitankar Pal
  Postdoctoral Researcher,
  Dept of Chemistry, Yale University
  New Haven, CT 06511

 --
 Thomas Holder
 PyMOL Developer
 Schrödinger Contractor


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 --
 Rhitankar Pal
 Postdoctoral Researcher,
 Dept of Chemistry, Yale University
 New Haven, CT 06511




 --
 Rhitankar Pal
 Postdoctoral Researcher,
 Dept of Chemistry, Yale University
 New Haven, CT 06511


 --
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 their applications. This 200-page book is written by three acclaimed
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Re: [PyMOL] Pymol error in Mac OS X 10.8.2

[David Hall]

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 it doesn't show the 'Molecular Graphics System' window but shows
 only the 'Pymol Viewer' window. In the terminal I have the following error
 message:
 
 Detected OpenGL version 2.0 or greater. Shaders available.
 Detected GLSL version 1.20.
 OpenGL graphics engine:
 GL_VENDOR: NVIDIA Corporation
 GL_RENDERER: NVIDIA GeForce GT 640M OpenGL Engine
 GL_VERSION: 2.1 NVIDIA-8.10.44 304.10.65f03
 Traceback (most recent call last):
 File /Library/Python/2.7/site-packages/pymol/__init__.py, line 450, in
 launch_gui
 __import__(self.invocation.options.gui)
 File /Library/Python/2.7/site-packages/pmg_tk/__init__.py, line 22, in
 module
 from PMGApp import *
 File /Library/Python/2.7/site-packages/pmg_tk/PMGApp.py, line 33, in
 module
 class PMGApp(Pmw.MegaWidget):
 File /Library/Python/2.7/site-packages/Pmw/Pmw_2_0_0/lib/PmwLoader.py,
 
 - Ignored:
 line 131, in __getattr__
 self._initialise()
 File /Library/Python/2.7/site-packages/Pmw/Pmw_2_0_0/lib/PmwLoader.py,
 line 89, in _initialise
 raise ImportError(msg)
 ImportError: No module named tkinter
 Detected 4 CPU cores. Enabled multithreaded rendering.
 
 Any help to resolve this issue would be greatly appreciated. Thanks
 
 Rhitankar
 
 -- 
 Rhitankar Pal
 Postdoctoral Researcher,
 Dept of Chemistry, Yale University
 New Haven, CT 06511 
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Re: [PyMOL] iPad pymol questions

[David Hall]

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 upper right corner, since the dropbox app has cached
them locally, PyMol just reads the file and doesn't need the internet

-David

On Wed, Nov 28, 2012 at 11:48 AM, Steve Williams wil...@appstate.edu wrote:
 I am a new subscriber to the pymol listserv.  I did look around a bit on the 
 listserv site, but did not find a way to search previous postings and 
 responses, so did not find if there is a known answer to my question.
 Minor question: is there a way to search the pymol message archive, and if 
 so, how to do it?
 Major question: I have been playing with the iPad version of pymol from 
 Schrodinger.  I know how to search pbd for structures,and how to view 
 structures I have already found and saved to my pymol app folder on Dropbox.  
 But I need to show some structures to an audience where I may not have wifi 
 access for my iPad, and I would like to have the pymol iPad app locally save 
 structure files so I can use them when I am off line.  Is there a way to do 
 this with the iPad?

 Thanks,
 Steve Williams

 Sent from my iPad
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Re: [PyMOL] Custom menus and shortcuts?

[David Hall]

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 call both
 
 * pml scripts, as well as
 * full python pymol scrpts
 
 Shortcuts
 =
 
 Similarly -- is there a way I can bind exectution of given
 
 * pml script, or
 * full python pymol script
 
 to a given key?
 
 The problem
 ===
 
 The basic problem
 -
 
 The basic problem is to automate tasks one repeats frequenlty. For example I 
 had to type::
 
   select notW, not (resn W)
   hide all
   show spheres, notW
 
 frequently.
 
 
 The problem which leads to the need of menu
 ---
 
 So I make a pml or full-python pymol script and load it.
 
 But then I have to remember the name of the script. Which is terrible -- 
 because I have custom scripts in each and every program that I use.
 
 
 The problem which leads to the need of custom shortcuts
 ---
 
 Having custom menu us great as a reminder of what scripts have You written. 
 But it's terrible to click through the menus. One is much better with 
 shorcuts (hotkeys). 
 
 
 
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Re: [PyMOL] I just built pymol, comes up but hangs on any attempt to view a test pdb.

