Re: [PyMOL] making a plane

2017-01-18 Thread Spencer Bliven
I have a script for calculating principal moments of inertia and displaying
them as axes: https://github.com/sbliven/principal_axes

If you look over the code it should be pretty easy to draw the first two
axes as a cgo plane instead of as arrows.

-Spencer

On Tue, Jan 17, 2017 at 3:38 PM, Tsjerk Wassenaar  wrote:

> Hi Vitaly,
>
> You have several options, but if the loops are nicely bent, the best is
> probably doing PCA on the coordinate sets of the loops and calculate the
> angle between the smallest eigenvectors.
>
> Is that enough information? Do you insist on drawing the planes?
>
> Cheers,
>
> Tsjerk
>
> On Jan 17, 2017 15:11, "chemocev marker"  wrote:
>
>> Hi
>> I am analyzing the dynamics of the loop and interested to define the loop
>> as plane. Is there is a way in the pymol, if I can define the loop as plane
>> and can measure the angle between these plane in different model??
>>
>> Best
>> J. Vitali
>>
>> 
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Re: [PyMOL] Save command output to a file in pymol

2017-01-13 Thread Spencer Bliven
This can be done using normal python file i/o:

f=open("ss.txt","w")
iterate n. CA, f.write(resi + ':' + ss+"\n")
f.close()

On Fri, Jan 13, 2017 at 10:38 AM, Academic Research 
wrote:

> That would be good as well, How?
>
> keep in mind, my protein is synthetic, it is not from the PDB database,
> and the .pdb file only contains ATOMS, no header or anything else.
>
> On Jan 13, 2017, at 12:37 pm, Albert  wrote:
>
> I think you can obtain it from your Linux  terminal
>
>
>
> On 01/13/2017 10:34 AM, Academic Research wrote:
>
> Pymol Professionals I need your help,
>
> I have the following command:
>
> iterate n. CA, print resi + ':' + ss
>
> I use this command in pymol to print out each residue number and its
> corresponding secondary structure. The command prints out the result in
> pymol itself.
>
> My question is: *How can I save the output from this command into a file?*
>
> AC Research
>
>
>
> 
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Re: [PyMOL] difficulty opening EmrE protein (pdb: 3B5D) in Pymol

2016-12-02 Thread Spencer Bliven
There is a cartoon variant too, although everything will look like a loop

set cartoon_trace_atoms, on
show cartoon, polymer

On Wed, Oct 26, 2016 at 12:27 AM, Yuxing Liao <
yuxing.l...@utsouthwestern.edu> wrote:

> Hi Mohsen,
>
> The PDB file of 3B5D only contains CA atoms, so most rendering like
> cartoon fails. You could try to visualize it by "set ribbon_trace_atoms, 1"
> and then show it as ribbon.
>
> Yuxing
>
> -Original Message-
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> pymol-users-requ...@lists.sourceforge.net]
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> Message: 4
> Date: Tue, 25 Oct 2016 21:34:01 +
> From: Mohsen Chitsaz 
> Subject: [PyMOL] difficulty opening EmrE protein (pdb: 3B5D) in Pymol
> To: "pymol-users@lists.sourceforge.net"
> 
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>  apcprd03.prod.outlook.com>
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>
> Hi everyone,
>
> Can someone please assist me opening this pdb file? I am trying to open
> EmrE protein (pdb: 3B5D) in Pymol a and show it as cartoon representation,
> but it opens up as many little cross signs seem to be corresponding to CA
> atoms. When I try to preset it pretty or any other preset options, it
> disappears. The command "show cartoon" is not doing anything on it.
>
> Cheers
> Mohsen
>
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Re: [PyMOL] PDB Format not correct for use in CHARMM

2016-11-28 Thread Spencer Bliven
It would be nice to have a setting that adds TER records only where the
chain or segi change (as opposed to whenever the residue numbers are
non-sequential). I believe that better captures the original intent for
terminating polymers. Of course, the real answer is that everyone should
switch to mmCIF.

On Mon, Nov 28, 2016 at 4:01 PM, Thomas Holder <
thomas.hol...@schrodinger.com> wrote:

> Hi Marko and Rui,
>
> The TER records can also be prevented with "set pdb_use_ter_records, off".
>
> https://pymolwiki.org/index.php/pdb_use_ter_records
>
> Cheers,
>   Thomas
>
> On 28 Nov 2016, at 05:03, Rui Sousa  wrote:
>
> > Hi Marko,
> >
> > For the order of the atoms, check if "retain_order" is set to 1; if not,
> > use "set retain_order, 1" before importing your PDB file. For the rest
> > of your problem, what exactly is being changed from the imported PDB
> > file and the saved one? Apart from the addition of TER, which is a
> > fairly trivial problem to solve.
> >
> > Best regards,
> >
> > Rui
> >
> > Le 28/11/2016 10:41, Marko Sever a écrit :
> >> Hello everybody,
> >>
> >> I'm working with a protein-protein complex and am fixing some stuff.
> >>
> >> When I save the fixed complex as a pdb the PDB format is not the same
> as it was in the imported pdb files (there it was the same as the CHARMM
> default pdb format).
> >>
> >> In the saved pdb it changed the line position of atoms in the pdb file.
> Residues are ok but atoms in a given residue are mixed up. It also added
> addition TER's which I had to manually delete.
> >>
> >> So how would I specify the output PDB format to be the same as in the
> original imported pdbs (before manipulation), so same as CHARMM pdb format.
> >>
> >> Please help,
> >>
> >> Marko
>
> --
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> PyMOL Principal Developer
> Schrödinger, Inc.
>
>
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Re: [PyMOL] Pair_fit syntax

2016-10-25 Thread Spencer Bliven
First off, when the documentation includes square brackets in the command
it indicates optional arguments. You don't include them in the command
itself. In this case, pair_fit takes alternating selections from obj1 and
obj 2. It also requires that the number of atoms in each selection be
equal. I usually use CA atoms.

>From you example it seems like you want to align two structures in chunks
of 254 residues, but in a permuted order. I would do it as follows. I'm
going to use the shorter "/obj1///1-255/CA" syntax to stand for "obj1 and
resi 1-255 and name CA").

pair_fit /obj2///256-510/CA, /obj1///1-255/CA, /obj2///1-255/CA,
/obj1///256-510/CA, /obj2///766-1020/CA, /obj1///511-765/CA,
/obj2///511-765/CA, /obj1///766-1020/CA

Note that if you have any missing residues you might get an error 'Atom
counts between selection sets don't match'. In this case you should make
sure that the obj2 selections have the same number of atoms as the obj1
selection.

-Spencer

On Fri, Oct 21, 2016 at 12:10 AM Subha K  wrote:

> Hi there,
>
> Could somebody please help me with the correct syntax for pair fit?
>
> I tried this, but this doesn't work.
>
> pairfit (obj2 and resi 256-510), (onj1 and resi 1-255), [(obj2 and resi
> 1-255), (obj1 and resi 256-510), [(obj2 and resi 766-1020), (obj1 and resi
> 511-765), [(obj2 and resi 511-765), (obj1 and resi 766-1020)]]]
>
> Thanks,
> Subha
>
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Re: [PyMOL] 3D printing

2016-10-04 Thread Spencer Bliven
I've done a bit of 3D printing of proteins. I found links in the previous
thread VRML2 export and edu pymol
helpful.

STL is the best supported format for the printers, but since it's not
supported by pymol I've used VRML2 (.wrl). Fortunately free tools to
convert are readily available. A bigger problem is ensuring that the
exported geometry is manifold. I've always had to do some cleanup in a 3D
modeling program (e.g. blender, sketchup, etc) to get 3D printing software
like Slic3r to accept it. Algorithms to automatically merge all geometry
would be really nice if you're improving Jmol's export functionality.

You don't need to worry about support material. That should be handled by
the slicing software, since it needs to know about the printer hardware to
be generated efficiently.

-Spencer


On Mon, Oct 3, 2016 at 9:50 PM, Sampson, Jared M.  wrote:

> Hi Bob -
>
> I also haven't done much of anything with 3D printing myself, but having
> worked on the COLLADA exporter as one of my POSF fellowship projects, I can
> share some info about the formats themselves and what data is being
> included in the output files.
>
> > Q: What output file types are supported? (WRL, X3D, STL[ASCII/binary],
> other)
>
> The list on the Save wiki page is fairly complete.  It reads:
>
> "The file format is autodetected if the extension is .pdb, .pqr, .mol,
> .sdf, .pkl, .pkla, .mmd, .out, .dat, .mmod, .pmo, .pov, .png, .pse, .psw,
> .aln, .fasta, .obj, .mtl, .wrl, .idtf, .dae, or .mol2."
>
> The 3D formats among these (that I recognize, anyway) are .obj (Wavefront
> Object), .mtl (Wavefront Material), .wrl (VRML2), .idtf (Intermediate Data
> Text Format), and .dae (COLLADA).
>
>
> > Q: Does the generation of these include algorithms for ensuring closure
> or for stitching together objects in order to not have ragged overlap?
>
> I'm not sure what you mean by "stitching together objects," but in
> general, as long as you have fully closed surfaces, it shouldn't be an
> issue.  The only situation I can think of that would be problematic is if
> you had clipping panes that cut through the object's representation and end
> up with a hollow, infinitesimally thin shell.  That would be pretty
> difficult to print.  :)
>
> > Q: What is needed to add support struts so that the model is connected
> and strong enough?
>
> No, this is related to what Paul was asking about recently.  My guess is
> some 3D printing software or sites might have more appropriate tools to put
> these in, although you could do it manually (and probably quite tediously)
> with CGO cylinders or distance dashes with dash_gap = 0 if you know the
> orientation you want to use.
>
> > Q: If features are not amenable to printing (labels,  perhaps?), are
> they automatically ignored? Need to be manually removed?
>
> As far as I know, none of the supported 3D formats include labels in their
> exported data.  Each one has its own implementation, but in general,
> representations stored within PyMOL as triangle meshes (surfaces and
> cartoons, primarily, although you can get everything as triangles with `set
> use_shaders, 0`) are supported by all of them.  The COLLADA exporter also
> handles spheres, cylinders, sausages (i.e. rounded cylinders, such as ) and
> cones.  VRML2 includes spheres, cylinders and sausages.  The .obj exporter
> has a bug in sphere export that I looked at about a year ago but got busy
> and didn't actually follow through on.  The others I don't know enough
> about to comment, but hopefully this gets you on the right track.
>
> If you want to look further into it, check out the
> RayRender{VRML2,IDTF,ObjMtl,COLLADA} functions in layer1/Ray.cpp or
> layer1/COLLADA.cpp and look for cPrimTriangle, cPrimSphere, etc. for the
> various primitive types.
>
> Hope that helps!
>
> Cheers,
> Jared
>
>
>
> >
> > Thanks,
> >
> > Bob Hanson
> > 
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Re: [PyMOL] Rotate protein to align principal axes

2016-09-01 Thread Spencer Bliven
Jingjie,

I've used a script for calculating the principal components (
https://github.com/sbliven/principal_axes). The computeprincipalaxes
function returns the axes. With a bit of linear algebra you should be able
to use that to get a transformation matrix to apply to the coordinates.
This can be passed to Transform_selection
.

