Re: [PyMOL] reproduce special vrml-output

[Sampson, Jared]

Hi Anke -

Try `as surface`, which is the equivalent of `hide everything; show surface`. 

Hope that helps.

Cheers,
Jared

Sent from my iPhone

> On May 19, 2017, at 6:43 AM, Anke Schultz  
> wrote:
> 
> Hi Thomas,
> 
> thanks for the explanation on adjusting view, it works fine. This leaves 
> me with one question: How do I get a .wrl-file containing only faces? 
> Using "show surface" and setting surface_type to 2 (triangles) gives me 
> sticks and spheres in the .wrl-file (sticks as edges, spheres at the 
> ends of every edge).
> 
> Cheers,
> 
> Anke
> 
> 
>> Am 19.05.2017 um 10:38 schrieb Thomas Holder:
>> Hi Anke,
>> 
>> The obvious difference I can see in your two samples is that the first one 
>> contains sticks and spheres representations, and the second one only has 
>> faces (could be surface or cartoon).
>> 
>> The other difference is the viewport z position (zoom distance), which is 
>> 0.0 in the second sample. This can be set as follows before exporting the 
>> file (note that the molecule might not be visible anymore, it could be 
>> behind the camera):
>> 
>> view = list(cmd.get_view())
>> view[11] = 0.0
>> cmd.set_view(view)
>> 
>> Hope that helps.
>> 
>> Cheers,
>>   Thomas
>> 
>>> On May 17, 2017, at 4:27 PM, Anke Schultz  
>>> wrote:
>>> 
>>> Hi all,
>>> 
>>> I've been experimenting with exporting surface meshes as .wrl-files. I 
>>> played with the geometry_export_mode setting and the set_view() options, 
>>> since I wanted to get the surface's coordinates corresponding to the atom's 
>>> coordinates of the sd-file I imported to pymol initially. I realized that 
>>> by exporting .wrl-format I got the camera-view instead of the "real" 
>>> coordinates as long as I left everything else on default. This resulted in 
>>> a shift between atom- and surface-coordinates.
>>> 
>>> While playing around to align camera and reality, I somehow managed to 
>>> change the way my .wrl-file looked in the end and it seems to be exactly 
>>> what I was looking for. I have tried for two days now, but unfortunately I 
>>> can't reproduce my steps leading to this special .wrl-file.
>>> 
>>> This is (part of) a .wrl-file without changing default settings:
>>> ###
>>> #VRML V2.0 utf8
>>> 
>>> Viewpoint {
>>>  position 0 0 20.39730644
>>>  orientation 1 0 0 0
>>>  description "Z view"
>>>  fieldOfView 0.465421
>>> }
>>> DirectionalLight {
>>>  direction -0.348155 -0.348155   -0.870
>>> }
>>> NavigationInfo {
>>>  headlight TRUE
>>>  type "EXAMINE"
>>> }
>>> Transform {
>>>  translation -1.820169 2.166291 -3.211221
>>>  rotation -0.199343 0.00 0.979930 2.401556
>>>  children [
>>>   Shape {
>>>geometry Cylinder {
>>> radius 0.024352
>>> height 0.139351
>>> bottom FALSE
>>> topFALSE
>>>}
>>>appearance Appearance {
>>>material Material { diffuseColor 0.9000 0.9000 0.9000
>>>specularColor 0.8 0.8 0.8
>>>shininess 0.8 }
>>>}
>>>   }
>>>   Transform {
>>>translation 0.0 0.069676 0.0
>>>children Shape {
>>> geometry Sphere { radius 0.024352 }
>>> appearance Appearance {
>>>material Material { diffuseColor 0.9000 0.9000 0.9000
>>>specularColor 0.8 0.8 0.8
>>>shininess 0.8 }
>>> }
>>>}
>>>   }
>>>   Transform {
>>>translation 0.0 -0.069676 0.0
>>>children Shape {
>>> geometry Sphere { radius 0.024352 }
>>> appearance Appearance {
>>>material Material { diffuseColor 0.9000 0.9000 0.9000
>>>specularColor 0.8 0.8 0.8
>>>shininess 0.8 }
>>> }
>>>}
>>>   }
>>>  ]
>>> }
>>> Transform {
>>>  translation -1.906664 2.148911 -3.187284
>>>  rotation 0.635566 0.00 0.772046 0.994256
>>> [...]
>>> ###
>>> 
>>> And this is (part of) the special .wrl-file I mysteriously created:
>>> 
>>> ###
>>> #VRML V2.0 utf8
>>> 
>>> Viewpoint {
>>>  position 0 0 -0.
>>>  orientation 1 0 0 0
>>>  description "Z view"
>>>  fieldOfView 0.465421
>>> }
>>> DirectionalLight {
>>>  direction -0.348155 -0.348155   -0.870
>>> }
>>> NavigationInfo {
>>>  headlight TRUE
>>>  type "EXAMINE"
>>> }
>>> Shape {
>>>  appearance Appearance {
>>>   material Material { diffuseColor 1.0 1.0 1.0 }
>>>  }
>>>  geometry IndexedFaceSet {
>>>   coord Coordinate {
>>>point [
>>> 1.121935 1.360173 -0.410155,
>>> 1.840800 1.307029 -0.904629,
>>> 1.445710 1.051540 -1.083943,
>>> 1.301289 0.550209 -1.380068,
>>> 1.445710 1.051540 -1.083943,
>>> 1.840800 1.307029 -0.904629,
>>> 2.165471 0.781700 -1.754629,
>>> 1.301289 0.550209 -1.380068,
>>> 1.840800 1.307029 -0.904629,
>>> 2.693056 1.515260 -1.343787,
>>> 2.165471 0.781700 -1.754629,
>>> 1.840800 1.307029 -0.904629,
>>> [...]
>>> ###

Re: [PyMOL] Pseudoatom for a cavity

[Sampson, Jared M.]

Hi Kanika -

You can get more information on the wiki: 
https://pymolwiki.org/index.php/Pseudoatom.

To answer your specific questions, to make a pseudoatom between the two 
terminal Ns of Arg 100 on chain A of myobj:

```
pseudoatom my_ps1, myobj and chain A and resi 100 and name NH1+NH2
```

and to place a pseudoatom at a specific XYZ coordinate, pass the `pos` 
parameter with a 3-tuple of floats:

```
pseudoatom my_ps2, pos=[1.0, 2.0, 3.0]
```

Hope that helps.

Cheers,
Jared


On Jan 26, 2017, at 8:58 AM, kanika sharma 
mailto:ksharma...@gmail.com>> wrote:



Dear PyMol Users,

​I asked this question but no body replied so I am trying again. ​

I am struggling here two things.
1). I want to place a pseudo
​ ​
atom in the charge centre of a non aromatic residue, like arginine.
2). Is it possible to place
​a
 pseudo
​ ​
atom in the centre of a cavity in the protein? I am thinking how can I define 
the co ordinates of the position where I wan t to place the pseudo
​ ​
atom?

​Thanks ​

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[PyMOL] New plugin: PyMOLProbity

[Sampson, Jared M.]

Dear PyMOL Users,

I am pleased to introduce a new plugin called 
PyMOLProbity which allows a PyMOL 
user to visualize MolProbity-style structural validation data directly in a 
PyMOL session. The programs Reduce, Flipkin, and Probe from the well-known 
MolProbity software package allow 
generation of data in "kinemage" (kinetic image) format to illustrate atom-atom 
contacts (dots) and clashes (spikes), and the new plugin now makes it possible 
to utilize the same programs to produce similar results in PyMOL scenes.

I have put together a page on the PyMOL 
Wiki with a brief summary of its 
features and basic how-to information.  (Please note that the MolProbity 
executables are only available for Linux/MacOS, so PyMOLProbity isn't yet 
useful on Windows.)

My work on this plugin was supported by the Warren L. DeLano Memorial PyMOL 
Open-Source Fellowship.  I would like once again to thank Schrödinger for the 
opportunity to work on this project, and in particular would like to thank the 
PyMOL developers for their support and feedback along the way.