[David Hall]

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, Mike Marchywka marchy...@hotmail.com wrote:

 
 
 
 fwiw, I never figured out why the out-of-the-box build hung  using the python 
 approach
 but I went through the ./cogifure, make make install route
 and did get the test molecules to display. However, I ran into lots of 
 problems with the ShaderMgr and
 ccealignmodule and then finally the link was missing -lGLEW.
 
 In any case it looks like I am all set but I thought the download would come 
 closer to working right
 away.
 
 And the xyz files I wanted to display do appear to come up just great.
 
 So do I need a license for the open source version?
 Thanks.
 
 
 
 note new address
 Mike Marchywka 2295 Collinworth Drive Marietta GA 30062.
 formerly 487 Salem Woods Drive Marietta GA 30067 404-788-1216 (C)- leave 
 message 989-348-4796 (P)- emergency
 
 
 
 
 From: marchy...@hotmail.com
 To: pymol-users@lists.sourceforge.net
 Date: Thu, 4 Oct 2012 15:43:53 -0400
 Subject: [PyMOL] I just built pymol, comes up but hangs on any attempt to 
 view a test pdb.
 
 
 
 
 Is there some common reason for this?
 CPU on one core stays at 100 percent and no more menu's come up.
 
 The larger window says at the bottom that the version is supposed to be 
 licensed
 but I just pulled it down from sourceforge and not sure that this version 
 needs a key
 to work.
 
 Thanks.
 
 
 note new address
 Mike Marchywka 2295 Collinworth Drive Marietta GA 30062.
 formerly 487 Salem Woods Drive Marietta GA 30067 404-788-1216 (C)- leave 
 message 989-348-4796 (P)- emergency
 
 
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[PyMOL] Pymol Rotated Screen

[David Hall]

With my macports pymol, I have a problem exhibited in the video below:
http://youtu.be/9u2GF6f9sTY

I have a monitor rotated 90 degrees. When I launch pymol on it, the
screen visually rotates back to the non-rotated state. If I launch on
my main monitor and drag the program onto the 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

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

[David Hall]

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 Emtekær Linnet wrote:

 Dear PyMolers.
   
 Reading crystallographic papers, and feeling the
 need for seing a papers annotation and explanation of important residues,
 I often have pymol at my hand.
   
 fetching the protein, and typing in commands to see the mentioned residues.
 That is time-consuming, but okay.
   
 Inspired by John Amraph's need for a preset.lig​and_cartoo​n, when loadning
 a paper, I would wish there were a: preset.as_article or a fetch 1SVN, 
 as_article.
   
 Simply a pymol script file that fetch the protein, shows it as cartoon, and 
 selecting/labelling/showing the
 mentioned important residues in the article. Or the catalytic triad, the 
 substrate channels... etc.
 You get the point. :-)
   
 So, does anyone know there already exist such a databank/annotation server?
 If it exist, could one make a script that can fetch and convert these 
 annotations to a pymol script?
 Or if doesnt exist, would it be a interesting project to pursue?
   
 Best
 Troels Emtekær Linnet
 PhD student
 SBiNLab, Copenhagen University
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Re: [PyMOL] GUI to improve interaction between user and PyMOL

[David Hall]

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 first point I should make though is that, as far as I know, you
*cannot* modify the existing PyMol windows, that is, you can't add an
item to the menu you get when you right click on a protein or make it
so there are additional per object menus on the right side of the
screen for your application.

Generally, for PyMol, your plugin interface is written using Tkinter,
which is widely documented across the internet (
http://wiki.python.org/moin/TkInter ).

http://www.pymolwiki.org/index.php/Plugins_Tutorial provides a simple
example of a plugin with a graphical interface. The __init__ adds your
plugin to the menu bar in PyMol and tells PyMol what to execute when
you click on the button. From there, it is just Tkinter with python
and pymol scripting.

The only pymol plugin I currently use with a graphical interface is
the Autodock plugin:
https://raw.github.com/Pymol-Scripts/Pymol-script-repo/master/plugins/autodock_plugin.py
It's a pretty complex piece of code, but it is a nice plugin that
seems highly reliable, so understanding looking at how it does things
can probably help you solve any issues you have along the way. There
are other plugins that you can find by browsing the pymolwiki that
also use graphical elements and may also be helpful.

-David




On Thu, Mar 22, 2012 at 4:39 PM, Suhaila Haji Mohd Hussin
bell_beaut...@hotmail.com wrote:
 Hello everyone.

 Is there any useful online reference that can be shared for me to learn how
 to add GUI executed by Python script?

 I know PyMOL can visualize the protein just by typing in on PyMOL command
 but my supervisor will  grade my group project higher if we can make it more
 interactive where the user can just use a mouse to click button or something
 and less typing on command.