Another approach might be to use the orient command, and then use get_view
to extract the view matrix. Applying the inverse of this to the coordinates
should orient them along the XY axes.

-Spencer


On Thu, Sep 1, 2016 at 3:46 PM, #YEO JINGJIE#  wrote:

> Hi Jared,
>
> Thank you very much for your information. However, it seems that orient
> only changes the viewpoint, may I know whether it would possible to change
> the coordinates accordingly and save it into a pdb?
>
> Best Regards,
> Jingjie
>
> On 31 Aug 2016, at 10:16 PM, Sampson, Jared M. 
> wrote:
>
> Hi Jingjie -
>
> The `orient ` command does
> this, although you can't specify which axis.  However, when combined with `
> turn ` or `rotate
> `, you can get the molecule
> aligned in whichever orientation you prefer.  E.g:
>
> orient myprotein
> turn x, 90
> turn y, -90
>
> Hope that helps.
>
> Cheers,
> Jared
>
>
>
> On Aug 31, 2016, at 6:10 PM, #YEO JINGJIE#  wrote:
>
> Dear Users,
>
> May I know whether there are any methods in pymol to rotate a protein such
> that it's longest principal axis is in a particular direction, for instance
> aligned to the x-axis?
>
> Best Regards,
> Jingjie
> **Disclaimer** The sender of this email does not represent Nanyang
> Technological University and this email does not express the views or
> opinions of the University.
>
> 
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Re: [PyMOL] Problem with feedback push

2016-03-13 Thread Spencer Bliven
Thanks, Thomas.

On Fri, Mar 11, 2016 at 6:21 PM, Thomas Holder <
thomas.hol...@schrodinger.com> wrote:

> Hi Spencer,
>
> Yes this is a bug in the feedback stack. As a workaround, you can enable
> "cmd" and "parser" feedback manually before popping:
>
> _ feedback enable, cmd parser, warnings errors results
> _ feedback pop
>
> Hope that helps.
>
> Cheers,
>   Thomas
>
> On 11 Mar 2016, at 04:48, Spencer Bliven <spencer.bli...@gmail.com> wrote:
>
> > Here's a minimal .pymolrc to demonstrate the issue:
> >
> > #prints response, as expected
> > get cartoon_power
> >
> > _ feedback push
> > _ feedback disable,all,everything
> >
> > # Nothing prints here, as expected
> > get cartoon_power_b
> >
> > _ feedback pop
> >
> > # Still nothing prints!
> > get cartoon_use_shader
> >
> >
> > P.S. The feedback docs don't mention the push/pop commands. I likely got
> them from MacOSX-specific_.pymolrc_file
> >
> >
> > On Fri, Mar 11, 2016 at 10:41 AM, Spencer Bliven <
> spencer.bli...@gmail.com> wrote:
> > Since time immemorial my .pymolrc file has been wrapped by the construct
> > _ feedback push
> > _ feedback disable,all,everything
> >
> > ...
> >
> > _ feedback pop
> >
> > However, I've noticed that my `get` command doesn't print anything
> unless I specifically re-enable all feedback after starting pymol (or use
> the unwieldy `print cmd.get("var")`). Removing the feedback manipulation
> from my pymolrc restores the expected output from get. Is this a bug with
> the feedback stack?
> >
> > -Spencer
>
> --
> Thomas Holder
> PyMOL Principal Developer
> Schrödinger, Inc.
>
>
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Re: [PyMOL] Problem with feedback push

2016-03-11 Thread Spencer Bliven
Here's a minimal .pymolrc to demonstrate the issue:

#prints response, as expected
get cartoon_power

_ feedback push
_ feedback disable,all,everything

# Nothing prints here, as expected
get cartoon_power_b

_ feedback pop

# Still nothing prints!
get cartoon_use_shader



P.S. The feedback <http://pymolwiki.org/index.php/Feedback> docs don't
mention the push/pop commands. I likely got them from
MacOSX-specific_.pymolrc_file
<http://www.pymolwiki.org/index.php/MacOSX-specific_.pymolrc_file>





On Fri, Mar 11, 2016 at 10:41 AM, Spencer Bliven <spencer.bli...@gmail.com>
wrote:

> Since time immemorial my .pymolrc file has been wrapped by the construct
>
> _ feedback push_ feedback disable,all,everything
> ..._ feedback pop
>
>
> However, I've noticed that my `get` command doesn't print anything unless
> I specifically re-enable all feedback after starting pymol (or use the
> unwieldy `print cmd.get("var")`). Removing the feedback manipulation from
> my pymolrc restores the expected output from get. Is this a bug with the
> feedback stack?
>
> -Spencer
>
>
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[PyMOL] Problem with feedback push

2016-03-11 Thread Spencer Bliven
Since time immemorial my .pymolrc file has been wrapped by the construct

_ feedback push_ feedback disable,all,everything
..._ feedback pop


However, I've noticed that my `get` command doesn't print anything unless I
specifically re-enable all feedback after starting pymol (or use the
unwieldy `print cmd.get("var")`). Removing the feedback manipulation from
my pymolrc restores the expected output from get. Is this a bug with the
feedback stack?

-Spencer
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Re: [PyMOL] PyMOL split_states error on [PDB: 1hho]

2016-02-22 Thread Spencer Bliven
This looks like a bug in the PDB's file, and you should definitely let them
know about it. It's a particularly weird case since the second model
doesn't correspond to any of the valid crystallographic operators. Probably
it is a problem with the very non-standard crystal frame specified by the
SCALE matrix in the PDB file. These are always problematic, to the point
that some tools (e.g. EPPIC ) will ignore them
completely.

While waiting for the PDB to fix the file, you can generate the biological
unit from the symmetry operators using:

fetch 1hho, async=0
symexp sym, 1hho, 1hho, 2

-Spencer

On Mon, Feb 22, 2016 at 10:19 AM, Jame R.Ketudat-Cairns 
wrote:

> Dear Ioannis,
>I was wondering about that, too.  Given the prominence of hemoglobin
> structure and oxygen binding in Biochemistry education, the 1 HHO structure
> seems to be a bad biological structure to calculate incorrectly.  I guess
> an email to the PDB might be in order (if it is intentional, they could at
> least explain it in that case).
> Best Regards,
>   Jim
> 
> From: Ioannis Michalopoulos 
> Sent: Monday, February 22, 2016 4:05 PM
> To: Jame R.Ketudat-Cairns
> Subject: Re: [PyMOL] PyMOL split_states error on [PDB: 1hho]
>
> Dear Jim,
>
> Thank you for your prompt answer which worked perfectly. I was writing a
> tutorial for my students and I found many incorrectly calculated biological
> units. I wonder if we should complain to PDB about it, or wait and see what
> PyMOL can do about it, first.
>
> Best Regards,
>
> Ioannis
>
> On Monday 22 of February 2016 02:09:05 you wrote:
> > Dear Ioannis,
> >The 1HHO biological unit seems to be calculated incorrectly (just spun
> > around the y-axis 180 degrees).  I found that the symexp command works
> for
> > this: symexp sym, 1hho, (1hho), 1
> > Best Regards,
> > Jim
> > 
> > From: Ioannis Michalopoulos 
> > Sent: Monday, February 22, 2016 3:39 AM
> > To: pymol-users@lists.sourceforge.net
> > Subject: [PyMOL] PyMOL split_states error on [PDB: 1hho]
> >
> > Dear PyMOL users,
> >
> > I run PyMOL 1.8.0.0 for Windows.
> >
> > I loaded the biological assembly of 1HHO:
> >
> > http://www.rcsb.org/pdb/files/1HHO.pdb1.gz
> >
> > When I tried:
> >
> > split_states 1hho
> >
> > PyMOL failed to produce the proper tetramer that is seen at:
> >
> >
> http://www.rcsb.org/pdb/explore/jmol.do?structureId=1HHO=3=1
> >
> > Instead PyMOL shows a weird tetramer. Is it a bug? This approach works
> > fine on other cases eg 1SVC. Is there any other way to do it?
> >
> > Thank you in advance.
> >
> > Best Regards,
> >
> > Ioannis
> > --
> > Dr Ioannis Michalopoulos
> > Staff Research Scientist - Associate Professor Level
> > Centre of Systems Biology
> >
> > Tel: +30 210 6597 127
> > Fax: +30 210 6597 545
> > Email: imicha...@bioacademy.gr
> > _
> > Biomedical Research Foundation, Academy of Athens
> > Soranou tou Efessiou 4, 115 27 Athens, Greece
> >
> >
> >
> 
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> --
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> Staff Research Scientist - Associate Professor Level
> Centre of Systems Biology
>
> Tel: +30 210 6597 127
> Fax: +30 210 6597 545
> Email: imicha...@bioacademy.gr
> _
> Biomedical Research Foundation, Academy of Athens
> Soranou tou Efessiou 4, 115 27 Athens, Greece
>
>
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Re: [PyMOL] regarding show_bumps

2016-01-28 Thread Spencer Bliven
You can automate generating the bump objects:

split_states *,prefix=split_
for n in cmd.get_object_list("(split_*)"): show_bumps(n, "bump_"+n);

However, unfortunately the bump cgo objects don't seem to be able to be
combined into a multi-state object (e.g. with `for n in
cmd.get_object_list("(split_*)"):
cmd.create("bumps","bump_"+n,target_state=-1)`). Thus you might have to
generate your movie using some python loops to enable/disable the bumps for
each frame, if you want to automate it.