I hope many of you will find it useful.  If you come across any bugs or have 
any feature requests or other suggestions, please feel free to email me 
directly or create a new 
issue on Github.

Happy PyMOLing!

Cheers,
Jared
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Re: [PyMOL] pymol in pthyon get_wizard() problems

[Sampson, Jared M.]

Hi Tim - It seems to me that cmd.get_wizard() needs some argument to be passed 
to it, because right now that function is returning `None`.  This explains the 
error, which states you're trying to call .set_dep() of a `None` object.

Hope that helps.

Cheers,
Jared

On Oct 11, 2016, at 2:48 PM, Timothy Craig 
mailto:utimcr...@gmail.com>> wrote:

Hello,
  I'm trying to adapt this script in python to do a variety of different 
mutations from a csv file using this previous message as a template.

https://sourceforge.net/p/pymol/mailman/message/11671708/

I'm a python novice so please excuse me if this is something simple. Here is a 
line that I have in my script that is giving me an error, which is now quite 
long so I don't want to post it all here now:
---

pymol.cmd.get_wizard().set_dep("dep")

error:

Error: unable to get setting type.

Traceback (most recent call last):

  File "pngCSVmutate.py", line 141, in 

pymol.cmd.get_wizard().set_dep("dep")

AttributeError: 'NoneType' object has no attribute 'set_dep'



It seems like something needs to go in the parentheses for get_wizard() since 
that's where the NoneType is coming from.  Sadly there is no pymol wiki page on 
get_wizard
 so I'm not sure where to look for the answer.  Does anyone have an idea or an 
example of the proper use of get_wizard() in python?
Thanks in advance for your help,
-Tim

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Re: [PyMOL] 3D printing

[Sampson, Jared M.]

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] VRML export

[Sampson, Jared M.]

Hi Paul - I'm not too familiar with 3D printing, so not sure if this will help 
you or not.  But if all you need is to have extra cylinders in your output wrl 
file, you could add them using either CGO or distance objects directly within 
PyMOL.

https://pymolwiki.org/index.php/Distance
https://pymolwiki.org/index.php/CGOCylinder

Cheers,
Jared



On Sep 23, 2016, at 4:18 PM, Paul Paukstelis 
mailto:shocksofmig...@gmail.com>> wrote:

Thanks, Jared.

I did ultimately find it there. Looks like what I was shooting for isn't likely 
to be very straightforward. From what I can tell, it doesn't seem that any of 
the atom information gets passed into RayRender.

--p

On 09/23/2016 12:34 PM, Sampson, Jared M. wrote:
Hi Paul -

The relevant function used for VRML export is RayRenderVRML2() in 
layer1/Ray.cpp.

Cheers,

Jared

On Sep 22, 2016, at 11:43 AM, Paul Paukstelis 
mailto:shocksofmig...@gmail.com>> wrote:

Greetings,

I've started playing with 3D printing some ball-and-stick models
(primarily nucleic acids). I've worked up some Blender scripts to enable
automatic pinning (e.g. add a small pin to cylinder of the O3'-P bond
and a correspond hole in the phosphate sphere), however, I'm trying to
further decrease the amount of user input needed in Blender to
ultimately export the model parts for printing. One thing that would be
really useful would be to define some custom child nodes in the VRML
output (atom names for example) and subsequently input that into Blender
as custom properties. Could someone point me to the most relevant pymol
files responsible for VRML output? I did some quick fgrep'ing and didn't
find too much that was of use. Blender side was pretty easy to
accomplish so far.

Thanks,

--paul

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Re: [PyMOL] VRML export

[Sampson, Jared M.]

Hi Paul - 

The relevant function used for VRML export is RayRenderVRML2() in 
layer1/Ray.cpp.

Cheers,

Jared

> On Sep 22, 2016, at 11:43 AM, Paul Paukstelis  
> wrote:
> 
> Greetings,
> 
> I've started playing with 3D printing some ball-and-stick models 
> (primarily nucleic acids). I've worked up some Blender scripts to enable 
> automatic pinning (e.g. add a small pin to cylinder of the O3'-P bond 
> and a correspond hole in the phosphate sphere), however, I'm trying to 
> further decrease the amount of user input needed in Blender to 
> ultimately export the model parts for printing. One thing that would be 
> really useful would be to define some custom child nodes in the VRML 
> output (atom names for example) and subsequently input that into Blender 
> as custom properties. Could someone point me to the most relevant pymol 
> files responsible for VRML output? I did some quick fgrep'ing and didn't 
> find too much that was of use. Blender side was pretty easy to 
> accomplish so far.
> 
> Thanks,
> 
> --paul
> 
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Re: [PyMOL] Session scene compatibility with MacPymol?

[Sampson, Jared M.]

Hi Paul -

I'm a little late on this thread, but thought I'd add my 2¢.  Probably the 
easiest way get around this issue (as you realize) is probably to save a 
1.7.4.5-compatible PSE file.  But, for the adventurous, there is another way:

With a small effort (and the willingness to use the command line), your 
students with Macs can replace the older Educational build of MacPyMOL with a 
current version of Open Source PyMOL for free using the command line package 
manager, Homebrew.  They just need to open up Terminal.app and 
type the following 3 commands:


# Install Homebrew (run the command below, which downloads the installer, and 
follow the prompts)
/usr/bin/ruby -e "$(curl -fsSL 
https://raw.githubusercontent.com/Homebrew/install/master/install)"

# Install XQuartz
brew install Caskroom/cask/xquartz

# Install PyMOL
brew install pymol


Pretty much everything homebrew installs goes into `/usr/local/Cellar` and gets 
symlinked to `/usr/local/bin`, and shouldn't interfere with any other standard 
software.  One notable exception is that Homebrew 
Cask items like Xquartz.app typically go into 
/Applications, because Cask handles the downloading of apps and installers and 
runs installers automatically.  Of course, you can just as easily download 
XQuartz from the project website and install it 
manually if you prefer.

It may take a few minutes to build PyMOL and its few dependencies. But that's 
it!  Now to open PyMOL they can open a Terminal window, `cd` to whatever 
directory they want to work in, and launch PyMOL by typing `pymol`.  This would 
not only get them a more up-to-date PyMOL version, but as an added bonus, a 
little exposure to a Unix command line environment.

Hope that helps.

Cheers,
Jared




On Sep 2, 2016, at 4:24 PM, Paul Paukstelis 
mailto:shocksofmig...@gmail.com>> wrote:

Are there known session issues with MacPymol? I've saved a session for
my students to look at using my linux incentive linux build and tried
various session compatibility settings (1.6, 1.74, 1.76) but in all
cases the preset scenes I've saved in the session are not loaded when
the session is opened in MacPymol (educational version 1.7.6 I believe).

Thanks,

--paul

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Re: [PyMOL] Pymol spheres/circles

[Sampson, Jared M.]

Hi Laura -

You can also choose single atom selection mode through the menu: click Mouse > 
Selection mode > Atoms and then click your alpha carbon atom.  However, it can 
be tricky to hit the right atom if you're only looking at a cartoon 
representation, so I usually prefer to use the PyMOL command line as Osvaldo 
mentioned with something like:

```
select mutant, myprotein and resi 2
show spheres, mutant and name CA
```

Hope that helps.

Cheers,
Jared



On Aug 30, 2016, at 8:18 AM, Smith, Laura 
mailto:laura.j.sm...@ucl.ac.uk>> wrote:

Hi,

I’m pretty new to Pymol and not that great with all the syntax etc.

I am wanting to easily show where a mutation is located in  cartoon model. I’ve 
tried to label the residues with spheres but it generates more than one dot and 
that’s not what I want. I just want one single sphere/circle/dot localised to 
an atom on the structure for me to label myself.

Basically like figure 2A in this paper >> 
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1326319/

Thanks,
Laura


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Re: [PyMOL] Active site in Pymol

[Sampson, Jared M.]

Hi Farzaneh -

Are you looking for something programmatic to use for many different 
structures, or just analyzing a single structure?