 Best regards,
 Suhaila

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Re: [PyMOL] Editing of the pdb structure

[David Hall]

On Tue, Mar 20, 2012 at 8:44 AM, Tsjerk Wassenaar tsje...@gmail.com 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 answer given (with TER statements) is not wrong, but from a
 chemical and biological point of view, and in light of the PDB format,
 is actually more correct.

The PDB format says:
The TER records occur in the coordinate section of the entry, and
indicate the last residue presented for each polypeptide and/or
nucleic acid chain for which there are determined coordinates. For
proteins, the residue defined on the TER record is the
carboxy-terminal residue; for nucleic acids it is the 3'-terminal
residue.
( http://www.wwpdb.org/documentation/format33/sect9.html#TER )

Chain breaks in crystal structures are generally not the
carboxy-terminal residues.

-David

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Re: [PyMOL] Little coordinate cross in Pymol?

[David Hall]

http://pymolwiki.org/index.php/Axes

-David

On Feb 27, 2012, at 5:38 AM, Gudrun Lotze gudrun.lo...@gmx.net 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 just want to show clearly which plane is shown when presenting the model in 
 my document.
 
 Thank you for your help.
 Kind regards
 Gudrun Lotze
 
 
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Re: [PyMOL] Open Source PyMOL v1.5.0.1

[David Hall]

On Mon, Feb 13, 2012 at 2:27 PM, Jason Vertrees
jason.vertr...@schrodinger.com 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 created. All of this is accessible form the
 PyMOL project page on SourceForge
 (http://sourceforge.net/projects/pymol/).

For those of you on openSUSE, I've updated the pymol packages in the
openSUSE Build Service to this release. You can test this new version
by visiting 
http://software.opensuse.org/download.html?project=devel:languages:pythonpackage=pymol
and choosing the appropriate openSUSE release and architecture.

-David

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Re: [PyMOL] Using super correctly

[David Hall]

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
super, the default value was 0.

-David

On Fri, Jan 13, 2012 at 7:44 AM, QT rdirect...@gmail.com wrote:
 Dear all,

 I'm having a tough time using the super command correctly.  I want to
 superimpose two 5S structures.

 In pymol, I'll do the following

 load 2awb.pdb
 load 3cc2.pdb

 create ec-5s, 2awb and chain a
 create hm-5s, 3cc2 and chain 9

 If I issue super ec-5s, hm-5s then the cryptic error ExecutiveAlign:
 invalid selections for alignment. would appear.

 Issuing super /ec-5s//a, /hm-5s//9 does not help either.

 What am I missing?  align /ec-5s//a, /hm-5s//9 works just fine though...

 Any help from the community would be very appreciated.

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

[David Hall]

On Fri, Jan 13, 2012 at 4:34 AM, tusi t...@enzim.hu 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 script, the png file does not arise:

 from pymol import cmd
 cmd.do('load tmp.pdb, tmp')
 cmd.do('png tmp.png')

 No any error is reported on pymol console.

Can you try doing

from pymol import cmd
cmd.load('tmp.pdb', 'tmp')
cmd.png('tmp.png')


-David

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Re: [PyMOL] Using super correctly

[David Hall]

I decided to dig in and answer my own question about what the seq argument does.

seq:
positive means use sequence and structure
0 means use only structure
negative means only use sequence

For super, I assume you only want to use structure, so messing with
that argument is silly advice.

The problem is that when you use structure, SelectorGetResidueVLA gets
an argument of true for ca_only

Obviously, nucleic acids don't have any c-alphas, so when
SelectorGetResidueVLA searches for residues using strcmp(ai1-name,
CA) == 0 , pymol finds no residues in the selections, then 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 li...@cowsandmilk.net wrote:
 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
 super, the default value was 0.

 -David

 On Fri, Jan 13, 2012 at 7:44 AM, QT rdirect...@gmail.com wrote:
 Dear all,

 I'm having a tough time using the super command correctly.  I want to
 superimpose two 5S structures.

 In pymol, I'll do the following

 load 2awb.pdb
 load 3cc2.pdb

 create ec-5s, 2awb and chain a
 create hm-5s, 3cc2 and chain 9

 If I issue super ec-5s, hm-5s then the cryptic error ExecutiveAlign:
 invalid selections for alignment. would appear.

 Issuing super /ec-5s//a, /hm-5s//9 does not help either.

 What am I missing?  align /ec-5s//a, /hm-5s//9 works just fine though...

 Any help from the community would be very appreciated.