-Spencer

On Thu, Jan 28, 2016 at 11:25 AM, ccp4 pymol <ccp4.py...@gmail.com> wrote:

> Dear Spencer
>
> Thank you for the suggestion. Well, I actually wanted to do it as a part
> of making a movie, so would have liked some automation.
>
> Thank you.
>
> Best Regards
> Priyan
>
> On Thu, Jan 28, 2016 at 2:39 PM, Spencer Bliven <spencer.bli...@gmail.com>
> wrote:
>
>> Priyan–
>>
>> You can use the split_states
>> <http://pymolwiki.org/index.php/Split_states> command to divide it into
>> multiple objects, then run the script on each state individually.
>>
>> -Spencer
>>
>> On Thu, Jan 28, 2016 at 3:45 AM, ccp4 pymol <ccp4.py...@gmail.com> wrote:
>>
>>> Hi
>>>
>>> I have a multi-state object loaded in PyMOL which represents transition
>>> of a domain from one orientation to the other. I tried using
>>> "show_bumps.py" to bring up clashes during the transition but the cgo that
>>> is written out shows clashes only for the first state. Am I doing something
>>> wrong or should we pass additional commands to show clashes for all states.
>>> Kindly post your replies with help/suggestions in this regard.
>>>
>>> Thank you
>>>
>>> Best Regards
>>> Priyan
>>>
>>>
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>>
>>
>
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Re: [PyMOL] show the long helix filament

2016-01-13 Thread Spencer Bliven
For such cases I generate the symmetry partners using either the symexp
 command or the supercell
 script. Both scripts result in
lots of extra objects, which you then have to winnow down to a single
helix. Supercell can be nice since you can specify how man unit cells to
generate along a particular axis and it draws the unit cells.

-Spencer

On Wed, Jan 13, 2016 at 10:35 AM, Lukáš Pravda  wrote:

> Hi Yeping,
>
>
>
> What is the PDB id you are working with? Perhaps you have to download the
> biological assembly rather than asymmetric unit. I’d suggest you to go to
> the PDBe entry (pdbe.org/PDBID) and from the quick links select download
> ‘Assembly composition XML’. Take a look which assembly id has ‘preferred’
> attribute se to ‘True’ and download corresponding assembly.
>
>
>
> Hope it helps
>
>
>
> Lukas Pravda
>
> Central European Institute of Technology (CEITEC)
>
>
>
> *From:* sunyeping [mailto:sunyep...@aliyun.com]
> *Sent:* Wednesday, January 13, 2016 9:31 AM
> *To:* pymol-users 
> *Subject:* [PyMOL] show the long helix filament
>
>
>
>
>
> Dear all,
>
>
>
> I am studying a published protein molecule which was claimed to be helical
> symmetric. The pdb file contain 3 copies of this molecule arranged in
> head-to-tail patern. The author claims that this interation
> is repeated in a directional manner along the P31 screw axis. Does anyone
> know how to show the whole long helix filament rather that just three
> protomer of this molecule? Can pymol do this?
>
>
>
> Best regards.
>
> Yeping Sun
>
> Institute of Microbiology, Chinese Academy of Sciences
>
>
>
>
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Re: [PyMOL] Problem using pymol

2015-12-10 Thread Spencer Bliven
> Please let me know how can I renumber protein chains to avoid overlap and
> give it a uniqu chain id.
>

You can manually modify chain IDs with the alter
 command. For instance, to rename
chain A to X:

alter chain A, chain = "X"

To automatically select unique chain IDs, you can install the flatten_obj
 script.


> How can I change .pse file to .pdb file?
>

Use the 'Save molecule' option in the file menu, or the save
 command.

-Spencer
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Re: [PyMOL] PyMOL with Python 3

2015-12-07 Thread Spencer Bliven
Nice work! It will be very nice to have python3 compatibility in the future.

It would be nice to organize a section of the pymol-script-repo for
python3-compatible scripts once this gets merged to SVN.

-Spencer

On Fri, Dec 4, 2015 at 8:12 PM Thomas Holder 
wrote:

> Hi all,
>
> We have refactored Open-Source PyMOL to work with Python 3. If you are
> interested, the patched code and the patch itself are currently available
> from the sourceforge download page:
>
> https://sf.net/projects/pymol/files/pymol/1.8/
> pymol-v1.8.0.0-r4145-py3.tar.bz2 (patched code)
> pymol-v1.8.0.0-r4145-py3.patch (diff agains current SVN)
>
> Disclaimer: If you have no particular interest in Python 3, then this is
> not for you. Most currently available PyMOL plugins and Python scripts will
> not work with this version, they will need to be refactored as well.
>
> If you find any bugs or unexpected behavior, please let us know. In Python
> 3, all strings (type "str") are unicode, while in Python 2 "str" is an
> alias for "bytes". This difference is probably the most significant one for
> PyMOL. Once the patch looks rock solid and also proves to still work fine
> with Python 2, we will check it in to SVN.
>
> Cheers,
>   Thomas
>
> --
> Thomas Holder
> PyMOL Principal Developer
> Schrödinger, Inc.
>
>
>
> --
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Re: [PyMOL] using "bymol" in combination with "within"

2015-12-02 Thread Spencer Bliven
Andrew,

The 'byres' selector expands the inner selection to include all covalently
bonded atoms. Thus, your selection #2 should be a superset of selection #1.
Are you sure that's not the case?

What do your 'wats' and 'solute' selections refer to? Are you trying to
find the water molecules to some selected organic solvent molecule? If so,
you might mean

select wats within 3 of (bymolecule solute)

This would first expand selection 'solute' to encompass any covalently
connected atoms, then would return any atoms from selection 'wats' which
are within 3Å of the resulting molecule.

A more complete explanation of what you're trying to select (and which PDB
entry, if applicable) would be helpful.

-Spencer

P.S. You might also be interested in the predefined keywords 'solvent' (all
waters) and 'organic' (ligands, buffers).

On Wed, Dec 2, 2015 at 3:32 PM Andrew Kalenkiewicz 
wrote:

> Dear PyMOL users,
>
> I'm wondering if anyone knows how exactly a selection is defined if you
> utilize both the "bymol" and "within" commands together. For instance,
> consider the following two selections:
>
> 1. "select closewats, wats within 3 of solute"
> 2. "select closewats, bymol (wats within 3 of solute)"
>
> In the latter case, it seems to me that the distance cutoff imposed by
> within is not by "closest atom" for each respective molecule (which is what
> I actually want). Visually, I can see that the first selection includes
> more total water molecules than the second selection. So what does the
> distance cutoff refer to? The geometrical center? Center of mass? I
> couldn't find anything on the PyMOL wiki that explains this.
>
> Thanks,
> Andrew
>
> --
> Andrew Kalenkiewicz
> Biomedical Engineering M.S.E. '15
> Cellular & Molecular Biology B.S. '13
> University of Michigan, Ann Arbor
> 734-709-0355
> aj...@umich.edu
>
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Re: [PyMOL] using "bymol" in combination with "within"

2015-12-02 Thread Spencer Bliven
Andrew,

Can you provide an example? In my tests the bymol and within operators work
as expected.

fetch 4FC1 #high-res neutron scattering structure with water hydrogens
select solvent w. 3 of resi 7
stored.i=0; cmd.iterate("sele", "stored.i+=1"); print stored.i #7 atoms
select bymol solvent w. 3 of resi 7
stored.i=0; cmd.iterate("sele", "stored.i+=1"); print stored.i #12 atoms

Is this an MD structure? It's a bit weird that you have hydrogens on your
waters. Some MD programs I've worked with give poorly constructed PDB
files, so I wonder if it could be a problem with your input structure.

-Spencer

On Wed, Dec 2, 2015 at 8:58 PM Andrew Kalenkiewicz <ajkalenkiew...@gmail.com>
wrote:

> Hi Spencer,
>
> Thanks for your response! I was also originally under the impression that
> my selection #2 should be a superset of selection #1, but that is
> definitely not the case. There are atoms in selection #1 that are not
> included in selection #2.
>
> What I want to do is select all the water molecules that have at least one
> of their atoms within 3 angstroms of my protein-ligand complex (the
> solute). Based on the above discrepancy, I know that selection #2 does not
> give me this. This is corroborated by an independent calculation I did in a
> different program (the Bio3D pacakge in R).
>
> All best,
> Andrew
>
> On Wed, Dec 2, 2015 at 10:53 AM, Spencer Bliven <spencer.bli...@gmail.com>
> wrote:
>
>> Andrew,
>>
>> The 'byres' selector expands the inner selection to include all
>> covalently bonded atoms. Thus, your selection #2 should be a superset of
>> selection #1. Are you sure that's not the case?
>>
>> What do your 'wats' and 'solute' selections refer to? Are you trying to
>> find the water molecules to some selected organic solvent molecule? If so,
>> you might mean
>>
>> select wats within 3 of (bymolecule solute)
>>
>> This would first expand selection 'solute' to encompass any covalently
>> connected atoms, then would return any atoms from selection 'wats' which
>> are within 3Å of the resulting molecule.
>>
>> A more complete explanation of what you're trying to select (and which
>> PDB entry, if applicable) would be helpful.
>>
>> -Spencer
>>
>> P.S. You might also be interested in the predefined keywords 'solvent'
>> (all waters) and 'organic' (ligands, buffers).
>>
>> On Wed, Dec 2, 2015 at 3:32 PM Andrew Kalenkiewicz <
>> ajkalenkiew...@gmail.com> wrote:
>>
>>> Dear PyMOL users,
>>>
>>> I'm wondering if anyone knows how exactly a selection is defined if you
>>> utilize both the "bymol" and "within" commands together. For instance,
>>> consider the following two selections:
>>>
>>> 1. "select closewats, wats within 3 of solute"
>>> 2. "select closewats, bymol (wats within 3 of solute)"
>>>
>>> In the latter case, it seems to me that the distance cutoff imposed by
>>> within is not by "closest atom" for each respective molecule (which is what
>>> I actually want). Visually, I can see that the first selection includes
>>> more total water molecules than the second selection. So what does the
>>> distance cutoff refer to? The geometrical center? Center of mass? I
>>> couldn't find anything on the PyMOL wiki that explains this.
>>>
>>> Thanks,
>>> Andrew
>>>
>>> --
>>> Andrew Kalenkiewicz
>>> Biomedical Engineering M.S.E. '15
>>> Cellular & Molecular Biology B.S. '13
>>> University of Michigan, Ann Arbor
>>> 734-709-0355
>>> aj...@umich.edu
>>>
>>> --
>>> Go from Idea to Many App Stores Faster with Intel(R) XDK
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>>
>>
>
>
> --
> Andrew Kalenkiewicz
> Biomedical Engineering M.S.E. '15
> Cellular & Molecular Biology B.S. '13
> University of Michigan, Ann Arbor
> 734-709-0355
> aj...@umich.edu
>
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Re: [PyMOL] on axis of the subunit