With just one structure (or a few) you can do most of this using the GUI by eye.

1. To find the length of each H-bond involving your ligand, (let's say the 
object or selection is called "my_ligand"), click "S (show) > Labels" for the 
'my_ligand_polar_conts' object that was created when finding the H-bonds.

2. To see which kinds of residues are involved, you can type on the PyMOL 
command line: `show sticks, byres (my_ligand within 4)` which will show sticks 
for the entire residue (byres) of any residue with any atom within 4 Å of 
my_ligand.

3. For the number of H-bonds in an individual active site, you can probably 
just count them by eye.

Alternatively, if you need a more automated approach, have a look at Thomas 
Holder's Polarpairs plugin: http://www.pymolwiki.org/index.php/Polarpairs

Hope that helps.

Cheers,
Jared



On Aug 23, 2016, at 2:39 AM, Farzaneh Namazifar 
mailto:f.namazifar706...@gmail.com>> wrote:

Hi Dear all;
I am a PyMol user.  I read the PyMOL 
tutorial
 about the hydrogen bond. I need some informations about hydrogen bond like:
1- length of hydrogen bond between two residue
2- which kind of residues are in the hydrogen bond
3- Number of hydrogen bond in active site
As above, I need informations about  Hydrophobicity of residues in the active 
site. and else information about pi-pi interaction in DNA... I need your help 
...
Best Regards.
Thank you in advance.
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Re: [PyMOL] What's wrong with my pymol script?

[Sampson, Jared M.]

Hi Dd H -

`cmd.set` is the wrong command to use here.  (It's for changing settings, not 
for going through states, although some settings can be applied to only a 
specific state).

Instead, you should use `cmd.frame(i)` to move to that frame (state) number.

Note that the `width` and `height` arguments to 
`cmd.png` are in pixels unless you include 
a unit suffix like '10in' or '10cm', and it also takes a `ray` keyword argument 
if you want to ray trace for a nicer image.  Also, this is in a PyMOL (.pml) 
script instead of a Python (.py) script, you need to enclose any statement that 
requires multiple lines (i.e. loops, if/else, etc.) within a `python` block.

```
python
for i in range(1, cmd.count_states()+1):
 cmd.frame(i)
 cmd.png("%d.png" % (i), width='10in', height='10in', dpi=300, ray=1)
python end
```

Hope that helps.

Cheers,
Jared


On Aug 14, 2016, at 9:48 AM, Dd H mailto:ddhe...@gmail.com>> 
wrote:

Hi everyone,
I want to render images of frames of my trajectory that loaded in pymol with 
the script below. After running this script, pymol outputs images and they are 
all the same. So what's wrong with my script?

for i in range(1, cmd.count_states()+1):
 cmd.set("state", i, "traj")
 cmd.png("%d.png" % (i), width=10, height=10, dpi=300)

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Re: [PyMOL] Modeling protein-dna complex

[Sampson, Jared M.]

Hi soumi - 

A command-line version of what David said is the following:

save new_complex.pdb, protein_selection or dna_selection

where `protein_selection` and `dna_selection` include all the atoms you want to 
have in the final PDB.  They could be object names if you have each protein and 
the DNA in separate objects.

Hope that helps.

Cheers,
Jared

> On Aug 13, 2016, at 12:15 PM, David Hall  wrote:
> 
> Select the protein you want and the dna, then save the selection as a PDB.
> 
> There are many ways to make a selection; visually, the easiest might be:
> 
> You said you’ve removed the DNA from the protein-dna complex, so now you 
> should have:
> 
> (1) an object that has just your protein that you want in the complex
> (2) an object that has just your DNA that you want in the complex
> 
> In the bottom right, where it typically says “Selecting Residues”, click 
> where it says Residues until that it says “Objects”
> 
> Click on your protein
> 
> Click on your dna
> 
> Click on File->Save Molecule and save “sele” as a PDB file.
> 
>> On Aug 13, 2016, at 8:22 AM, soumi  wrote:
>> 
>> Hi,
>>I carry on my research work on protein-dna complex system.I have one dna 
>> pdb and one protein-dna complex pdb.I want to make new protein-dna complex 
>> pdb taking  dna from single pdb and protein from protein-dna complex.Protein 
>> possess similar DNA-binding specificities.I superimpose two pdb file and 
>> remove dna from protein-dna complex pdb .But I can not save new protein-dna 
>> complex.Please let me know by pymol how I would be able to model of the 
>> referred paper was done.
>> Thanks
>> soumi
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Re: [PyMOL] Scripting in Pymol (+)

[Sampson, Jared M.]

Hi James -

For the first part, you should use split_states and super or cealign, as in my 
response to one of your emails last month.

https://sourceforge.net/p/pymol/mailman/message/35156097/

Then, once you have aligned all the trajectory structures (let's say they're 
called traj_01 through traj_10), you can create new objects from each of the 
snapshots and the heme using the `or` operator in the selection passed to 
`create`.

create heme_traj_01, traj_01 or resn HEM
create heme_traj_02, traj_02 or resn HEM
etc.

Hope that helps.

Cheers,
Jared

For 1, you need to get your MD simulatio
On Jul 12, 2016, at 3:05 AM, James Starlight 
mailto:jmsstarli...@gmail.com>> wrote:

Dear Pymol Users!

Here I desice to continue my topic regarding scripting in Pymol;

My current task:
I have 1 X-ray structure of cythochrome-C with HEME residue embedded
within the protein as a cofactor
I have 10 snapshots of cythochrome-C from MD trajectory where HEME was
not present explicitly

What I need from pymol to write some script, which will
1) align (superimpose) each MD snapshot againt reference
2) copy HEME residue from reference to each of the superimpsoed
snapshot within the same position.

Thanks so much for any suggestions regarding realization !

James

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[PyMOL] Resetting PyMOL via API for unit testing

[Sampson, Jared M.]

tl;dr: Is there a way to fully stop and restart PyMOL "sessions" using the API 
to avoid crossover between unit tests?

Hi everyone -

I'm working on unit testing for a plugin and have been trying to figure out how 
to test some functionality from within a PyMOL session.  I have a partially 
working solution, but the problem arises that I can't adequately reinitialize 
PyMOL between tests, and sometimes end up getting carryover between tests.

Here's a working example of this behavior using the built-in `unittest` testing 
framework:

```
import unittest

import __main__
__main__.pymol_argv = ['pymol','-qkc']
import pymol
from pymol import cmd

class TestPymolApi(unittest.TestCase):
def setUp(self):
pymol.finish_launching()
cmd.reinitialize()

def tearDown(self):
#cmd.quit()  # ***this line hangs if uncommented***
pass

def test_1(self):
'''No value for stored.foo.'''
from pymol import stored
with self.assertRaises(AttributeError):
stored.foo

def test_2(self):
'''Sets a value for stored.foo.'''
from pymol import stored
stored.foo = 'bar'

#def test_3(self):
#'''Fails due to carryover from test_2.'''
#self.test_1()

if __name__ == '__main__':
unittest.main()
```


Running `python basic_tests.py` yields the following output (each dot 
represents a successful test):

```
$ python basic_tests.py
..
--
Ran 2 tests in 0.043s

OK
```


But if I uncomment `test_3` and re-run (the tests are executed in standard 
string-sorting order by function name), it fails because the value of 
`stored.foo` is retained even after reinitialization after `test_2`.  (The 
`setUp` and `tearDown` functions are run before and after each test, 
respectively.)

```
$ python basic_tests.py
..F
==
FAIL: test_3 (__main__.TestPymolApi)
--
Traceback (most recent call last):
  File "basic_tests.py", line 32, in test_3
self.test_1()
  File "basic_tests.py", line 24, in test_1
stored.foo
AssertionError: AttributeError not raised

--
Ran 3 tests in 0.110s

FAILED (failures=1)
```

Maybe this is a bug in `cmd.reinitialize()`?  If not, it is unexpected behavior 
(at least in my opinion), and could be improved.

