Re: [PyMOL] making a plane

[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

[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

[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-
> From: pymol-users-requ...@lists.sourceforge.net [mailto:
> pymol-users-requ...@lists.sourceforge.net]
> Sent: Tuesday, October 25, 2016 4:50 PM
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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"
> 
> Message-ID:
>  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

[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

[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

[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

[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

[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  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

[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 
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

[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]

[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&opt=3&bionumber=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] ignore_case in next PyMOL version

[Spencer Bliven]

Restoring the old ignore_case behaviour seems pragmatic.

Can you explain the difference with the new ignore_case_chain setting? Is
the idea that we would want case-insensitive element symbols
(ignore_case=off) but case-sensitive chains (ignore_case_chain=on)? Are
there other places where case is important in the selections or structures
(e.g. insertion codes)?

-Spencer

On Tue, Feb 9, 2016 at 4:18 PM, Thomas Holder  wrote:

> Hi all,
>
> Quick update on the "ignore_case" issue:
>
> - ignore_case=on default restored in PyMOL 1.8.0.5 and latest SVN
> - latest SVN introduces new "ignore_case_chain" setting
>
> Cheers,
>   Thomas
>
> On 02 Feb 2016, at 14:38, Thomas Holder 
> wrote:
>
> > Greetings,
> >
> > I like to let you know that we plan another change for the "ignore_case"
> setting behavior. We want to restore the old default (ignore_case=on) and
> introduce a new setting "ignore_case_chain=off", which will affect the
> "chain" and "segi" identifiers.
> >
> > As you may (or should) know, we changed the default of the "ignore_case"
> setting in PyMOL 1.8 from "on" to "off". The rationale was to have default
> settings which properly support PDB files which mix upper and lower case
> chain identifiers (e.g. 3a0b). Users who still prefer a case insensitive
> selection language can put a "set ignore_case" line in their pymolrc file.
> >
> > However, we now realized that this is not very practical. One reason is
> that too many scripts and code samples use lower case resn and name
> selections, fixing those historic resources is often not feasible or
> desirable. Another reason is that PyMOL inconsistently stores element
> symbols, for example chlorine is "CL" when loaded from a PDB file, but "Cl"
> when loaded from SDF. The logical conclusion is that PyMOL should handle
> chain and segi different from resn, name and elem.
> >
> > See also: http://pymolwiki.org/index.php/ignore_case
> >
> > Any kind of feedback regarding the planned change will be appreciated.
> >
> > Cheers,
> >  Thomas
>
> --
> Thomas Holder
> PyMOL Principal Developer
> Schrödinger, Inc.
>
>
>
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Re: [PyMOL] regarding show_bumps

[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  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 
> 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  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] regarding show_bumps

[Spencer Bliven]

Priyan–

You can use the 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  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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Re: [PyMOL] show the long helix filament

[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

[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

[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"

[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 
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 
> 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
>>>
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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] using "bymol" in combination with "within"

[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] on axis of the subunit

[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] on PDB

[Spencer Bliven]

Smith–

The code is intended to be saved to a file ("save_transformed.py") and then
loaded into pymol using `run /path/to/save_transformed.py`. There's some
general info on running pymol scripts: Simple_Scripting
 Running_Scripts


The script defines a new command which can be run e.g. `save_transformed
, `. You don't have to replace anything in the script
yourself.

Note that the save_transformed command modifies the object it's run on, so
you might want to run it on a backup copy by first calling `create
_backup, `

-Spencer

On Thu, Nov 26, 2015 at 8:33 AM, Smith Liu  wrote:

> Dear All,
>
> For get view, we get something like
>
>  set_view (\
>0.999876618,   -0.000452542,   -0.015699286,\
>0.000446742,0.99821,   -0.000372844,\
>0.015699454,0.000365782,0.999876678,\
>0.0,0.0, -150.258514404,\
>11.842411041,   20.648729324,8.775371552,\
>118.464958191,  182.052062988,0.0 )
>
> For save trasformed pdb file, we need sonething like
>
> ttt = [m[0], m[1], m[2], 0.0,
>m[3], m[4], m[5], 0.0,
>m[6], m[7], m[8], 0.0,
>0.0,   0.0,  0.0, 1.0]
> Will you please show me how to replace m[0], m[1] from what we get by
> get_view? Which item is which item?
>
> In addition, for the save_transformed.py, the last sentence is
> "cmd.extend('save_transformed',save_transformed)". Should we replace the
> second save_transformed with something, for example *.pdb? Ortherwise how
> to get the output modified PDB?
>
>
> I am looking forward to getting a reply from you.
>
> Smith
>
>
>
>
>
>
>
>
>
> At 2015-11-26 14:24:15, "Andreas Forster"  wrote:
>
> http://www.pymolwiki.org/index.php/Modeling_and_Editing_Structures
>
>
> Andreas
>
>
> On Thu, Nov 26, 2015 at 2:24 AM, Smith Liu  wrote:
>
>> Dear Shane,
>>
>> get_view is a nice command. Is any way to change the original PDB based
>> on what we get by set_view to get the new pdb?
>>
>> Smith
>>
>>
>>
>>
>>
>>
>> At 2015-11-26 03:54:32, "Shane Caldwell" 
>> wrote:
>>
>> Hi Smith,
>>
>> You can type
>>
>> >get_view
>>
>> and copy the output into a txt file for later use. The output set_view
>> command will return the window to the same camera settings
>>
>> Shane
>>
>> Shane Caldwell
>> McGill University
>>
>> On Tue, 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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>>>
>>
>>
>>
>>
>>
>>
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>>
>
>
>
>
>
>
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Re: [PyMOL] Is it possible to install PyMOL .app on Mac?

[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

[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

[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

[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)

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

[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

[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

[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  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

[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

[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  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

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

[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  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  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:
> >>
> >> PyMOL>iterate 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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[PyMOL] Interleaved atoms when creating from two objects

[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:

PyMOL>iterate 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

[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  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] select state not working

[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  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_fatcat&mol=PDP:4BVNAa&mol=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  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  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 
>>> 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 
>>>> 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

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

[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  wrote:

> also http://www.pymolwiki.org/index.php/Transform_selection
>
> and
>
> PyMOL>help rotate
>
> DESCRIPTION
>
> "rotate" rotates the atomic coordinates of atoms in a selection
> about an axis.  Alternatively, it modifies the matrix associated
> with a particular object or object state.
>
> USAGE
>
> rotate axis, angle [, selection [, state [, camera [, object
> [, origin ]
>
>
>
> On Mon, Nov 17, 2014 at 7:03 AM, Tsjerk Wassenaar 
> wrote:
>
>> Hey :)
>>
>> PyMOL>help 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 
>> 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 :
>>>
 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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>>>
>>>
>>>
>>> --
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>>>
>>>
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>>
>>
>>
>> --
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>>
>>
>>
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Re: [PyMOL] sequence alignment function

[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  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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>
> Research Associate @Schief Lab
> The Scripps Research Institute
> 10550 N. Torrey Pines Rd.
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> Phone: 1-858-784-1000 ext: 43377
>
>
>
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Re: [PyMOL] Problem with MacPyMOL's linalg package

[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  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
>
> --
> Thomas Holder
> PyMOL Principal Developer
> Schrödinger, Inc.
>
>
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Re: [PyMOL] wiki.pymol.org

[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  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
>
> --
> Thomas Holder
> PyMOL Principal Developer
> Schrödinger, Inc.
>
>
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Re: [PyMOL] Super, algorithm

[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 
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] wiki.pymol.org

[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
).

-Spencer
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[PyMOL] Problem with MacPyMOL's linalg package

[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

[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  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  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  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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>>
>>
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Re: [PyMOL] select state not working

[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  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  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

[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

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

[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  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 :
> > 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
>
> --
> Thomas Holder
> PyMOL Developer
> Schrödinger, Inc.
>
>
>
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Re: [PyMOL] symmetry mates

[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
 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  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:
>  A>generate>symmetry mates>4A, 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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>
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Re: [PyMOL] how to get the surface representation look better?