2015-12-01 Thread Spencer Bliven
Note that the elbow formula assumes that the two vectors are normalized.
Remember the dot product 
equation

 = |x| * |y| * cos( theta )

-Spencer



On Tue, Dec 1, 2015 at 4:34 AM Sampson, Jared M. 
wrote:

> Hi Smith -
>
> Check out how I did it in the http://pymolwiki.org/index.php/Elbow_angle 
> script.
> As long as you have the vectors, the angle is easy.  In particular, have a
> look at this line:
>
> elbow = int(numpy.degrees(numpy.arccos(numpy.dot(direction_v, 
> direction_c
>
> i.e. the angle (in radians) will be given by the arccos of the dot product
> of the two vectors.  For the elbow angle script, I converted to degrees and
> reported an integer value.
>
> Cheers,
> Jared
>
> —
> Jared Sampson
> Graduate Student
> Department of Biochemistry and Molecular Biophysics
> Columbia University
>
> On Nov 30, 2015, at 8:33 PM, Smith Liu  wrote:
>
> Thanks Jared, it works.
>
> In addition, if by your way I created 2 vectors for 2 different chains,
> will you please show me how to determine the angle formed by the 2 vectors
> created?
>
> Smith
>
>
>
>
>
>
>
> At 2015-12-01 00:51:46, "Sampson, Jared M." 
> wrote:
>
> Hi Smith -
>
> I’m not quite sure what you mean by "axis of a subunit."  If you mean the
> principal axis of that selection of atoms, `orient my_selection` will get
> it aligned along one of the axes.  Then you can create pseudoatoms on that
> axis and create a dash between them with the distance command.
>
> # Get it lined up with the viewport axes.
> select domain, chain A and resi 1-100
> orient domain
>
> # Here I’m assuming this put the long axis of the domain along the
> # x axis.  We move the view along the x axis, and place pseudoatoms
> # at the viewport center in two places.  You can change the length of the
> # displayed axis based on how far you move.
> move x, -10
> pseudoatom ps1
> move x, 20
> pseudoatom ps2
> move x, -10
> distance axis, ps1, ps2
>
> This is a bit clumsy and not a rigorous approach, but it will work for any
> other kind of vector you want to show, as long as you can get it aligned
> with one of the view axes.
>
> Cheers,
> Jared
>
> —
> Jared Sampson
> Graduate Student
> Department of Biochemistry and Molecular Biophysics
> Columbia University
>
> On Nov 29, 2015, at 7:42 AM, Smith Liu  wrote:
>
> Dear All,
>
> Will you please show me how to display an axis of a subunit or a domain by
> pymol?
>
> Smith
>
>
>
>
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Re: [PyMOL] Is it possible to install PyMOL .app on Mac?

2015-11-08 Thread Spencer Bliven
Luke,

You have the right download. .app files are for mac programs, not for
Linux. However, I believe that macpymol 1.3 doesn't work on recent os x
versions. You'll need at least version 1.4. You can install the open source
version 1.7 from a number of places, including macports and homebrew.

-Spencer

On Sun, Nov 8, 2015, 11:25 PONGPAWAN SETHANANT <
pongpawan@student.mahidol.ac.th> wrote:

> Dear all,
>
> I am having trouble installing the previous version (v1.3) of PyMOL
> educational version on Mac.
>
> The file name says something like PyMOL for mac, but it is a .app file,
> which is particularly for Linux.
>
> So, is it possible to install it on Mac?
>
> I would really appreciate all your help,
> Luke
>
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Re: [PyMOL] PyMol Question

2015-11-03 Thread Spencer Bliven
Mohsen–

set transparency , .5, sele

Cheers,
Spencer

On Tue, Nov 3, 2015 at 3:18 AM, Mohsen Chitsaz <
mohsen.chit...@flinders.edu.au> wrote:

> Hi there,
>
>
>
> I was wondering how I can make the surface of a selected part of a protein
> transparent? I tried transparency command, but, I came up with a message
> that “transparency” was not found.
>
>
>
> Thank you
>
>
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Re: [PyMOL] Biological assembly unit

2015-11-02 Thread Spencer Bliven
Faiza–

If what you're actually interested in is a model for the structure of the
human dimeric Phenylalanine-4-hydroxylase, I suggest that rather than
building it in pymol you use one from the protein model portal:
http://www.proteinmodelportal.org/query/up/P00439

If you want to make such a model yourself in pymol, it is basically just a
matter of aligning a copy of 1phz onto each chain from the 1j8u biological
assembly. Just load 1phz twice, and align each copy to one chain of the
flattened 1j8u BA.

fetch 1j8u, type=pdb1
fetch 1phz
create 1phz_2, 1phz
flatten_obj 1j8u_ba, 1j8u
align 1phz, /1j8u_ba//A
align 1phz_2, /1j8u_ba//B

Of course, the interface will not be optimized with this method and could
lead to clashes.

-Spencer

P.S. Please reply to questions on the mailing list rather than directly.


On Mon, Nov 2, 2015 at 7:45 AM, faiza iftikhar 
wrote:

> Hi Spencer,
>
> I didn't get my desired structure. I am new to pymol and what I want to do
> is to create a dimer containing N-terminal of 1phz and 1j8u.
>
> Regards,
> Faiza
>
> --
> From: spencer.bli...@gmail.com
> Date: Fri, 30 Oct 2015 15:26:16 +0100
> Subject: Re: [PyMOL] Biological assembly unit
> To: faizaaiftik...@hotmail.com
> CC: pymol-users@lists.sourceforge.net
>
>
> Dealing with multi-state models is tricky. I wrote a flatten_obj
>  script to combine the
> multiple states into a single object. (Thanks for the motivation to finally
> upload my script to the wiki!) This allows you to use the normal
> align/super/cealign commands to superimpose them as expected. Your example:
>
> run flatten_obj.py
> fetch 1phz 1j8u, type=pdb1
> flatten_obj 1j8u_ba, 1j8u
> flatten_obj 1phz_ba, 1phz
> cealign /1phz_ba//A, /1j8u_ba//A
>
> Note that the dimer interface shifts somewhat between the two structures,
> so it may be preferable to superimpose two copies of the 1ju8 asymmetric
> unit onto both chains of 1phz_ba (or vice versa, depending on which
> interface you consider more relevant).
>
> -Spencer
>
> On Thu, Oct 29, 2015 at 1:26 PM, faiza iftikhar <
> faizaaiftik...@hotmail.com> wrote:
>
> Hi,
>
> I would like to know is there any way to combine N-terminal of 1phz
> (biological assembly structure not asymmetric one) to 1j8u(biological
> structure) in Pymol.
>
> Regards,
> Faiza
>
>
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Re: [PyMOL] Biological assembly unit

2015-10-30 Thread Spencer Bliven
Dealing with multi-state models is tricky. I wrote a flatten_obj
 script to combine the multiple
states into a single object. (Thanks for the motivation to finally upload
my script to the wiki!) This allows you to use the normal
align/super/cealign commands to superimpose them as expected. Your example:

run flatten_obj.py
fetch 1phz 1j8u, type=pdb1
flatten_obj 1j8u_ba, 1j8u
flatten_obj 1phz_ba, 1phz
cealign /1phz_ba//A, /1j8u_ba//A

Note that the dimer interface shifts somewhat between the two structures,
so it may be preferable to superimpose two copies of the 1ju8 asymmetric
unit onto both chains of 1phz_ba (or vice versa, depending on which
interface you consider more relevant).

-Spencer

On Thu, Oct 29, 2015 at 1:26 PM, faiza iftikhar 
wrote:

> Hi,
>
> I would like to know is there any way to combine N-terminal of 1phz
> (biological assembly structure not asymmetric one) to 1j8u(biological
> structure) in Pymol.
>
> Regards,
> Faiza
>
>
> --
>
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Re: [PyMOL] Common atoms in two selections (and their indices)

2015-10-27 Thread Spencer Bliven
Tsjerk–

You might be able to extract the ids of the aligned residues from an
alignment object:

cmd.align(sele1,sele2copy,object="aln")
[a.id for a in cmd.get_model('aln').atom]

Since the alignment is sequential, I think this should contain all the
aligned atoms from sele1 concatenated with the aligned atoms from sele2.
However, as far as I know the internals of the alignment objects aren't
documented, so I'm not sure if this can be relied upon.

-Spencer


On Tue, Oct 27, 2015 at 12:22 PM, Tsjerk Wassenaar 
wrote:

> Hi Osvaldo,
>
> Probably that's the trick, although I'd need the indices, but that's
> simple enough.
> The 'equivalence' one is still standing though :)
>
> Thanks,
>
> Tsjerk
>
> On Tue, Oct 27, 2015 at 11:44 AM, Osvaldo Martin 
> wrote:
>
>> So, you want to know the best way to do this?
>>
>> Z = [at_x for at_x in X for at_y in Y if at_x.id == at_y.id]
>>
>> Or am I still not getting it right?
>>
>> Cheers,
>> Osvaldo.
>>
>> On Tue, Oct 27, 2015 at 10:56 AM, Tsjerk Wassenaar 
>> wrote:
>>
>> Hi Osvaldo,
>>>
>>> I could have been more clear I guess. First of all, let's say I have
>>> obtained the atom list of a selection:
>>>
>>> X = cmd.get_model(selection1).atom
>>>
>>> I'm doing stuff with that (PCA, to be exact), but now I want to display
>>> the result only for a subselection. Probably getting the intersection of
>>> the selections and then check which atoms there match with the original
>>> selection is an approach. The question there is what the best way is for
>>> checking identity of the atoms.
>>>
>>> The second issue is when there is no intersection of the selections, but
>>> there may be correspondence, as in alignment.
>>>
>>> Thanks for thinking along,
>>>
>>> Tsjerk
>>>
>>> On Tue, Oct 27, 2015 at 10:44 AM, Osvaldo Martin 
>>> wrote:
>>>
 Hi Tsjerk,

 Do you mean something like this?

 cmd.index("sel_1 and sel_2")

 I do not get the differences between your two cases. Whats the
 difference between “atoms which are both in selection 1 and 2” and
 “matching atoms in the two selections”

 Cheers,

 Osvaldo.