Anyway, this is why I'm trying to figure out another way to reset PyMOL using 
the API.  So if I then uncomment the `cmd.quit()` line to try to get complete 
shut down and restart of PyMOL, unittest hangs on the tearDown of the first 
test and I have to interrupt the process with .

I found an old 
thread where Jason 
mentioned using (admittedly experimental) `pymol2.PyMOL().start/stop()` to, 
well, start and stop PyMOL sessions.  However, in Open Source PyMOL 1.8.2.1, it 
appears to be broken:

```
$ python
>>> import pymol2
>>> p = pymol2.PyMOL()
>>> p.start()
Segmentation fault: 11
```

So, again, my question is: Is there any way to reliably start and stop multiple 
PyMOL sessions or completely reset it using the API?

Looking forward any suggestions or further discussion.

Cheers,
Jared








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Re: [PyMOL] Analysis of docking poses from 2 nmr-ensembles

[Sampson, Jared M.]

Hi James -

First, it will be useful to split the 
states.

split_states ensemble1
split_states ensemble2
delete ensemble1
delete ensemble2

Then, superimpose all structures onto a 
reference structure for easier visualization.  This won't affect your distance 
measurements, but will make it easier to see the changes from one object to the 
next.

python
ref = 'ensemble1_0001'   # your reference object
for obj in cmd.get_names():
if obj != ref:
cmd.super(obj, ref)
python end

For your residue pair analysis, you have to decide what kind of distance you 
want to measure (e.g. CA-CA; average position of all atoms in the residue; 
closest atoms, which would require looping through all atom pairs in each 
residue pair and keeping only the shortest distance).  Then create selection 
strings based on those criteria, use them in 
distance measurement, and print 
them or add them to a variable to be output.  If you want to create and 
visualize distance objects, use `distance` instead of `get_distance` and pass a 
distance object name as the first parameter before the selections.

python
sel1 = "resi 100 and name CA"
sel2 = "resi 200 and name CA"
sel3 = "resi 300 and name CA"
for obj in cmd.get_names():
d12 = cmd.get_distance("{} and {}".format(obj, sel1), "{} and 
{}".format(obj, sel2))
d23 = cmd.get_distance("{} and {}".format(obj, sel2), "{} and 
{}".format(obj, sel3))
print "{}: '{}' to '{}' distance = {}".format(obj, sel1, sel2, d12)
print "{}: '{}' to '{}' distance = {}".format(obj, sel2, sel3, d23)
python end

This is just a very quick example; really there are many different ways to do 
this, and you'll have to find what kind of analysis your particular structure 
needs.  Also, if you want to look at H-bonds, it will be more complicated, 
because the angle is important as well.  In this case you may want to look at 
Thomas' Polarpairs script.

Hope that helps.

Cheers,
Jared



On Jun 13, 2016, at 9:41 AM, James Starlight 
mailto:jmsstarli...@gmail.com>> wrote:

Dear Pymol users!

I am studying protein-protein assosiation using 2 different proteins
as test case by means of variety of computational methods.
For my particular caseI need to compare binding poses emerged as the
result of protein-protein docking (ensemble 1: which  consists of 20
snapshots according to docking ranking) as well as MD simulation
(ensemble 2: which consists of 10 snapshots each of which represents
binding pose which has been established during long MD run).
Loading those two ensembles in pymol as 2 different models (in
NMR-like model format)  I need to performs some analysis  to find some
shared trends in each of them e.g RMSD of the distances between common
residues-pairs found in contact map analysis
or something else. What are most trivial suggestions might be in that
particular case?


Thanks for the suggestions!


James

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Re: [PyMOL] Dynamic reloading of plugin

[Sampson, Jared M.]

Hi Martin - 

I've also experienced this kind of tedium.  Depending on the type of extension 
it is, you could also consider writing tests for your function that can be run 
by either:

a) importing PyMOL commands into a python (.py) script and running e.g. 
`nosetests` or other unit testing software

```extension_tests.pml
import pymol
from pymol import cmd
pymol.finish_launching()
...do stuff here...
```

or,

b) run PyMOL (.pml) scripts in command line only mode.

For example, I've used approach (b) before with a setup something like this:

```test1.pml
from pymol import cmd
frag ala
python
if 'ala' in cmd.get_names(): 
   print 'OK'
else: 
   print 'Not OK'
python end
```

Then run each test from the shell:

```
pymol -cq test1.pml
```

For running many tests automatically, I've also used a "run_tests.sh" that 
looks something like this:

```run_tests.sh
#!/bin/bash
function run_test() {
 PML="test${1}.pml"
 if [ -f "$PML" ]; then
   echo ""
   echo 
""
   echo "Running Test ${1}: $PML"
   echo ""
   pymol -ckq $PML
   echo ""
 fi
}

# call `./run_tests.sh` with no args to run all the tests (up to 100)
if [ $# -lt 1 ]; then
 for i in {1..100}  # increase if you have more than 100 tests
 do
   run_test $i
 done

# call with args, e.g. `./run_tests.sh 1 2 4 7` to run specific test(s)
else
 for i in $@
 do
   run_test $i
 done
fi 
```

Hope this is helpful.  Good luck!

Cheers,
Jared




> On Apr 25, 2016, at 11:06 AM, Thomas Holder  
> wrote:
> 
> Hi Martin,
> 
> how about:
> 
> set_key F1, run script.py; function_from_script()
> 
> Reduces step 3) and 4) to hitting "F1" on the keyboard.
> 
> Cheers,
> Thomas
> 
> On 24 Apr 2016, at 06:36, Martin Hediger  wrote:
> 
>> Hi all
>> 
>> When working on a PyMOL extension script, my workflow is currently something 
>> like this:
>> 
>> 1) Start PyMOL
>> 2) Work on script
>> 3) PyMOL> run script.py
>> 4) PyMOL> function_from_script()
>> 5) See if function works, go back to 2)
>> 
>> Is it possible to have PyMOL automatically re-run the script everytime i 
>> save it?
>> 
>> Thanks and best regards
>> Martin
>> 
>> -- 
>> Martin R. Hediger, PhD
>> Mittlere Strasse 65
>> 4056 Basel
> 
> -- 
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> PyMOL Principal Developer
> Schrödinger, Inc.
> 
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Re: [PyMOL] on the alignment command

[Sampson, Jared M.]

Hi Smith -

`Align` takes selections as arguments, so something like the following should 
work.

align protA and chain A+B+C, protB and chain E+F+G

You could also use `super` or `cealign` instead of align, although with 
cealign, you should reverse the order of the arguments to achieve the same 
result.

Cheers,
Jared


On Apr 12, 2016, at 5:11 AM, Smith Liu 
mailto:smith_liu...@163.com>> wrote:

Dear All,

Suppose my protein A PDB contains chian A, B, C, D, and my protein B PDB 
contains chain E, F, G, H, I want to align all protein A without chain D, with 
all protein B without chain H, will you please tell me the align command?

Smith



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Re: [PyMOL] pymolrc location

[Sampson, Jared M.]

It should be a plain text file with no filename extension (i.e. no ".txt") in 
your home directory, with the full path:

/Users/yourusername/.pymolrc

You can do this with any text editor (including TextEdit--press Cmd-Shift-T to 
make it plain text), or, alternatively, the shell command:

echo "set auto_show_classified" >> ~/.pymolrc

which appends the quoted text to a new line in .pymolrc, creating the file if 
it doesn't exist.

Cheers,
Jared

On Apr 8, 2016, at 11:42 AM, harold steinberg 
mailto:h.adam.steinb...@gmail.com>> wrote:

Sorry to be inept… I've never had the opportunity to learn beyond the basics of 
Unix.

create a txt file or create a pml file?
Place it on the hard drive next to the library and system folder?
Or place it in the User folder next to the library folder?


On Apr 8, 2016, at 9:47 AM, David Hall 
mailto:li...@cowsandmilk.net>> wrote:

Make a file at ~/.pymolrc

-David

On Apr 8, 2016, at 10:35 AM, harold steinberg 
mailto:h.adam.steinb...@gmail.com>> wrote:

where in OS X is pymolrc located?