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

[David Hall]

the builds on 
https://build.opensuse.org/package/show?package=pymolproject=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 marius.s.rete...@gmail.com wrote:

 Could you please specified what exactly did the gcc 4.5 broke in Pymol?
 Maybe this is not the case for every linux distribution.

 Cheers,
 Marius

 2011/12/2 Troels Emtekær Linnet tlin...@gmail.com:
 Try Following this script.

 http://www.pymolwiki.org/index.php/Linux_Install#Ubuntu.2FMint_Compile_and_install_with_MPEG_support

 Please report if you are successful.
 It would be interesting to see how it works on CentOS

 /T



 2011/12/2 grantaka36 grantak...@gmail.com

 Referring the following, I'm trying to install PyMOL 1.4.1 with
 attached 'compile_pymol.sh', but no success. Would you please help to
 finish installation, or give me some advices? If information
 inadequate, please contact me.

 http://www.pymolwiki.org/index.php/Linux_Install
 - Requirements
 - Get latest Source from SVN
 - Compile and install
 - Problems - gcc-4.5 is broken for pymol install, use gcc-4.4
 -- My distribution has gcc4.5, so installed /usr/bin/gcc44,
 /usr/bin/g++44.

 Attached 'install_error.txt' gathers some information:
 - Original module files are in $HOME/install_module/pymol-archive
 - Intends to install in $HOME/pymol-svn
 - Original log has some Japanese messages so I added /* means ... */

 Regards,
 Masataka


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Re: [PyMOL] Show Sticks - Turns Molecule Blue

[David Hall]

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:pythonpackage=pymol

-David

2011/9/11 Troels Emtekær Linnet tlin...@gmail.com:
 This should get you on the way on compiling from svn.

 http://www.pymolwiki.org/index.php/Linux_Install#Mint11_Linux_.28Ubuntu.29_-_Tested_for_PyMOL_1.4.1

 Best
 Troels


 2011/9/9 Sean Law magic...@hotmail.com

 Hi PyMOLers,

 I have tried installing both PyMOL 1.3 and PyMOL 1.4.1 on OpenSuse (old
 Pentium 4) and am finding that when I load a molecule and click Show --
 Sticks that the entire molecular gets colored blue (originally the green
 default lines color).  After trying to change the color (Color --
 Elements), it doesn't alter the color at all.  However, hiding the sticks
 representation takes me back to the hidden green default lines color.  I'm
 not sure if this is because I'm using an old computer or if I'm missing
 something (i.e. libraries).

 Any suggestions would be greatly appreciated.

 Thanks

 Sean


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Re: [PyMOL] Pymol no longer fetches from pdb

[David Hall]

Resolves fine for me.

-David

On Mar 22, 2011, at 12:30 PM, Jason Vertrees jason.vertr...@schrodinger.com 
wrote:

 Hi Roger,
 
 On Tue, Mar 22, 2011 at 9:20 AM, Roger Rowlett rrowl...@colgate.edu 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 investigate
 further. This may be the issue with pymol if it is using that server path.
 
 This is clearly the reason for the error.  PyMOL looks for PDBs at the
 main PDB site at the following path:
 
 ftp://ftp.wwpdb.org/pub/pdb/data/structures/divided/pdb/
 
 and then appends the appropriate extension, which resolves and lists
 PDBs just fine (from my machine).
 
 Is anyone else having this error or just Roger?
 
 Cheers,
 
 -- Jason
 
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Re: [PyMOL] using pymol from python script

[David Hall]

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 )

The -- makes it so mymolecule.xyz is passed as an argument to the
python script instead of as an argument to pymol

Then examply.py is just

from pymol import cmd
import argv
import mymodule

cmd.load(sys.argv[1])
cmd.hide()
cmd.show(spheres)
mymodule.dosomething()


Note, that pymol has to be able to find mymodule, which if you're
using a Delano Scientific/Schrodinger binary can be annoying, but it
looks like that is already working for you.

Also, http://pymolwiki.org/index.php/Python_Integration makes it look like
pymol -l examply.py -- mymolecule.xyz

may work, but I've never done it, so no idea how the behavior differs.

-David


On Thu, Feb 17, 2011 at 3:05 AM, John Russo lamaro...@gmail.com wrote:
 Thanks, that is what I was looking for! I just made a simple
 script out of it which looks like this

 #!/usr/bin/env python

 import pymol
 from pymol import cmd
 import mymodule

 pymol.finish_launching()

 cmd.load(mymolecule.xyz)
 cmd.hide()
 cmd.show(spheres)
 mymodule.dosomething()


 I've noticed something strange though. The dosomething() function just
 colors atoms according to some order parameter. If I execute in the script
 above it is quite slow, I can see individual atoms being colored. Instead if
 I execute dosomething() from within the pymol interpreter it is much faster.
 Any reason for this?