 On Mon, Oct 26, 2015 at 10:33 AM, Tsjerk Wassenaar 
 wrote:


> Hi Thomas e.a.,
>
> Given two selections, would there be an easy way to
>
> 1. find the atoms which are both in selection 1 and 2, and the indices
> of those in the selections
>
> and
>
> 2. find the matching atoms in the two selections, like align does, and
> the indices of those in the selections
>
> Thanks,
>
> Tsjerk
>
> --
> Tsjerk A. Wassenaar, Ph.D.
>
>
>
> --
>
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 ​

>>>
>>>
>>>
>>> --
>>> Tsjerk A. Wassenaar, Ph.D.
>>>
>>> ​
>>
>
>
>
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>
>
>
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Re: [PyMOL] superimposing and aligning

2015-10-26 Thread Spencer Bliven
Or cealign !

On Tue, Oct 20, 2015 at 4:14 PM, Osvaldo Martin 
wrote:

> Hi Raag,
>
> You can use align  or super
> , the main difference is that
> super does not use sequence information.
>
> Cheers,
>
> Osvaldo.
>
> On Tue, Oct 20, 2015 at 4:04 PM, Raag Saluja 
> wrote:
>
> Hi! how do you align two molecules when you superimpose? Can you please
>> tell me the exact command?
>>
>> Thank you so much and sorry for the bother!
>>
>> --
>> Regards,
>> Raag
>>
>>
>> --
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[PyMOL] Interrupting slow commands

2015-10-26 Thread Spencer Bliven
Is there any way to interrupt slow commands without killing pymol? For
instance, if you accidentally add an extra 0 to the raytracing resolution.

On a related note, it would be nice to programmatically access the progress
bar and abort button from scripts and plugins (I know it has been discussed
previously on this list) rather than have to make a custom UI for
monitoring progress. Then I would have less time to write feature requests
while my slow scripts grind to completion. :)

Cheers,
-Spencer
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Re: [PyMOL] Pymol crash when deleting callback object

2015-09-30 Thread Spencer Bliven
awesome, thanks

On Tue, Sep 29, 2015 at 7:39 PM, Thomas Holder <
thomas.hol...@schrodinger.com> wrote:

> Hi Spencer,
>
> This was a threading issue, I have fixed the script.
>
> Passing a wrong name to PutCenterCallback results in the same threading
> issue. Should also be fixed.
>
> Cheers,
>   Thomas
>
> On 29 Sep 2015, at 10:47, Spencer Bliven <spencer.bli...@gmail.com> wrote:
>
> > I'm using the callback version of the Axes script (third script at
> http://www.pymolwiki.org/index.php/Axes). In MacPyMol 1.7.6.3 syspython,
> deleting the constructed axes object causes Pymol to crash. It's an old
> script and I'm guessing not well maintained, but the crash is still
> unfortunate.
> >
> > As an aside, you can also crash many versions of pymol by making
> mistakes in the callback, such as passing a different name for the callback
> and the cgo object (yes, this is a silly thing to try, but it shouldn't
> crash).
> >
> > -Spencer
>
> --
> Thomas Holder
> PyMOL Principal Developer
> Schrödinger, Inc.
>
>
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[PyMOL] Pymol crash when deleting callback object

2015-09-29 Thread Spencer Bliven
I'm using the callback version of the Axes script (third script at
http://www.pymolwiki.org/index.php/Axes). In MacPyMol 1.7.6.3 syspython,
deleting the constructed axes object causes Pymol to crash. It's an old
script and I'm guessing not well maintained, but the crash is still
unfortunate.

As an aside, you can also crash many versions of pymol by making mistakes
in the callback, such as passing a different name for the callback and the
cgo object (yes, this is a silly thing to try, but it shouldn't crash).

-Spencer
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Re: [PyMOL] Pymol crash when raytracing empty graphics

2015-08-18 Thread Spencer Bliven
Thanks for the quick fix! I would love to get a hotfix if possible.

The PDBe API is a nice solution. I think that detecting CA traces will fix
90% of the cases. There are still a few edge cases besides CA which don't
have a cartoon mode (e.g. 1hzs, which has a polydeoxyribonucleotide polymer
type but lacks phosphate atoms needed for cartoon), but these are rare
enough to be handled individually.

-Spencer

On Mon, Aug 17, 2015 at 7:54 PM, Thomas Holder 
thomas.hol...@schrodinger.com wrote:

 Hi Spencer,

 Thank you for the bug report. We could reproduce and fix the crash, if you
 want I can send you a hotfix build. I will also push the fix to the open
 source SVN repository soon.

 I second John's suggestions to query the ca_p_only property from the
 PDBe API. Also, the next PyMOL version will read that property from the
 mmCIF file and automatically set the cartoon_trace_atoms and
 ribbon_trace_atoms settings.

 Cheers,
   Thomas

 On 17 Aug 2015, at 10:58, John Berrisford j...@ebi.ac.uk wrote:

  Dear Spencer
  It is possible to work this out using the PDBe API.
  for our interactive API see:
  http://www.ebi.ac.uk/pdbe/api/doc/
  The molecules url will give you this information:
  http://www.ebi.ac.uk/pdbe/api/pdb/entry/molecules/1a1q
  entity 1 has ca_p_only: true,
  which means cartoon will not work for this chain - so we use ribbon
 instead with the command
  pymol.cmd.set(ribbon_trace_atoms, 1)
  This test allows us to make images such as those shown on the entry page
 for 1a1q at PDBe
  http://www.ebi.ac.uk/pdbe/entry/pdb/1a1q
  The images are made with pymol (currently 1.6, but also works in 1.7)
  Regards
  John
  PDBe
  On Monday 17 August 2015 15:40:14 Spencer Bliven wrote:
   We have a pipeline that uses pymol to create images using the headless
   command line interface. I've discovered that PyMOL 1.7.4 and 1.7.6 (at
   least) crash if you try to ray-trace an empty viewport.
  
   Example:
  
   pymol -q -c -d 'fetch 1a1q,async=0;as cartoon;ray'
  
   This particular example only has CA atoms, so the cartoon mode doesn't
 show
   anything. In interactive mode I would `set cartoon_trace_atoms,1` but
 when
   batch processing there isn't a good way of detecting whether anything
 is
   showing or not.
  
   The error is:
  
   *** glibc detected ***
   /home/user/software/packages/pymol-v1.7.4.4/pymol.exe: double free or
   corruption (out): 0x7f11f8744f40 ***
  
   I've reproduced the error on Redhat 6 and Ubuntu 14.04, with PyMOL
 1.7.4.1
   through 1.7.6.3.
  
   Attached is a stack trace.
  
  
   Any suggestions on ensuring that there are some polygons in frame would
   also be appreciated. Say, if there was a way to detect that cartoon
 would
   fail so that I can switch to a lines or nonbonded representation (I
 wish
   that was the default fallback for cartoon).
  
   Thanks,
   Spencer
  
  --
  John Berrisford
  PDBe
  European Bioinformatics Institute (EMBL-EBI)
  European Molecular Biology Laboratory
  Wellcome Trust Genome Campus
  Hinxton
  Cambridge CB10 1SD UK
  Tel: +44 1223 492529

 --
 Thomas Holder
 PyMOL Principal Developer
 Schrödinger, Inc.



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[PyMOL] Pymol crash when raytracing empty graphics

2015-08-17 Thread Spencer Bliven
We have a pipeline that uses pymol to create images using the headless
command line interface. I've discovered that PyMOL 1.7.4 and 1.7.6 (at
least) crash if you try to ray-trace an empty viewport.

Example:

pymol -q -c -d 'fetch 1a1q,async=0;as cartoon;ray'

This particular example only has CA atoms, so the cartoon mode doesn't show
anything. In interactive mode I would `set cartoon_trace_atoms,1` but when
batch processing there isn't a good way of detecting whether anything is
showing or not.

The error is:

*** glibc detected ***
/home/user/software/packages/pymol-v1.7.4.4/pymol.exe: double free or
corruption (out): 0x7f11f8744f40 ***

I've reproduced the error on Redhat 6 and Ubuntu 14.04, with PyMOL 1.7.4.1
through 1.7.6.3.

Attached is a stack trace.


Any suggestions on ensuring that there are some polygons in frame would
also be appreciated. Say, if there was a way to detect that cartoon would
fail so that I can switch to a lines or nonbonded representation (I wish
that was the default fallback for cartoon).

Thanks,
Spencer


pymol_crash.log
Description: Binary data
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[PyMOL] Interleaved atoms when creating from two objects

2015-04-22 Thread Spencer Bliven
I'm working on a script which involves joining two objects together, which
I do using the create command. The input objects have different chain
identifiers, but identical residue numbers. When I create the joined
object, I would expect all atoms from the first object to be added,
followed by all atoms from the second object (with atom IDs being unchanged
for the first object, and then continuing sequentially for the second
object). Instead, the produced object alternates between atoms of each of
the input objects:

PyMOLiterate joined, print (ID,chain,name)
(0, 'A', 'N')
(1, 'B', 'N')
(2, 'A', 'CA')
(3, 'B', 'CA')
(4, 'A', 'C')
(5, 'B', 'C')
(6, 'A', 'O')
(7, 'B', 'O')
...


This order breaks cartoon and ribbon representations, as well as makes the
sequence view display each atom individually rather than combining residues.

A somewhat convoluted but reproducible case follows (Using MacPyMOL 1.7.4):

fetch 4rp9, type=pdb1
split_states 4rp9
alter 4rp9_0002, chain = 'B'
create joined, 4rp9_* and resi 282

I've tried various combinations of the rebuild and sort commands, as well
as manually changing the IDs of the objects, but I haven't been able to
find a workaround yet. Sort seems to operate on the resi and ignores the ID
 chain.