On Apr 7, 2016, at 2:39 PM, Thomas Holder 
mailto:thomas.hol...@schrodinger.com>> wrote:

pymolrc

H. Adam Steinberg
7904 Bowman Rd
Lodi, WI 53555
608/592-2366


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608/592-2366


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Re: [PyMOL] The Wiki appears outdated or in error

[Sampson, Jared M.]

Hi Jim -

Here's a patch for Open Source PyMOL (rev4153) that adds the 
"collada_background_box" setting (default=0).  If you're using Open Source 
PyMOL and are up to applying it and rebuilding, feel free to use it.  
Otherwise, I already sent it to Thomas, so hopefully it will be incorporated 
into SVN and Incentive PyMOL soon.

Cheers,
Jared

--
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Columbia University

On Mar 24, 2016, at 2:26 PM, Sampson, Jared M. 
mailto:jms2...@cumc.columbia.edu>> wrote:

Hi Jim -

When I

set geometry_export_mode, 1

in PyMOL, then save myfile.dae, then import into MeshLab, MeshLab hangs.

I can confirm that this happens for me, too.  I guess maybe Meshlab requires 
the camera?

As a workaround, you can go back to the previous version with 
collada_geometry_mode=1 and simply delete the box.  You can do this within 
Meshlab by using the "Select Connected Components in a region" tool to select a 
corner the box, then clicking the "Delete the current set of selected faces and 
all the vertices surrounded by that faces" button (see attached screenshot).  
Then, if you zoom in (the box is 100x larger than the largest dimension of the 
scene), your scene will be there.

I'm working on a patch right now to exclude the bounding background box from 
default COLLADA output and make it optional via a new `collada_background_box` 
setting.

Sorry for the confusion, hope this clears it up.

Cheers,
Jared

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collada_background_box.patch
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Re: [PyMOL] The Wiki appears outdated or in error

[Sampson, Jared M.]

Hi Jim -

When I

set geometry_export_mode, 1

in PyMOL, then save myfile.dae, then import into MeshLab, MeshLab hangs.

I can confirm that this happens for me, too.  I guess maybe Meshlab requires 
the camera?

As a workaround, you can go back to the previous version with 
collada_geometry_mode=1 and simply delete the box.  You can do this within 
Meshlab by using the "Select Connected Components in a region" tool to select a 
corner the box, then clicking the "Delete the current set of selected faces and 
all the vertices surrounded by that faces" button (see attached screenshot).  
Then, if you zoom in (the box is 100x larger than the largest dimension of the 
scene), your scene will be there.

I'm working on a patch right now to exclude the bounding background box from 
default COLLADA output and make it optional via a new `collada_background_box` 
setting.

Sorry for the confusion, hope this clears it up.

Cheers,
Jared

--
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Columbia University

On Mar 24, 2016, at 1:05 PM, James Kress 
mailto:jimkress...@kressworks.org>> wrote:

Hi Jared,

When I

set geometry_export_mode, 1

in PyMOL, then save myfile.dae, then import into MeshLab, MeshLab hangs.  Is 
there an alternative to MeshLab I can use to generate the u3d file?

Thanks.

Jim

James Kress Ph.D., President
The KressWorks® Foundation
An IRS Approved 501 (c)(3) Charitable, Nonprofit Organization
“Engineering The Cure” ©
(248) 605-8770

Learn More and Donate At:
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From: Sampson, Jared M. [mailto:jms2...@cumc.columbia.edu]
Sent: Wednesday, March 23, 2016 10:53 PM
To: jimkress...@kressworks.org<mailto:jimkress...@kressworks.org>
Cc: pymol-users 
Subject: Re: [PyMOL] The Wiki appears outdated or in error

Hi Jim -

This is something we've been talking about changing.  The entire scene as 
viewed within PyMOL is inside that block, including the camera position.   (The 
interior surface of the block itself provides the background color of the 
scene.)  Some viewers, e.g. Mac Preview.app, default to displaying from the 
camera position, but others, including MeshLab, don't, which is understandably 
confusing.

To export only the geometry without any of the scene information, you can `set 
geometry_export_mode, 1` in PyMOL before saving the .dae.

Hope that helps!

Cheers,
Jared

P.S. if you are able to work out a protocol/workflow for generating 3D PDFs 
that is better than what's on the wiki, I hope you will consider updating the 
wiki to help others who might try it in the future.

Jared Sampson
Columbia University

On Mar 23, 2016, at 8:26 PM, James Kress 
mailto:jimkress...@kressworks.org>> wrote:

I installed v 1.8.0.6

When I save ‘myfile.dae’ and then import into MeshLab, all I get is a solid 
gray block.

What do I need to do in PyMOL to export my DNA structure?

Thanks.

Jim

James Kress Ph.D., President
The KressWorks® Foundation
An IRS Approved 501 (c)(3) Charitable, Nonprofit Organization
“Engineering The Cure” ©
(248) 605-8770

Learn More and Donate At:
Website: http://www.kressworks.org<http://www.kressworks.org/>
Facebook: https://www.facebook.com/KressWorks.Foundation/
Twitter: @KressWorksFnd

Confidentiality Notice | This e-mail message, including any attachments, is for 
the sole use of the intended recipient(s) and may contain confidential or 
proprietary information. Any unauthorized review, use, disclosure or 
distribution is prohibited. If you are not the intended recipient, immediately 
contact the sender by reply e-mail and destroy all copies of the original 
message.

From: Sampson, Jared M. [mailto:jms2...@cumc.columbia.edu]
Sent: Tuesday, March 22, 2016 1:40 PM
To: jimkress...@kressworks.org<mailto:jimkress...@kressworks.org>
Cc: pymol-users 
mailto:pymol-users@lists.sourceforge.net>>
Subject: Re: [PyMOL] The Wiki appears outdated or in error

Hi Jim -

The COLLADA exporting code was incorporated into Open Source PyMOL starting 
with 1.7.3.2 (SVN 4097), but I'm not sure when it made it into Incentive PyMOL, 
so if that's what you're using, 1.7.4 might be just barely too early to have 
that capability.  You could try saving as VRML2, (`save myfile.wrl`) and use 
MeshLab to convert that instead of the COLLADA file--I think VRML output is 
more complete than IDTF.

Alternatively, you could install a more recent open source PyMOL using 
instructions available on the wiki: 
http://www.pymolwiki.org

Re: [PyMOL] The Wiki appears outdated or in error

[Sampson, Jared M.]

Hi Jim -

This is something we've been talking about changing.  The entire scene as 
viewed within PyMOL is inside that block, including the camera position.   (The 
interior surface of the block itself provides the background color of the 
scene.)  Some viewers, e.g. Mac Preview.app, default to displaying from the 
camera position, but others, including MeshLab, don't, which is understandably 
confusing.

To export only the geometry without any of the scene information, you can `set 
geometry_export_mode, 1` in PyMOL before saving the .dae.

Hope that helps!

Cheers,
Jared

P.S. if you are able to work out a protocol/workflow for generating 3D PDFs 
that is better than what's on the wiki, I hope you will consider updating the 
wiki to help others who might try it in the future.

Jared Sampson
Columbia University

On Mar 23, 2016, at 8:26 PM, James Kress 
mailto:jimkress...@kressworks.org>> wrote:

I installed v 1.8.0.6

When I save ‘myfile.dae’ and then import into MeshLab, all I get is a solid 
gray block.

What do I need to do in PyMOL to export my DNA structure?

Thanks.

Jim

James Kress Ph.D., President
The KressWorks® Foundation
An IRS Approved 501 (c)(3) Charitable, Nonprofit Organization
“Engineering The Cure” ©
(248) 605-8770

Learn More and Donate At:
Website: http://www.kressworks.org<http://www.kressworks.org/>
Facebook: https://www.facebook.com/KressWorks.Foundation/
Twitter: @KressWorksFnd

Confidentiality Notice | This e-mail message, including any attachments, is for 
the sole use of the intended recipient(s) and may contain confidential or 
proprietary information. Any unauthorized review, use, disclosure or 
distribution is prohibited. If you are not the intended recipient, immediately 
contact the sender by reply e-mail and destroy all copies of the original 
message.