 On 02/17/2011 04:33 PM, Tsjerk Wassenaar wrote:
 Hi John,

 Is this what you're looking for?:

 http://www.pymolwiki.org/index.php/Launching_From_a_Script

 Cheers,

 Tsjerk

 On Thu, Feb 17, 2011 at 8:19 AM, John Russolamaro...@gmail.com  wrote:
 Hi,
 I'm sorry for making such beginner's questions but searching the manual,
 google
 or the wiki didn't help me.

 I know how to extend pymol by writing python functions (through the
 extend command).
 But is it possible to do the opposite? I want to write a script that
 loads a molecule, does something
 to it and then displays the pymol window or outputs a png file. I want
 to this without having to
 enter commands in the pymol command line, since I need to put these
 operations in a script,
 without interactive control on pymol.

 Example. I want to write a script examply.py with which I can do

 ./examply.py mymolecule.xyz

 And for output I want to get mymolecule.png or the pymol window with all
 the operations
 already done.

 Any hints? Thank you.


    John



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Re: [PyMOL] Start PyMOL session in web browser

[David Hall]

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 source.

In the html5 world, you have jolecules http://jolecule.appspot.com/ , canvasmol 
http://alteredqualia.com/canvasmol/ , and chemdoodle web components 
http://web.chemdoodle.com/

-David

On Dec 19, 2010, at 7:37 AM, Martin Hediger ma@bluewin.ch wrote:

 Dear all
 Is it possible to start a PyMOL viewer through a web browser? What I 
 mean by this is, is it possible to view a protein over the internet 
 where the viewing features are provided by some limited PyMOL server? 
 The only thing able to do that right now is Jmol, but i think its very 
 inconvenient to use when viewing large structures such as proteins.
 
 Thanks for your answers
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[PyMOL] label_size in pymol 1.3 on Mac

[David Hall]

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 log indicating a fix that might
have been added since whatever source fink and macports declared 1.3.

-David

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Re: [PyMOL] OpenDX files from opendx.org

[David Hall]

Thanks,

Clearly my assumption about using the VMD plugins was wrong (and the
reader in dxplugin.cpp doesn't appear to even read that line, much
less assume it will say double).  As a more general question, does
pymol use the plugins in contrib/uiuc/plugins/molfile_plugin at all or
is that a relic from some earlier time?  Since the directory was still
being updated in June 2009, I assume it is at least used for some
files?

-David

On Mon, Oct 18, 2010 at 11:49 AM, Michael Lerner mgler...@gmail.com wrote:
 Hi David,
 As far as I know, PyMOL is still using its own DX reading functions
 (primarily ObjectMapDXStrToMap in layer2/ObjectMap.c if anyone's curious).
 I don't think it would be too much work to get PyMOL to read regular.dx. As
 far as I can tell, the only problem is that PyMOL is expecting the line that
 starts with object 3 to say object 3 class array type double instead of
 object 3 class array float.
 As for regularskewed.dx, PyMOL *does* support non-orthogonal maps (see
 e.g. http://www.mail-archive.com/pymol-users@lists.sourceforge.net/msg05870.html),
 but I'm not sure that PyMOL's DX reader supports them directly.
 I have not looked into the VMD plugins. If they support non-orthogonal DX
 maps out of the box, that might be a quick and easy solution.
 Cheers,
 -Michael

 On Fri, Oct 15, 2010 at 5:51 PM, David Hall li...@cowsandmilk.net wrote:

 I have long been happy reading .dx files produced by apbs and my own
 programs into pymol.  Everything works great.

 Interestingly, when I save a .dx file from OpenDX (http://opendx.org),
 pymol seems to not be able to read it.

 I've attached two files that come from OpenDX's samples directory
 where loading into pymol gives the error ObjectMap-Error: Error
 reading map.

 Any help in what's wrong with these files (or how to patch the VMD
 plugins that I believe pymol uses to read in dx files) would be
 appreciated.

 -David


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[PyMOL] OpenDX files from opendx.org

[David Hall]

I have long been happy reading .dx files produced by apbs and my own
programs into pymol.  Everything works great.

Interestingly, when I save a .dx file from OpenDX (http://opendx.org),
pymol seems to not be able to read it.

I've attached two files that come from OpenDX's samples directory
where loading into pymol gives the error ObjectMap-Error: Error
reading map.

Any help in what's wrong with these files (or how to patch the VMD
plugins that I believe pymol uses to read in dx files) would be
appreciated.