Is this a bug or am I doing something wrong?

Thanks,
Spencer
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Re: [PyMOL] Interleaved atoms when creating from two objects

2015-04-22 Thread Spencer Bliven
Thanks, it was indeed due to the autodock plugin setting retain_order. That
would have taken me quite a while to debug on my own!

-Spencer

On Wed, Apr 22, 2015 at 6:03 PM, Matthew Baumgartner mp...@pitt.edu wrote:

 Hi,

 I had problems with the retain order setting as well. The autodock vina
 pulgin turns it on. Unload the plugin to fix it, or manually set it
 after plugins are loaded.

 Matt

 On 4/22/15 8:56 PM, Thomas Holder wrote:
  Hi Spencer,
 
  please check your retain_order setting, it should be off (default). If
 it's on, also check your pymolrc if you're setting it there.
 
  http://www.pymolwiki.org/index.php/Retain_order
  http://www.pymolwiki.org/index.php/Pymolrc
 
  Cheers,
 Thomas
 
  On 22 Apr 2015, at 20:39, Spencer Bliven sbli...@ucsd.edu wrote:
 
  I'm working on a script which involves joining two objects together,
 which I do using the create command. The input objects have different chain
 identifiers, but identical residue numbers. When I create the joined
 object, I would expect all atoms from the first object to be added,
 followed by all atoms from the second object (with atom IDs being unchanged
 for the first object, and then continuing sequentially for the second
 object). Instead, the produced object alternates between atoms of each of
 the input objects:
 
  PyMOLiterate joined, print (ID,chain,name)
  (0, 'A', 'N')
  (1, 'B', 'N')
  (2, 'A', 'CA')
  (3, 'B', 'CA')
  (4, 'A', 'C')
  (5, 'B', 'C')
  (6, 'A', 'O')
  (7, 'B', 'O')
  ...
 
 
  This order breaks cartoon and ribbon representations, as well as makes
 the sequence view display each atom individually rather than combining
 residues.
 
  A somewhat convoluted but reproducible case follows (Using MacPyMOL
 1.7.4):
 
  fetch 4rp9, type=pdb1
  split_states 4rp9
  alter 4rp9_0002, chain = 'B'
  create joined, 4rp9_* and resi 282
 
  I've tried various combinations of the rebuild and sort commands, as
 well as manually changing the IDs of the objects, but I haven't been able
 to find a workaround yet. Sort seems to operate on the resi and ignores the
 ID  chain.
 
  Is this a bug or am I doing something wrong?
 
  Thanks,
  Spencer
 



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Re: [PyMOL] holes in isosurface representation

2015-01-06 Thread Spencer Bliven
Hey Jacob,

Are Lagging_A and Leading_B selections or objects? Generally for surfaces
to display right you have to create a new object for the part you want
(using either the create or extract commands). Otherwise you get holes in
the surface where the selection contacts the rest of the object.

-Spencer

On Tue, Dec 30, 2014 at 10:16 PM, Jacob Lewis jl...@uowmail.edu.au wrote:

 Hi all,

 I am using the maps and isosurface to represent a large protein protein
 complex, however whenever I generate a a map then isosurface it has holes
 in it areas that are not complete. I don’t understand as it surface
 representation it is a complete, closed surface? Anyone have any ideas as
 to why this is happening? Below is how I generate the maps and isosurface.

 remove solvent
 alter all, b=40
 alter all, q=1
 set gaussian_resolution,15
 set surface_quality, 2

 # Clamp Loader Maps
 # Lagging A
 map_new Lagging_A-MAP, gaussian, 1, Lagging_A, 3
 isosurface Lagging_A-SURF, Lagging_A-MAP

 # Leading B
 map_new Leading_B-MAP, gaussian, 1, Leading_B, 3
 isosurface Leading_B-SURF, Leading_B-MAP

 Any help is greatly appreciated,

 Cheers,

 Jacob

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

2014-12-05 Thread Spencer Bliven
You can translate and rotate objects using the Editing mouse mode ('Mouse'
 '3 Button Editing'). Objects can be rotated with shift-left click or
translated with shift-middle click. You can also modify just a segment by
'picking' the boundaries (command/ctrl left click). Use the 'unpick'
command to get back to moving the whole molecule.

The editing mode is pretty powerful, but not that well documented. It's
also missing undo capabilities, so save your session before attempting
anything.

-Spencer

On Mon, Nov 17, 2014 at 1:35 PM, David Hall li...@cowsandmilk.net wrote:

 also http://www.pymolwiki.org/index.php/Transform_selection

 and

 PyMOLhelp rotate

 DESCRIPTION

 rotate rotates the atomic coordinates of atoms in a selection
 about an axis.  Alternatively, it modifies the matrix associated
 with a particular object or object state.

 USAGE

 rotate axis, angle [, selection [, state [, camera [, object
 [, origin ]



 On Mon, Nov 17, 2014 at 7:03 AM, Tsjerk Wassenaar tsje...@gmail.com
 wrote:

 Hey :)

 PyMOLhelp translate

 DESCRIPTION

 translate translates the atomic coordinates of atoms in a
 selection.  Alternatively, is modifies the matrix associated with
 a particular object or object-state.

 USAGE

 translate vector [, selection [, state [, camera [, object 

 ###

 Alternatively, alter_state can be used.

 Cheers,

 Tserk

 On Mon, Nov 17, 2014 at 10:42 AM, Folmer Fredslund folm...@gmail.com
 wrote:

 Hi Cacau,

 You can move objects independently of each other, but not selections
 inside objects AFAIK.

 So, you would need to *extract* or *create* new objects and then
 manipulate them with the editing mode.

 Best regards,
 Folmer

 2014-11-17 9:57 GMT+01:00 Cacau Centurion cacaucenturi...@gmail.com:

 Hi all,

 I am wondering if it is possible to move different subunits
 independently with Pymol. Can anyone let me know about it?

 Yours,
 Cacau


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Re: [PyMOL] select state not working

2014-12-05 Thread Spencer Bliven
I noticed that my response didn't go through due to the attachment being to
big. The PDB file is here:
https://dl.dropboxusercontent.com/u/41995424/4BVNAa-2Z73Aa.pdb

-Spencer

On Thu, Nov 6, 2014 at 2:44 PM, Spencer Bliven sbli...@ucsd.edu wrote:

 I hadn't heard about any plans to convert biological assemblies to mmcif
 format, although that would certainly be a logical move. As far as I know,
 only split entries will be discontinued in December. I'm not sure if even
 mmCIF has a clean solution to the problem that we would sometimes like to
 display and access multiple copies of the asymmetric unit in different
 positions. The issue is broader than just the assembly files, and it is
 also a problem when dealing with PPIs or when doing structural comparisons.

 I've attached a PDB file with two non-identical states. It was saved from
 the RCSB protein comparison tool (
 http://rcsb.org/pdb/workbench/getaligned.do?action=pw_fatcatmol=PDP:4BVNAamol=PDP:2Z73Aa).
 Of course, that doesn't mean that this use of MODEL was blessed by the
 wwPDB format committee, but it is a useful hack to save multiple objects in
 a single PDB file (and works great in Jmol).

 -Spencer


 On Thu, Nov 6, 2014 at 12:51 PM, David Hall li...@cowsandmilk.net wrote:

 I would tell you to use mmcif (especially since the structures I believe
 you are describing will no longer be available in pdb format in a month),
 but it might not solve part of your problem. I'm still not sure what PDB id
 has a chain in state 1 that does not have exactly the same internal
 coordinates as the chain in state 2 though, can you provide an example.

 On Thu, Nov 6, 2014 at 6:19 AM, Spencer Bliven sbli...@ucsd.edu wrote:

 One possible reason for this behavior would be code that assumes atom
 IDs are unique. In fact, both the ID and the state are required to uniquely
 identify an atom. This would be consistent with some other problems I've
 observed when working with multi-state objects, such as the fact that
 cartoon representation does not work on states which don't match the atoms
 of state 1. Does anyone familiar with the code know if that's the case? If
 so it's probably not a trivial fix.

 -Spencer

 On Thu, Nov 6, 2014 at 10:18 AM, Spencer Bliven sbli...@ucsd.edu
 wrote:

 Thanks for the response, David!

 You can fetch biological assemblies from the PDB using `fetch PDBID,
 type=pdb1` (or the PDB Loader Service plugin). This gives you the proper
 oligomeric state, rather than just the asymmetric unit. However, since it
 can potentially have chains from multiple asymmetric units, the chain IDs
 are not necessarily unique. The RCSB's solution to this is to put each
 asymmetric unit in a different state (arguably an abuse of the MODEL
 record, but they write the spec).

 Intra_fit won't work for me because I want to align two different
 objects. I can't use split_states because I want the whole multi-state
 object to move together, but I want to only align based on a single
 state/chain combo. Trying to do `align` on a multi-state object fails badly
 because it aligns to the average position of equivalently-named atoms in
 all states, which falls along a single line for symmetric structures. Thus
 align basically just superimposes the centers of mass, even very similar
 structures.

 I should also mention that I use most of the alignment methods
 (pair_fit, align, super, cealign, etc), so fixing the select command or
 adding selection language would be preferable to just fixing single
 commands.

 -Spencer

 On Wed, Nov 5, 2014 at 1:03 PM, David Hall li...@cowsandmilk.net
 wrote:

 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

Re: [PyMOL] sequence alignment function

2014-12-03 Thread Spencer Bliven
PyMOL includes Biopython, so I would just use their sequence aligner. For
instance:

from Bio import pairwise2 alignments = pairwise2.align.globalxx(ACCGT, ACG)

See http://biopython.org/DIST/docs/api/Bio.pairwise2-pysrc.html

-Spencer



On Wed, Dec 3, 2014 at 9:33 AM, Jordan Willis jwillis0...@gmail.com wrote:

 Hi,

 I know Pymol has a built-in sequence alignment function that ‘align’ uses
 before it does alignment. I was wondering how one could access this
 function generically for any given strings. I wanted to use this in a
 module and don’t want to rely on importing alignment modules from other
 packages if I don’t have to.