From: Sampson, Jared M. [mailto:jms2...@cumc.columbia.edu]
Sent: Tuesday, March 22, 2016 1:40 PM
To: jimkress...@kressworks.org<mailto:jimkress...@kressworks.org>
Cc: pymol-users 
Subject: Re: [PyMOL] The Wiki appears outdated or in error

Hi Jim -

The COLLADA exporting code was incorporated into Open Source PyMOL starting 
with 1.7.3.2 (SVN 4097), but I'm not sure when it made it into Incentive PyMOL, 
so if that's what you're using, 1.7.4 might be just barely too early to have 
that capability.  You could try saving as VRML2, (`save myfile.wrl`) and use 
MeshLab to convert that instead of the COLLADA file--I think VRML output is 
more complete than IDTF.

Alternatively, you could install a more recent open source PyMOL using 
instructions available on the wiki: 
http://www.pymolwiki.org/index.php/Category:Installation.

Cheers,
Jared

--
Jared Sampson
Columbia University

On Mar 21, 2016, at 5:46 PM, James Kress 
mailto:jimkress...@kressworks.org>> wrote:

Hi Jared,

The version of PyMOL I am using (1.7.4.0) does not recognize the dae file type.

Here is the message PyMOL generates:

PyMOL>save output_no_H2O.dae
Save-Warning: Unrecognized file type -- defaulting to PDB format.
Save: wrote "output_no_H2O.dae".

I get the same error message if I use the command ‘save output_no_H2O.dae’

Jim


James Kress Ph.D., President
The KressWorks® Foundation
An IRS Approved 501 (c)(3) Charitable, Nonprofit Organization
“Engineering The Cure” ©
(248) 605-8770

Learn More and Donate At:
Website: http://www.kressworks.org<http://www.kressworks.org/>
Facebook: https://www.facebook.com/KressWorks.Foundation/
Twitter: @KressWorksFnd

Confidentiality Notice | This e-mail message, including any attachments, is for 
the sole use of the intended recipient(s) and may contain confidential or 
proprietary information. Any unauthorized review, use, disclosure or 
distribution is prohibited. If you are not the intended recipient, immediately 
contact the sender by reply e-mail and destroy all copies of the original 
message.

From: Sampson, Jared M. [mailto:jms2...@cumc.columbia.edu]
Sent: Wednesday, March 16, 2016 2:28 PM
To: jimkress...@kressworks.org<mailto:jimkress...@kressworks.org>
Cc: pymol-users@lists.sourceforge.net<mailto:pymol-users@lists.sourceforge.net>
Subject: Re: [PyMOL] The Wiki appears outdated or in error

Hi James -

If I remember correctly, PyMOL's IDTF output currently only supports triangles 
meshes (not cylinders or spheres, e.g.), so unfortunately you're basically 
limited to surface representations for output directly into that format.

As a workaround, you could try saving your scene in COLLADA format (`save 
myfile.dae`), and use an external program (e.g. Blender, Meshlab) to convert to 
IDTF or U3D.  When doing so, please note that you'll probably need to `set 
collada_geometry_mode=1` to specifically use the subset of COLLADA elements 
supported by those two programs (they only allow  elements to 
describe the triangles, which are a more general, verbose description than the 
more concise  and  output generated with t

Re: [PyMOL] color an isosurface with a rainbow

[Sampson, Jared M.]

Hi H. Adam -

Try the http://pymolwiki.org/index.php/Distancetoatom script by Andreas 
Warnecke and use it to set b (or your own custom property in recent Incentive 
PyMOL versions) based on the distance from a point.

Hope that helps.

Cheers,
Jared

--
Jared Sampson
Columbia University

On Mar 23, 2016, at 5:20 PM, harold steinberg 
mailto:h.adam.steinb...@gmail.com>> wrote:

I have a pdb ‘xyz1’ and create a mapA, then create a surfA.

set surface_quality, 1
alter all, b=50
alter all, q=1
set gaussian_resolution,5
map_new mapA, gaussian, 1, sele or pdb, 6
isosurface surfA, mapA

I can then color that surfA with any solid color.

How can one color the surfA with a rainbow affect that radiates out from the 
center, or similar.

This is easy to do with a protein (pdb) but I cannot get a ramp to work with a 
surf.


H. Adam Steinberg
7904 Bowman Rd
Lodi, WI 53555
608/592-2366

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Re: [PyMOL] The Wiki appears outdated or in error

[Sampson, Jared M.]

Hi Jim -

The COLLADA exporting code was incorporated into Open Source PyMOL starting 
with 1.7.3.2 (SVN 4097), but I'm not sure when it made it into Incentive PyMOL, 
so if that's what you're using, 1.7.4 might be just barely too early to have 
that capability.  You could try saving as VRML2, (`save myfile.wrl`) and use 
MeshLab to convert that instead of the COLLADA file--I think VRML output is 
more complete than IDTF.

Alternatively, you could install a more recent open source PyMOL using 
instructions available on the wiki: 
http://www.pymolwiki.org/index.php/Category:Installation.

Cheers,
Jared

--
Jared Sampson
Columbia University

On Mar 21, 2016, at 5:46 PM, James Kress 
mailto:jimkress...@kressworks.org>> wrote:

Hi Jared,

The version of PyMOL I am using (1.7.4.0) does not recognize the dae file type.

Here is the message PyMOL generates:

PyMOL>save output_no_H2O.dae
Save-Warning: Unrecognized file type -- defaulting to PDB format.
Save: wrote "output_no_H2O.dae".

I get the same error message if I use the command ‘save output_no_H2O.dae’

Jim


James Kress Ph.D., President
The KressWorks® Foundation
An IRS Approved 501 (c)(3) Charitable, Nonprofit Organization
“Engineering The Cure” ©
(248) 605-8770

Learn More and Donate At:
Website: http://www.kressworks.org<http://www.kressworks.org/>
Facebook: https://www.facebook.com/KressWorks.Foundation/
Twitter: @KressWorksFnd

Confidentiality Notice | This e-mail message, including any attachments, is for 
the sole use of the intended recipient(s) and may contain confidential or 
proprietary information. Any unauthorized review, use, disclosure or 
distribution is prohibited. If you are not the intended recipient, immediately 
contact the sender by reply e-mail and destroy all copies of the original 
message.

From: Sampson, Jared M. [mailto:jms2...@cumc.columbia.edu]
Sent: Wednesday, March 16, 2016 2:28 PM
To: jimkress...@kressworks.org<mailto:jimkress...@kressworks.org>
Cc: pymol-users@lists.sourceforge.net
Subject: Re: [PyMOL] The Wiki appears outdated or in error

Hi James -

If I remember correctly, PyMOL's IDTF output currently only supports triangles 
meshes (not cylinders or spheres, e.g.), so unfortunately you're basically 
limited to surface representations for output directly into that format.

As a workaround, you could try saving your scene in COLLADA format (`save 
myfile.dae`), and use an external program (e.g. Blender, Meshlab) to convert to 
IDTF or U3D.  When doing so, please note that you'll probably need to `set 
collada_geometry_mode=1` to specifically use the subset of COLLADA elements 
supported by those two programs (they only allow  elements to 
describe the triangles, which are a more general, verbose description than the 
more concise  and  output generated with the default 
setting).

Hope that helps.

Cheers,
Jared

--
Jared Sampson
Columbia University

On Mar 12, 2016, at 11:24 PM, James Kress 
mailto:jimkress...@kressworks.org>> wrote:

Among the export functions, a particular interest of mine is the as a
idtf file as "precursor" for a 3d pdf mentioned at

http://www.pymolwiki.org/index.php/3d_pdf

where I experience difficulties I want to address here.