-David


regular.dx
Description: Binary data


regularskewed.dx
Description: Binary data
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[PyMOL] Super Bug Report

[David Hall]

In preparing my test for the odd request that I just sent, I came
across what seems to be a bug in super.  It has to do with this weird
nucleic acid thing I was talking about.

Here's the script this time:
from pymol import cmd

cmd.fetch('1acb', async=0)
cmd.fetch('1acb', '1acb_2', async=0)
cmd.fetch('426d', async=0)


print 1acb_2; print cmd.super('1acb', '1acb_2')[0]
print 426d; print cmd.super('1acb', '426d')[0]
print 1acb_2_again; print cmd.super('1acb', '1acb_2')[0]

~ ~/src/pymol_trunk_20100922/pymol -qrkc script2.py
PyMOLrun script2.py,main
1acb_2
0.0
426d
0.0
1acb_2_again
2.80655193329

super should give an rms between 1acb and 1acb_2 of 0.0, which it does
at first.  But once you super your protein to a nucleic acid that has
a calcium ion, when you run exactly the same command, you all of a
sudden get 2.8.  Very weird...

Note, this does not happen if you use 100d, which is a nucleic acid
without a calcium ion, does not happen if you use a pdb file with a
calcium ion, and does happen with 1d56, which is another nucleic acid
with a calcium ion I just pulled out.

In pymol 1.2, it also behaved incorrectly:
~ pymol -qrkc script2.py
PyMOLrun script2.py,main
1acb_2
0.0
426d
nan
1acb_2_again
nan


-David

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[PyMOL] Request: Change in behavior of super on nucleic acids?

[David Hall]

I realize this is an edge case, where behavior is not always well
defined in programs, but I have a request for a behavior (and the
behavior actually seemed to change between 1.2 and 1.3)

My example script:
from pymol import cmd

cmd.fetch('1acb', async=0)
cmd.fetch('1acb', '1acb_2', async=0)
cmd.fetch('100d', async=0)
cmd.fetch('426d', async=0)

print 1acb_2; print cmd.super('1acb', '1acb_2')[0]
print 1zna; print cmd.super('1acb', '100d')[0]
print 426d; print cmd.super('1acb', '426d')[0]


To explain, 1acb is a protein, 100d is a nucleic acid, 426d is also a
nucleic acid, but with a calcium, whose CA atom seems to impact the
behavior of super.  I want to be able to tell that 1acb and 1acb_2 are
identical.

In 1.2, when I ran this:
 pymol -qrkc script.py
PyMOLrun script.py,main
1acb_2
0.0
1zna
 ExecutiveAlign: invalid selections for alignment.
2.79037312189e-38
426d
nan

I can see that 1acb_2 is different from the others.  I like the 426d
behavior or reporting nan, but I can deal with looking for the
ExecutiveAlign error I see with 100d.


In pymol trunk, when I ran this:
~ ~/src/pymol_trunk_20100922/pymol -qrkc script.py
PyMOLrun script.py,main
1acb
0.0
1zna
 ExecutiveAlign: invalid selections for alignment.
0.0
426d
0.0

I can still look for the ExecutiveAlign error for 100d, but I don't
have any indication of differences between 426d and 1acb.  In this
case, I can do rms_cur or something to differentiate them, but in my
real desired use case, this is not possible.

I would love it if in the case of errors in alignment or rms, when
there are no atoms used or matching, it would return nan as it used to
for 426d.  If you think I should just stop doing silly things like
trying to use pymol's super to tell if a pdb is a nucleic acid, that's
an understandable response though.

-David

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Re: [PyMOL] for evaluation only

[David Hall]

The quick answer is Don't use an evaluation build.

You have 3 main options:
1) become a sponsor and get builds of the latest code
http://pymol.org/funding.html
2) use the free builds that are several years old http://pymol.org/rel/099/
3) build pymol from source.  There are instructions on
http://www.pymolwiki.org/ for building on windows, mac, and  linux,
and solutions to many common problems you might face can be found by
searching the archives of the list (linked to at the bottom of each
message).  If you run into any problems not discussed in the wiki or
archives, people around here are nice and will likely help you out.

-David

On Thu, Apr 29, 2010 at 6:03 PM, victor kenyon vicken...@gmail.com wrote:
 hi all,
 i am an academic using pymol and the new build places a for
 evaluation only graphic on top of the rendered structure. not very
 helpful for presentations, publications and the like. how do i
 circumvent this without using chimera to generate my images for pubs.
 thanks.
 victor

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[PyMOL] Load without bonding

[David Hall]

Is it possible to load a pdb file and have pymol skip making bonds?
There's a bunch of undocumented options to load, but I don't think any
of them do what I want.  I have a file where there's a bunch of
jumbled atoms and there's no relation between them, just thousands in
the same place and pymol spends a long time loading it presumably
trying to make these bonds.