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Re: [PyMOL] wiki.pymol.org

2014-12-01 Thread Spencer Bliven
Great, I appreciate the clarification!

On Wed, Nov 26, 2014 at 5:40 PM, Thomas Holder 
thomas.hol...@schrodinger.com wrote:

 Hi Spencer,

 We have no plans to move the community wiki to the pymol.org domain.
 Schrödinger keeps wiki.pymol.org as a read-only backup mirror of
 pymolwiki.org, and it's up-to-date with sometimes a few days delay.
 Thanks for your suggestion about the sitenotice - we've put it into place.

 Cheers,
   Thomas

 On 26 Nov 2014, at 05:48, Spencer Bliven sbli...@ucsd.edu wrote:

  What's the deal with wiki.pymol.org? It looks like a mirror of
 pymolwiki.org from June 9th. Are there plans to move the community wiki
 into the pymol namespace?
 
  Since google indexes them both now, it would be nice to have a
 indication on wiki.pymol.org that the information is not fully up-to-date
 (e.g. through a sitenotice).
 
  -Spencer

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Re: [PyMOL] Problem with MacPyMOL's linalg package

2014-12-01 Thread Spencer Bliven
Thanks for the workaround. It works for me, although it will be a bit hard
to incorporate into fully portable scripts. I think I'll avoid using scipy
where possible.

-Spencer

On Wed, Nov 26, 2014 at 6:09 PM, Thomas Holder 
thomas.hol...@schrodinger.com wrote:

 Hi Spencer,

 thanks for bringing this to our attention. Since OS X 10.9 ships with
 scipy preinstalled, you can try this workaround which imports scipy from
 the system python:

 import sys
 sys.path.insert(1,
 '/System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python')
 import scipy.linalg

 Hope that helps.

 Cheers,
   Thomas

 On 25 Nov 2014, at 04:46, Spencer Bliven sbli...@ucsd.edu wrote:

  Importing scipy.linalg in MacPyMOL crashes the program for me. Probably
 the linalg module shipped with MacPyMOL is corrupt or incorrectly linked.
 I've reproduced it with MacPyMOL 1.6 and 1.7, with both X11 and aqua, and
 on Mac OS 10.9 and 10.10.
 
  I discovered this problem because importing the full pymol script repo
 crashes, due to the pyanm plugin. Maybe this will save someone a headache
 in the future.
 
  -Spencer

 --
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[PyMOL] wiki.pymol.org

2014-11-26 Thread Spencer Bliven
What's the deal with wiki.pymol.org? It looks like a mirror of pymolwiki.org
from June 9th. Are there plans to move the community wiki into the pymol
namespace?

Since google indexes them both now, it would be nice to have a indication
on wiki.pymol.org that the information is not fully up-to-date (e.g.
through a sitenotice
http://www.mediawiki.org/wiki/Manual:Interface/Sitenotice).

-Spencer
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Re: [PyMOL] Super, algorithm

2014-11-26 Thread Spencer Bliven
I would also be interested if there is any documentation about the super
algorithm and the differences to align.

-Spencer

On Fri, Nov 14, 2014 at 10:25 PM, Osvaldo Martin aloctavo...@gmail.com
wrote:

 Hi,

 Exactly which algorithm is behind the super command? How the outliers
 pairs are defined?  The is some scientific paper related to super or it is
 really an experimental idea?

 Thanks.


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[PyMOL] Problem with MacPyMOL's linalg package

2014-11-25 Thread Spencer Bliven
Importing scipy.linalg in MacPyMOL crashes the program for me. Probably the
linalg module shipped with MacPyMOL is corrupt or incorrectly linked. I've
reproduced it with MacPyMOL 1.6 and 1.7, with both X11 and aqua, and on Mac
OS 10.9 and 10.10.

I discovered this problem because importing the full pymol script repo
crashes, due to the pyanm plugin. Maybe this will save someone a headache
in the future.

-Spencer
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Re: [PyMOL] select state not working

2014-11-06 Thread Spencer Bliven
Thanks for the response, David!

You can fetch biological assemblies from the PDB using `fetch PDBID,
type=pdb1` (or the PDB Loader Service plugin). This gives you the proper
oligomeric state, rather than just the asymmetric unit. However, since it
can potentially have chains from multiple asymmetric units, the chain IDs
are not necessarily unique. The RCSB's solution to this is to put each
asymmetric unit in a different state (arguably an abuse of the MODEL
record, but they write the spec).

Intra_fit won't work for me because I want to align two different objects.
I can't use split_states because I want the whole multi-state object to
move together, but I want to only align based on a single state/chain
combo. Trying to do `align` on a multi-state object fails badly because it
aligns to the average position of equivalently-named atoms in all states,
which falls along a single line for symmetric structures. Thus align
basically just superimposes the centers of mass, even very similar
structures.

I should also mention that I use most of the alignment methods (pair_fit,
align, super, cealign, etc), so fixing the select command or adding
selection language would be preferable to just fixing single commands.

-Spencer

On Wed, Nov 5, 2014 at 1:03 PM, David Hall li...@cowsandmilk.net wrote:

 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] select state not working

2014-11-06 Thread Spencer Bliven
One possible reason for this behavior would be code that assumes atom IDs
are unique. In fact, both the ID and the state are required to uniquely
identify an atom. This would be consistent with some other problems I've
observed when working with multi-state objects, such as the fact that
cartoon representation does not work on states which don't match the atoms
of state 1. Does anyone familiar with the code know if that's the case? If
so it's probably not a trivial fix.

-Spencer

On Thu, Nov 6, 2014 at 10:18 AM, Spencer Bliven sbli...@ucsd.edu wrote:

 Thanks for the response, David!

 You can fetch biological assemblies from the PDB using `fetch PDBID,
 type=pdb1` (or the PDB Loader Service plugin). This gives you the proper
 oligomeric state, rather than just the asymmetric unit. However, since it
 can potentially have chains from multiple asymmetric units, the chain IDs
 are not necessarily unique. The RCSB's solution to this is to put each
 asymmetric unit in a different state (arguably an abuse of the MODEL
 record, but they write the spec).

 Intra_fit won't work for me because I want to align two different objects.
 I can't use split_states because I want the whole multi-state object to
 move together, but I want to only align based on a single state/chain
 combo. Trying to do `align` on a multi-state object fails badly because it
 aligns to the average position of equivalently-named atoms in all states,
 which falls along a single line for symmetric structures. Thus align
 basically just superimposes the centers of mass, even very similar
 structures.

 I should also mention that I use most of the alignment methods (pair_fit,
 align, super, cealign, etc), so fixing the select command or adding
 selection language would be preferable to just fixing single commands.

 -Spencer

 On Wed, Nov 5, 2014 at 1:03 PM, David Hall li...@cowsandmilk.net wrote:

 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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[PyMOL] select state not working

2014-11-05 Thread Spencer Bliven
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] naming of chain id

2014-09-17 Thread Spencer Bliven
Are there plans to support 4-letter chain IDs, as defined by the current
xPDB/mmCIF specification?

-Spencer

On Tue, Sep 16, 2014 at 3:36 PM, Thomas Holder 
thomas.hol...@schrodinger.com wrote:

 Hi Folmer and Yeping,

 to support upper and lower case letters, set this setting:

 PyMOL set ignore_case, off

 Cheers,
   Thomas

 On 16 Sep 2014, at 02:44, Folmer Fredslund folm...@gmail.com wrote:
  Hi Yeping Sun,
 
  Did you solve your problem?
 
  According to http://www.wwpdb.org/procedure.html#toc_4
  
  What is the maximum number of chain IDs in a file?
 
  Up to 62 chains can be included in the PDB entry. Upper case letters and
 numbers (0-9) should be used first for chain IDs. Lower case letters should
 be used only after all upper letters and numbers have been used. Symbols
 should never be used for chain IDs.
 
  you can use numbers and also small letters in the PDB file format.
 
 
 
  I don't know if PyMOL will let you do this, though.
 
  Regards,
 
  Folmer
 
 
  2014-09-02 10:41 GMT+02:00 sunyeping sunyep...@aliyun.com:
  I have a protein which contains 32 chains. By using A-Z can only name 26
 chains. Can I use expression containing two character such as A1, AB, etc.
 to as chain id? Will this change the format of the pdb files?
 
  Yeping Sun
 
  Institute of Microbiology, Chinese Academy of Sciences
 
  --
  Folmer Fredslund

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Re: [PyMOL] how to get the surface representation look better?

2014-08-27 Thread Spencer Bliven
Yeping–

You have to make a new object with the desired atoms. Try 'help extract' or
'help create'.

Also, dropbox lets you share a link to any file. The file is visible at
https://www.dropbox.com/s/j2lkd2lvu0eb2l1/surface1.tif?dl=0. I would change
your password.

-Spencer


On Wed, Aug 27, 2014 at 6:00 AM, sunyeping sunyep...@aliyun.com wrote:

 Dear all,

 Please see the figure (surface1.tif) I deposited in dropbox (
 https://www.dropbox.com/home, Account sunyep...@aliyun.com, Password:
 pymolusers). A is taken from a literature, and B is prepared by myself. In
 A, the stick representation of the side chains of residues P3, D156, R97,
 etc., is wraped around in a representation that looks like having a
 transparent stereoscopic volume. I guess this represnetation is some kind
 of surface. However, in B, although I show the surface represnetation for
 residue E63, it looks like a curved surface locate aside E63 and doesn't
 wrap around the side chain of E63 as in A. Could anyone tell me how the
 effect of the surface representation (if I am correct) was prepared?

 Best regards.

 Yeping Sun

 Institute of Microbiology, Chinese Academy of Sciences



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Re: [PyMOL] symmetry mates

2014-08-27 Thread Spencer Bliven
Sometimes it is easier to see the overall structure when looking at a
single unit cell rather than the symmetry mates within a certain distance.
You might want to try the supercell
http://www.pymolwiki.org/index.php/Supercell script. Otherwise I tend to
generate symmetry mates multiple times and then hide or delete the ones
that don't match the expected biological assembly.