   While the export via the CLI works fine for creating a *.png picture
or a VRML *.wrl-geometry, the similar export as *.idtf creates only a
header to describe the scenery, but not the (expected) spheres and tubes
to represent atoms and molecular bonds.  The file generated is the same,
regardless if I request the data export via

save /home/user directory/target directory/test.idtf

or the recommended

save /home/user directory/target directory/test.idtf,*

Marking/highlighting the molecule in question does not alter the situation.

   The relative orientation of the model in regard to the observer is
provided, however, in the programs command line, like

3Daac=20.0, 3Droll=0, 3Dc2c=0 0 1, 3Droo=50.00, 3Dcoo=0 0 -50.00

  In addition, there is no *.tex file written -- well in contrast to the
pymol-wiki page -- that I would expect to be created in the very same
directory, too.  (This is contrast to jmol offering export as *.idtf
while simultaneously writing a *.tex file, too.)  Should I look up in a
different directory instead?  May be a mistake during the installation
be a reason why I do not obtain (yet) a functional *.idtf?  Do I need to
load another / an additional plugin to enlarge the export functions?

Thanks.

Jim

James Kress Ph.D., President
The KressWorks® Foundation
An IRS Approved 501 (c)(3) Charitable, Nonprofit Organization
“Engineering The Cure” ©
(248) 605-8770

Learn More and Donate At:
Website: http://www.kressworks.org<http://www.kressworks.org/>
Facebook: https://www.facebook.com/KressWorks.Foundation/
Twitter: @KressWorksFnd

Confidentiality Notice | This e-mail message, including any attachments, is for 
the sole use of the intended recipient(s) and may contain co

Re: [PyMOL] The Wiki appears outdated or in error

[Sampson, Jared M.]

Hi James -

If I remember correctly, PyMOL's IDTF output currently only supports triangles 
meshes (not cylinders or spheres, e.g.), so unfortunately you're basically 
limited to surface representations for output directly into that format.

As a workaround, you could try saving your scene in COLLADA format (`save 
myfile.dae`), and use an external program (e.g. Blender, Meshlab) to convert to 
IDTF or U3D.  When doing so, please note that you'll probably need to `set 
collada_geometry_mode=1` to specifically use the subset of COLLADA elements 
supported by those two programs (they only allow  elements to 
describe the triangles, which are a more general, verbose description than the 
more concise  and  output generated with the default 
setting).

Hope that helps.

Cheers,
Jared

--
Jared Sampson
Columbia University

On Mar 12, 2016, at 11:24 PM, James Kress 
mailto:jimkress...@kressworks.org>> wrote:

Among the export functions, a particular interest of mine is the as a
idtf file as "precursor" for a 3d pdf mentioned at

http://www.pymolwiki.org/index.php/3d_pdf

where I experience difficulties I want to address here.

   While the export via the CLI works fine for creating a *.png picture
or a VRML *.wrl-geometry, the similar export as *.idtf creates only a
header to describe the scenery, but not the (expected) spheres and tubes
to represent atoms and molecular bonds.  The file generated is the same,
regardless if I request the data export via

save /home/user directory/target directory/test.idtf

or the recommended

save /home/user directory/target directory/test.idtf,*

Marking/highlighting the molecule in question does not alter the situation.

   The relative orientation of the model in regard to the observer is
provided, however, in the programs command line, like

3Daac=20.0, 3Droll=0, 3Dc2c=0 0 1, 3Droo=50.00, 3Dcoo=0 0 -50.00

  In addition, there is no *.tex file written -- well in contrast to the
pymol-wiki page -- that I would expect to be created in the very same
directory, too.  (This is contrast to jmol offering export as *.idtf
while simultaneously writing a *.tex file, too.)  Should I look up in a
different directory instead?  May be a mistake during the installation
be a reason why I do not obtain (yet) a functional *.idtf?  Do I need to
load another / an additional plugin to enlarge the export functions?

Thanks.

Jim

James Kress Ph.D., President
The KressWorks® Foundation
An IRS Approved 501 (c)(3) Charitable, Nonprofit Organization
“Engineering The Cure” ©
(248) 605-8770

Learn More and Donate At:
Website: http://www.kressworks.org
Facebook: https://www.facebook.com/KressWorks.Foundation/
Twitter: @KressWorksFnd

Confidentiality Notice | This e-mail message, including any attachments, is for 
the sole use of the intended recipient(s) and may contain confidential or 
proprietary information. Any unauthorized review, use, disclosure or 
distribution is prohibited. If you are not the intended recipient, immediately 
contact the sender by reply e-mail and destroy all copies of the original 
message.

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Re: [PyMOL] How to store matrix settings for individual scenes?

[Sampson, Jared M.]

Hi Carsten -

Could you wrap the `scene` function and include storing/recalling of the 
matrices as well as the scenes?  I just whipped together the following:

```
from pymol import stored
from pymol import cmd
stored.scene_matrices = {}

def scene_store(scn):
obj_matrices = {}
# only store matrices for enabled objects
for obj in cmd.get_names(enabled_only=1):
print 'storing matrix for %s' % obj
m = cmd.get_object_matrix(obj)
print m
obj_matrices[obj] = m

stored.scene_matrices[scn] = obj_matrices
cmd.scene(scn, 'store')

def scene_recall(scn):
obj_matrices = stored.scene_matrices[scn]
for obj in cmd.get_names():
# don't try to reset objects that aren't in the recalled scene
if obj in obj_matrices.keys():
cmd.matrix_reset(obj)
cmd.transform_selection(obj, obj_matrices[obj])
cmd.scene(scn, 'recall')

cmd.extend('scene_store', scene_store)
cmd.extend('scene_recall', scene_recall)
```

This works for me with, e.g.

```
fetch 1shv, async=0
fetch 3opl, async=0
scene_store F1

super 3opl, 1shv  # changes the 3opl matrix
scene_store F2

scene_recall F1  # restores the original 3opl matrix
```

Not sure if that's closer to what you're looking for...hope it helps!

Cheers,
Jared
--
Jared Sampson
Columbia University

On Mar 7, 2016, at 12:35 PM, Schubert, Carsten [JRDUS] 
mailto:cschu...@its.jnj.com>> wrote:

Yeah, but not my preferred choice. Tried to do this the elegant way, but 
bumping up against Pymol’s limits unless Thomas has a workaround.

From: Sampson, Jared M. [mailto:jms2...@cumc.columbia.edu]
Sent: Monday, March 07, 2016 12:15 PM
To: Schubert, Carsten [JRDUS]
Cc: pymol-users@lists.sourceforge.net<mailto:pymol-users@lists.sourceforge.net>
Subject: Re: [PyMOL] How to store matrix settings for individual scenes?

Hi Carsten -

I'd probably create new objects and use those for superimposition, rather than 
moving the originals.  That would leave your scenes intact.

Cheers,
Jared

--
Jared Sampson
Columbia University

On Mar 7, 2016, at 12:10 PM, Schubert, Carsten [JRDUS] 
mailto:cschu...@its.jnj.com>> wrote:

Hi,

I am trying to create a session file of a multimeric protein, in which each 
monomer is displayed first using the original  matrix settings broken out into 
individual scenes. After that all monomers are overlayed on top of each other 
and the superposition matrices are copied and applied to the ligands, etc. So 
far so good, however once the matrices are applied this also affects the 
matrices for the scenes created previous to the overlay and matrix_copy. Any 
way I can store the matrices in each scene instead of having them applied 
globally once?

Cheers,

Carsten
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Re: [PyMOL] How to store matrix settings for individual scenes?

[Sampson, Jared M.]

Hi Carsten -

I'd probably create new objects and use those for superimposition, rather than 
moving the originals.  That would leave your scenes intact.

Cheers,
Jared

--
Jared Sampson
Columbia University

On Mar 7, 2016, at 12:10 PM, Schubert, Carsten [JRDUS] 
mailto:cschu...@its.jnj.com>> wrote:

Hi,

I am trying to create a session file of a multimeric protein, in which each 
monomer is displayed first using the original  matrix settings broken out into 
individual scenes. After that all monomers are overlayed on top of each other 
and the superposition matrices are copied and applied to the ligands, etc. So 
far so good, however once the matrices are applied this also affects the 
matrices for the scenes created previous to the overlay and matrix_copy. Any 
way I can store the matrices in each scene instead of having them applied 
globally once?