-David

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Re: [PyMOL] Load without bonding

[David Hall]

actually, you can ignore this email, it seems pymol was having issues
because there were a bunch of CONECT records, if I delete those, pymol
actually loads it really fast.  Kind of odd behavior, but interesting.

-David

On Thu, Apr 22, 2010 at 2:14 PM, David Hall li...@cowsandmilk.net wrote:
 Is it possible to load a pdb file and have pymol skip making bonds?
 There's a bunch of undocumented options to load, but I don't think any
 of them do what I want.  I have a file where there's a bunch of
 jumbled atoms and there's no relation between them, just thousands in
 the same place and pymol spends a long time loading it presumably
 trying to make these bonds.

 -David


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Re: [PyMOL] Load without bonding

[David Hall]

I started a pymolwiki page for this at
http://www.pymolwiki.org/index.php/Connect_mode so I had something to
benchmark.  If someone knows what connect_mode=3 does, please fill it
in.  The code in layer2/ObjectMolecule2.c is probably where to start
if you want to take a stab at figuring it out.

-David

On Thu, Apr 22, 2010 at 2:43 PM, Jason Vertrees
jason.vertr...@schrodinger.com wrote:
 Hi David,

 Check out the connect_mode setting:

 set connect_mode, 1

 # no bonds

 fetch 1cll

 Cheers,

 -- Jason

 On Thu, Apr 22, 2010 at 2:14 PM, David Hall li...@cowsandmilk.net wrote:
 Is it possible to load a pdb file and have pymol skip making bonds?
 There's a bunch of undocumented options to load, but I don't think any
 of them do what I want.  I have a file where there's a bunch of
 jumbled atoms and there's no relation between them, just thousands in
 the same place and pymol spends a long time loading it presumably
 trying to make these bonds.

 -David

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Re: [PyMOL] Automatic modification of structures in PyMOL

[David Hall]

I think what you're asking for is one of the examples included in the
PyMol source code.  You can do this manually using the mutagenesis
wizard, but it is possible to drive this wizard through scripts.  The
two examples can be found at:
http://pymol.svn.sourceforge.net/viewvc/pymol/trunk/pymol/examples/devel/mutate01.pml?view=markup
and
http://pymol.svn.sourceforge.net/viewvc/pymol/trunk/pymol/examples/devel/mutate02.py?view=markup

On Mon, Apr 19, 2010 at 8:15 AM, Angela Gray
angela.gray...@googlemail.com wrote:
 Hi everyone,

 I am trying to find a way, in Pymol, to remove an amino acid from a peptide
 and insert any other amino acid. I have been able to do this for one residue
 at a time using the command

 editor.attach_fragment(‘pk1′,’my_fragment_name’,11,0)

 but I have to do this in two parts so that the new amino acid binds at both
 ends. I was wondering if there is a way in which Pymol can “swap” an
 existing side chain at position N on the peptide for any other side chain in
 an automated fashion?

 Any help much appreciated.

 Angela

 --
 Angela Gray

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Re: [PyMOL] pyMol executing python script: file path

[David Hall]

I think you'll be saddened to discover that if you try what Petr (the
original poster) was doing, sys.argv[0] won't work.

$ cat test.py
print sys.argv[0]
$ pymol -qrc test.py
PyMOLrun test.py,main
/sw/lib/pymol-py26/modules/pymol/__init__.py

This quite clearly gives the behavior that Petr had issues with.

Instead, this is what is needed is a secret variable called
pymol.__script__ e.g.:
import pymol
print pymol.__script__

which can be parsed to give the directory component and such.  For
example, to get the directory name reliably:
import pymol
from os import path
print path.dirname(path.abspath(pymol.__script__))

I don't have the ability to test this on Windows, but it works on both
Mac and Linux.

-David

On Thu, Apr 15, 2010 at 1:43 AM, Yerko Escalona yescal...@ug.uchile.cl wrote:
 Hi
 how do I determine the path of the script???
 the answer is sys.argv[0]
 for more information see this page
 http://diveintopython.org/functional_programming/finding_the_path.html

 PS sorry for the mistake Jason Vertrees

 --
 Yerko Ignacio Escalona Balboa
 Ingeniero en Biotecnología Molecular
 Universidad de Chile
 http://zeth.ciencias.uchile.cl/~yescalona/

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Re: [PyMOL] how to install pymol in Mac?