[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  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] Detecting Plugins menu

[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  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  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

[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  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

[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

[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
>
> --
> Thomas Holder
> PyMOL Developer
> Schrödinger, Inc.
>
>
>
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[PyMOL] UCSD pymol workshop

[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

[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  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
>
> --
> Thomas Holder
> PyMOL Developer
> Schrödinger Contractor
>
>
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Re: [PyMOL] Fwd: Script writing

[Spencer Bliven]

James,

If the CA position is acceptable as the residue coordinate (as assumed in
Jason's answer), then you don't need to bother with pseudoatoms. Here's the
easiest way to display all the distances for a figure:

select resn LYS and n. CA
dist (sele), (sele)

Aside: this doesn't work for me as `dist sele, sele`. Anyone know why? Is
that a bug or a feature?

If you need to print the individual distances rather than display them,
this gets slightly harder :

atms=[]
iterate resn LYS and n. CA, atms.append( (model,ID,resi) )
# print residue IDs and CA-CA distance
print "\n".join([ "%s, %s, %s" % ( atms[i][2],atms[j][2],
cmd.distance("dist","%s and ID %s" % atms[i][:2], "%s and ID
%s"%atms[j][:2])) for i in xrange(1,len(atms)) for j in xrange(i)])


BTW, are you studying crosslinking?

-Spencer


On Thu, Aug 22, 2013 at 3:57 PM, Jason Vertrees <
jason.vertr...@schrodinger.com> wrote:

> Hi James,
>
> It could look something like this:
>
> # for_rutley.py
>
> # fetch a protein
> cmd.fetch("1rx1", async=0)
>
> # make a blank list
> l=[]
>
> # iterate over all lysine's alpha carbons
> cmd.iterate_state(1, "n. CA and resn lys", "l.append((x,y,z))")
>
> # set a counter to 0 for controlling unique names
> p=0
>
> # iterate over all coordinates and create a
> # pseudoatom at each lysine's alpha carbon
> for ca in l:
> p+=1
> cmd.pseudoatom("pseudo%s" % (p), pos=ca)
>
> # measure the pairwise distances across all pseudoatoms just created
> cmd.distance("/pseudo*", "/pseudo*")
>
> I bet someone like Thomas or Tsjerk could code this in half the number of
> lines, but this should be a starting point.
>
> Cheers,
>
> -- Jason
>
>
> On Thu, Aug 22, 2013 at 9:55 AM, James Rutley  wrote:
>
>>
>>
>> -- Forwarded message --
>> From: James Rutley 
>> Date: 22 August 2013 14:50
>> Subject: Script writing
>> To: pymol-users@lists.sourceforge.net
>>
>>
>> Hi,
>>
>> I am new to Pymol and programming. What's the best way to approach
>> creating a script that does the following:
>>
>> [image: Inline images 3]
>>
>> Thanks,
>>
>> James,
>> UCL
>>
>>
>>
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Re: [PyMOL] Passing parameters to pymol aliases

[Spencer Bliven]

Thanks, Troels. The import/extend pattern worked for me. Specifically,
lines like

import color_obj
cmd.extend("co",color_obj.color_obj)

Thanks!


On Thu, May 16, 2013 at 7:38 AM, Troels Emtekær Linnet wrote:

> In your .pymolrc, you probably just import the file/module, and then issue
> an extend command to the module.function with the wanted new shortcut name
> Den 16/05/2013 01.29 skrev "Spencer Bliven" :
>
>> I have a number of python scripts that I use regularly. I would like to
>> create shortcuts for these in my .pymolrc. For instance,
>>
>> alias co, color_obj
>>
>> Unfortunately, aliases cannot take arguments (using MacPyMOL 1.3). Is
>> there a way to create aliases for commands that require arguments? I could
>> modify the cmd.extend() call in each python script, but I'd rather do it
>> from my .pymolrc since some scripts are shared.
>>
>> Thanks!
>> -Spencer
>>
>>
>>
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[PyMOL] Passing parameters to pymol aliases

[Spencer Bliven]

I have a number of python scripts that I use regularly. I would like to
create shortcuts for these in my .pymolrc. For instance,

alias co, color_obj

Unfortunately, aliases cannot take arguments (using MacPyMOL 1.3). Is there
a way to create aliases for commands that require arguments? I could modify
the cmd.extend() call in each python script, but I'd rather do it from my
.pymolrc since some scripts are shared.

Thanks!
-Spencer
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