-Spencer


On Fri, Aug 15, 2014 at 9:26 AM, sunyeping sunyep...@aliyun.com wrote:

 Dear pymol users,

 I want to operate a structure whose crystal structure has one molecule in
 one asymmetry unit. I try to display its  polymer. I loaded the structure
 and used generate command in the pymol GUI interface:
  Ageneratesymmetry mates4A, and then many copies of this molecure
 appeared but in a quite disoder pattern. According to the paper that
 published this structure, it is a polymer arranged in a linear pattern.
 Could you tell me how can I display this linear polymer? Thanks in advance.

 Yeping Sun

 Institute of Microbiology, Chinese Academy of Sciences



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Re: [PyMOL] Detecting Plugins menu

2014-04-22 Thread Spencer Bliven
I just found the pymol._ext_gui property, which seems to be None if X11 is
off and a positive number if X11 is present. Seeing as it's a private
variable, is it ok to use this to check for X11 presence?

-Spencer


On Thu, Apr 17, 2014 at 10:21 AM, Spencer Bliven sbli...@ucsd.edu wrote:

 Here's what I'm currently using. It seems to work so far. Looking through
 the PyMol binary I see about 50 possible names though, so it would be nice
 if there were a built-in way to detect X11.

 def hasTk():
  Make an educated guess as to whether Tk is installed,
 hopefully without triggering any installation on Macs
 
 hasTk = True
 if sys.platform==darwin: #Mac
 # Hack: check the path for entries containing 'X11'
 hasTk = any([ X11 in p.upper() for p in sys.path])

 if hasTk:
 try:
 import Tkinter
 except ImportError:
 hasTk = False

 return hasTk


 On Mon, Apr 14, 2014 at 10:46 AM, Spencer Bliven sbli...@ucsd.edu wrote:

 I'm working on a plugin with a command line interface and a light-weight
 tk interface through the plugins menu. This works fine on Linux, Windows,
 and open-source Mac builds, but not on MacPyMol.app. Importing Tkinter
 causes PyMol to quit with a prompt to install X11 (but not an ImportError,
 as far as I can tell). If X11 is installed there are no errors, but there
 is not a plugins menu, so I'd rather not bother loading and initializing
 the Tk interface to the plugin.

 How can I detect whether Tk is available?

 I can think of two approaches, but haven't figured out the correct
 commands for either. (1) Check the name that pymol was started with.
 MacPyMol.app does not have Tk, while PyMOLX11Hybrid.app does.  I'm not
 sure how to get the name (maybe could be guessed from sys.path?), and I
 know there are a lot more variants than those two available. (2) Check for
 the existence of the plugins menu. But this would have to be done without
 importing Tk and triggering the X11 check.

 Is there a simple way to do this I'm overlooking?

 Thanks,
 -Spencer



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Re: [PyMOL] Detecting Plugins menu

2014-04-17 Thread Spencer Bliven
Here's what I'm currently using. It seems to work so far. Looking through
the PyMol binary I see about 50 possible names though, so it would be nice
if there were a built-in way to detect X11.

def hasTk():
 Make an educated guess as to whether Tk is installed,
hopefully without triggering any installation on Macs

hasTk = True
if sys.platform==darwin: #Mac
# Hack: check the path for entries containing 'X11'
hasTk = any([ X11 in p.upper() for p in sys.path])

if hasTk:
try:
import Tkinter
except ImportError:
hasTk = False

return hasTk


On Mon, Apr 14, 2014 at 10:46 AM, Spencer Bliven sbli...@ucsd.edu wrote:

 I'm working on a plugin with a command line interface and a light-weight
 tk interface through the plugins menu. This works fine on Linux, Windows,
 and open-source Mac builds, but not on MacPyMol.app. Importing Tkinter
 causes PyMol to quit with a prompt to install X11 (but not an ImportError,
 as far as I can tell). If X11 is installed there are no errors, but there
 is not a plugins menu, so I'd rather not bother loading and initializing
 the Tk interface to the plugin.

 How can I detect whether Tk is available?

 I can think of two approaches, but haven't figured out the correct
 commands for either. (1) Check the name that pymol was started with.
 MacPyMol.app does not have Tk, while PyMOLX11Hybrid.app does.  I'm not
 sure how to get the name (maybe could be guessed from sys.path?), and I
 know there are a lot more variants than those two available. (2) Check for
 the existence of the plugins menu. But this would have to be done without
 importing Tk and triggering the X11 check.

 Is there a simple way to do this I'm overlooking?

 Thanks,
 -Spencer

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[PyMOL] Detecting Plugins menu

2014-04-14 Thread Spencer Bliven
I'm working on a plugin with a command line interface and a light-weight tk
interface through the plugins menu. This works fine on Linux, Windows, and
open-source Mac builds, but not on MacPyMol.app. Importing Tkinter causes
PyMol to quit with a prompt to install X11 (but not an ImportError, as far
as I can tell). If X11 is installed there are no errors, but there is not a
plugins menu, so I'd rather not bother loading and initializing the Tk
interface to the plugin.

How can I detect whether Tk is available?

I can think of two approaches, but haven't figured out the correct commands
for either. (1) Check the name that pymol was started with. MacPyMol.app
does not have Tk, while PyMOLX11Hybrid.app does.  I'm not sure how to get
the name (maybe could be guessed from sys.path?), and I know there are a
lot more variants than those two available. (2) Check for the existence of
the plugins menu. But this would have to be done without importing Tk and
triggering the X11 check.

Is there a simple way to do this I'm overlooking?

Thanks,
-Spencer
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Re: [PyMOL] manual superposition with pymol--and another question

2014-04-08 Thread Spencer Bliven
Suzanne,

There isn't an easy way to do this, as far as I know. `pair_fit` can be
used to do a superposition based on an arbitrary alignment, but it is very
tedious to specify each aligned pair individually, and it's hard to modify
the alignment.

I've used NCBI's Cn3D program for detailed manual alignments, as it has a
good alignment editor and can show the superpositions internally after each
modification. However, it doesn't output two-model pdb files like most of
the structure alignment tools (eg pdb.org's structure comparison tool).
Thus you still might have to write an arduous pair_fit command (or a python
script to parse cn3 file) if you want to get it into pymol for nice
graphics. Cn3D has a confusing interface, so if you want to try it out I
can send you my notes on creating alignments off-list.

-Spencer




On Mon, Apr 7, 2014 at 9:11 PM, Lapolla, Suzanne M (HSC) 
suzanne-lapo...@ouhsc.edu wrote:

 This worked--thanks. I have another ? that may have been addressed
 previously but do not know the answer.  Is there a way to do an alignment
 (or maybe docking is a better word) on two structures/selections and input
 a constraint for that alignment? For example, i am working on generating a
 model RE a dimer of two molecules, and I have some data suggesting a range
 of distances between certain residues of the selection. Is there a way to
 input that data into Pymol before it completes the alignment, or do I need
 to use other docking programs to do that? Hope that makes sense.  Thanks.
 
 From: Lapolla, Suzanne M (HSC)
 Sent: Friday, April 04, 2014 5:11 PM
 To: Thomas Holder
 Subject: RE: [PyMOL] manual superposition with pymol

 Thank you! I will try this and get back to you.
 
 From: Thomas Holder [thomas.hol...@schrodinger.com]
 Sent: Friday, April 04, 2014 3:16 PM
 To: Lapolla, Suzanne M (HSC)
 Cc: pymol-users@lists.sourceforge.net
 Subject: Re: [PyMOL] manual superposition with pymol

 Hi Suzanne,

 looks like you only deprotected the CA atoms. If you have this as a named
 selection, try A  modify  complete  molecules and deprotect again. Or
 type:

 PyMOL deprotect bymol (sele)

 Instead of working with one object and protecting/deprotecting of subsets
 of atoms, I suggest to extract the selection that you want to move to its
 own object. That's usually easier to handle.

 Cheers,
   Thomas

 On 04 Apr 2014, at 13:38, Lapolla, Suzanne M (HSC) 
 suzanne-lapo...@ouhsc.edu wrote:

  I am using pymol 1.3 and having trouble with doing manual superposition
 with my structures. I am able to download my structures, select the portion
 I want to move manually and, after deprotecting it using the action menu
 move it using the shift-mouse editing command. When I do this with my
 selection shown in cartoon mode, things look great, but then when i switch
 to show my selected residues as  sticks,  the sticks become huge --they
  get bigger  and/or  smaller as I move the structure.  Ideas on what I may
 be doing wrong? Hope this makes sense. Thanks, Suzanne

 --
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 PyMOL Developer
 Schrödinger, Inc.



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[PyMOL] UCSD pymol workshop

2013-11-20 Thread Spencer Bliven
We've been discussing putting together a PyMol workshop for the UCSD
undergrad bioinformatics club (http://ubic.ucsd.edu/). I wanted to ping
this list and see if anyone in the San Diego area would be interested,
either as attendants or as an instructor or assistant.

I would like hearing if anyone has resources they found particularly useful
when learning to use pymol - tutorials, slides, etc.

Thanks!

Spencer
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Re: [PyMOL] new metals keyword

2013-09-10 Thread Spencer Bliven
Excellent! I had previously been using things like 'not elem c+n+o+h+s' in
my scripts. Using 'metal' will match my intent much better. 'Sidechain'
will be appreciated as well.

I would suggest 'ligand' and 'ptm' selectors to distinguish nonbonded and
covalently bonded hetatms. Although I'm not sure how non-standard amino
acids would fit in to those terms.

-Spencer


On Sun, Sep 8, 2013 at 4:54 AM, Thomas Holder thomas.hol...@schrodinger.com
 wrote:

 Greetings,

 we added backbone, bb. and sidechain, sc. keywords (SVN rev
 4041). They select polymer (protein and nucleic acid) backbone and
 sidechain atoms, based on PDB atom names. The internal GUI menu items
 with main chain and side chain use the new keyword, which adds
 nucleic acid support for those since they previously only considered
 protein atom names.

 Cheers,
   Thomas

 Thomas Holder wrote, On 08/13/13 17:56:
  Greetings,
 
  this is a quick announcement that we added the metals keyword to the
  selection language (SVN code revision 4039).
 
  Since PyMOL's selection language is one of the powerful core features
  that make so many complex tasks so easy, we plan to add more useful
  keywords and operators. For example selecting by x,y,z coordinates, or
  selecting by secondary structure element. If you have a good idea for a
  new keyword or operator, please file a feature request on sourceforge.
 
  Cheers,
Thomas

 --
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 PyMOL Developer
 Schrödinger Contractor


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