[David Hall]

The error below shows that you don't have gcc, which means you have to
install Apple's Developer tools to compile pymol.

That said, the easiest way right now is probably using macports.
Follow the instructions at http://www.macports.org/install.php for
installing macports, then you can run port install pymol and you
should be good to go.

-David

On Thu, Apr 15, 2010 at 10:54 AM, Young-Jin Cho youngji...@gmail.com wrote:
 Dear pymol users,
 I had to install pymol on my Macbook. I downloaded the files from
 SouceForge.net. When I typed  as following I got error messages:

  python setup.py build install
 running build
 running build_py
 running build_ext
 building 'pymol._cmd' extension
 gcc -fno-strict-aliasing -Wno-long-double -no-cpp-precomp
 -mno-fused-madd -fno-common -dynamic -DNDEBUG -g -Os -Wall
 -Wstrict-prototypes -DMACOSX -I/usr/include/ffi -DENABLE_DTRACE -arch
 i386 -arch ppc -pipe -D_PYMOL_MODULE -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE
 -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5
 -I/usr/X11R6/include
 -I/Users/youngjin25/Downloads/trunk/pymol/ext/include
 -I/Users/youngjin25/Downloads/trunk/pymol/ext/include/GL
 -I/Users/youngjin25/Downloads/trunk/pymol/ext/include/freetype2
 -Imodules/cealign/src -Imodules/cealign/src/tnt
 -I/System/Library/Frameworks/Python.framework/Versions/2.5/include/python2.5
 -c modules/cealign/src/ccealignmodule.cpp -o
 build/temp.macosx-10.5-i386-2.5/modules/cealign/src/ccealignmodule.o
 unable to execute gcc: No such file or directory
 error: command 'gcc' failed with exit status 1

 Could you tell me how I can handle this problem?

 Thanks in advance,

 Young-Jin

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Re: [PyMOL] RMSD for ALL ATOMS against ALL ATOMS

[David Hall]

rms and fit gave you different values?  They have never given me different
values.

Example:
from pymol import cmd

cmd.fetch('1nmr')
cmd.split_states('1nmr')
for i in xrange(1,21):
for j in xrange(1,21):
prot_i = '1nmr_%04d' %i
prot_j = '1nmr_%04d' %j

rms_val = cmd.rms(prot_i, prot_j)
fit_val = cmd.fit(prot_i, prot_j)

print rms_val-fit_val

prints 400 lines of 0.0

-David

On Wed, Apr 14, 2010 at 11:29 AM, Renuka Robert renukarob...@ymail.comwrote:

 Hi  All Pymol users

 I have a set of 40 X-ray crystallographic structures complexed with
 inhibitors belonging to a specific family of kinases. Binding site residues
 within 5 angstrom from the inhibitor were selected for each PDB structure
 and saved separately. Now i have a set of 40 PDB files which has only the
 binding site residues.


  I want to perform RMSD for ALL ATOMS against ALL ATOMS. The first
 structure should be fixed and compared with the remaining 39 structures. For
 the next time, second structure is fixed and so on for all the 40
 structures. Literally it should look like a 40X40 matrix table.


  I used align, fit and rms commands. Each one gives different values.
 Which is the best? Can you help me?


  Thank you in advance

 Renuka



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[PyMOL] Fedora Graphics Test Week

[David Hall]

I just learned about Fedora Graphics Test Week with nVidia being
tested today and ATI/AMD and Intel later in the week.  I figure many
PyMol users use proprietary drivers, but would be much happier if they
could use open source drivers instead.  There's even a Live CD, so you
don't need to be currently running Fedora or even Linux to
participate.  So, if you have some time to spare this week, you can
run all the tests on your system and hopefully help move open source
graphics on linux forward.

Announcement and details can be found at:
http://lwn.net/Articles/383156/

-David Hall

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Re: [PyMOL] Charged Surface Calculation at different pHs?

[David Hall]

I know little of the apbs-pymol integration, but in general, you can
use the PROPKA support built into PDB2PQR to assign protonation at
different pHs and then feed your pqr to apbs.

See http://www.poissonboltzmann.org/pdb2pqr/user-guide/using-pdb2pqr
for the --with-ph option.

There's also a whole different world of using apbs to determine pKa
(see http://www.poissonboltzmann.org/apbs/examples/pka-calculations )

-David

On Wed, Apr 7, 2010 at 12:49 PM, Soisson, Stephen M
stephen_sois...@merck.com wrote:
 Hi-

 Does anyone know if it is possible to calculate the charged surface using
 apbs at different pHs?  I am assuming the default pH is 7.

 Thanks in advance-

 Steve

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