Cheers,

Carsten
--
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Re: [PyMOL] How to tell from within a script if a plugin is loaded?

[Sampson, Jared M.]

Hi Thomas -

Thanks for the clarification on cmd.extend() and the difference between how 
commands and functions are made available. I hadn't thought to just add the 
function to cmd directly.  This will come in handy!

Cheers,
Jared

--
Jared Sampson
Columbia University

On Feb 18, 2016, at 1:14 PM, Thomas Holder 
mailto:thomas.hol...@schrodinger.com>> wrote:

Hi Jared,

The plugin system isn't really tuned for API extension. As Tsjerk pointed out, 
cmd.extend only registers a command, not a cmd. function. Also, scripts 
which are installed as plugins get loaded asynchronously from the external GUI. 
I suggest you do the following:

1) Inside your plugin (Python module), do:

from pymol import cmd
def my_func(): ...
cmd.my_func = my_func
cmd.extend('my_func', my_func)

2) The plugin's __init_plugin__ (or __init__) function should only be 
responsible for adding Plugin menu entries, not for anything else.

3) Inside your test file, do:

from pymol import cmd
import pmg_tk.startup.my_plugin
# (now cmd.my_func should be available immediately)

Hope that helps.

Cheers,
 Thomas

On 17 Feb 2016, at 11:32, Sampson, Jared M. 
mailto:jms2...@cumc.columbia.edu>> wrote:

Hi Tsjerk -

Thanks for the suggestion.  I tried this with:

import time
from pymol import cmd
while not hasattr(cmd, 'my_func'):
time.sleep(0.5)

Unfortunately that also causes everything to hang.  I think I might need to do 
this in a separate thread.  I'll have to look into how to do that.

Cheers,
Jared

--
Jared Sampson
Columbia University

On Feb 16, 2016, at 2:47 PM, Tsjerk Wassenaar 
mailto:tsje...@gmail.com>> wrote:

Hi Jared,

The extend function must set an attribute "my_func" on cmd. You can test for 
that with hasattr:

while not hasattr(cmd, "my_func"):
   # wait some more

Hope it helps,

Tsjerk

On Feb 16, 2016 20:07, "Sampson, Jared M." 
mailto:jms2...@cumc.columbia.edu>> wrote:
To my previous message I should add that it works fine if I do:

```
import pmg_tk.startup.my_plugin as mp
mp.my_func()
```

but I'd like to use the `cmd.my_func()` version, so that `my_func` will work in 
a .pml script.

>From `help(cmd)` I found `cmd.kw_list`, but this apparently doesn't include 
>"extended" functions, even after the function is loaded.

```
PyMOL>print 'ray' in cmd.kw_list
True
PyMOL>print 'my_func' in cmd.kw_list
False
```

Looking forward to any suggestions.  Thanks!

Cheers,
Jared

--
Jared Sampson
Columbia University

On Feb 16, 2016, at 1:50 PM, Sampson, Jared M. 
mailto:jms2...@cumc.columbia.edu>> wrote:

Hi PyMOLers -

Maybe some more experienced users/developers can help me out here.  I'm trying 
to write some automated test scripts for the plugin I'm writing, but the test 
functions end up running before the plugin is loaded.  Is there a way to tell 
if a plugin has been loaded from within a .pml or .py script?  For example, if 
the plugin makes commands available via `cmd.extend('my_func', my_func)`, how 
can I run `cmd.myfunc()` from a script and not have it execute before the 
plugin finishes loading?

I've tried something like this:

```
import time
from pymol import cmd
loaded = 0
while not loaded:
   try:
   cmd.my_func()  # if it's loaded no exception will be raised
   loaded = 1
   except:
   time.sleep(0.5)
```

But this just hangs, as apparently `time.sleep()` halts the execution of all 
threads, so the plugin won't ever be loaded.

Thanks,
Jared

--
Jared Sampson
Columbia University

--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.

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Re: [PyMOL] How to tell from within a script if a plugin is loaded?

[Sampson, Jared M.]

Hi Tsjerk -

Thanks for the suggestion.  I tried this with:

import time
from pymol import cmd
while not hasattr(cmd, 'my_func'):
time.sleep(0.5)

Unfortunately that also causes everything to hang.  I think I might need to do 
this in a separate thread.  I'll have to look into how to do that.

Cheers,
Jared

--
Jared Sampson
Columbia University

On Feb 16, 2016, at 2:47 PM, Tsjerk Wassenaar 
mailto:tsje...@gmail.com>> wrote:


Hi Jared,

The extend function must set an attribute "my_func" on cmd. You can test for 
that with hasattr:

while not hasattr(cmd, "my_func"):
# wait some more

Hope it helps,

Tsjerk

On Feb 16, 2016 20:07, "Sampson, Jared M." 
mailto:jms2...@cumc.columbia.edu>> wrote:
To my previous message I should add that it works fine if I do:

```
import pmg_tk.startup.my_plugin as mp
mp.my_func()
```

but I'd like to use the `cmd.my_func()` version, so that `my_func` will work in 
a .pml script.

>From `help(cmd)` I found `cmd.kw_list`, but this apparently doesn't include 
>"extended" functions, even after the function is loaded.

```
PyMOL>print 'ray' in cmd.kw_list
True
PyMOL>print 'my_func' in cmd.kw_list
False
```

Looking forward to any suggestions.  Thanks!

Cheers,
Jared

--
Jared Sampson
Columbia University

On Feb 16, 2016, at 1:50 PM, Sampson, Jared M. 
mailto:jms2...@cumc.columbia.edu>> wrote:

Hi PyMOLers -

Maybe some more experienced users/developers can help me out here.  I'm trying 
to write some automated test scripts for the plugin I'm writing, but the test 
functions end up running before the plugin is loaded.  Is there a way to tell 
if a plugin has been loaded from within a .pml or .py script?  For example, if 
the plugin makes commands available via `cmd.extend('my_func', my_func)`, how 
can I run `cmd.myfunc()` from a script and not have it execute before the 
plugin finishes loading?

I've tried something like this:

```
import time
from pymol import cmd
loaded = 0
while not loaded:
try:
cmd.my_func()  # if it's loaded no exception will be raised
loaded = 1
except:
time.sleep(0.5)
```

But this just hangs, as apparently `time.sleep()` halts the execution of all 
threads, so the plugin won't ever be loaded.

Thanks,
Jared

--
Jared Sampson
Columbia University

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Re: [PyMOL] How to tell from within a script if a plugin is loaded?

[Sampson, Jared M.]

To my previous message I should add that it works fine if I do:

```
import pmg_tk.startup.my_plugin as mp
mp.my_func()
```

but I'd like to use the `cmd.my_func()` version, so that `my_func` will work in 
a .pml script.

>From `help(cmd)` I found `cmd.kw_list`, but this apparently doesn't include 
>"extended" functions, even after the function is loaded.

```
PyMOL>print 'ray' in cmd.kw_list
True
PyMOL>print 'my_func' in cmd.kw_list
False
```

Looking forward to any suggestions.  Thanks!

Cheers,
Jared

--
Jared Sampson
Columbia University

On Feb 16, 2016, at 1:50 PM, Sampson, Jared M. 
mailto:jms2...@cumc.columbia.edu>> wrote:

Hi PyMOLers -

Maybe some more experienced users/developers can help me out here.  I'm trying 
to write some automated test scripts for the plugin I'm writing, but the test 
functions end up running before the plugin is loaded.  Is there a way to tell 
if a plugin has been loaded from within a .pml or .py script?  For example, if 
the plugin makes commands available via `cmd.extend('my_func', my_func)`, how 
can I run `cmd.myfunc()` from a script and not have it execute before the 
plugin finishes loading?

I've tried something like this:

```
import time
from pymol import cmd
loaded = 0
while not loaded:
try:
cmd.my_func()  # if it's loaded no exception will be raised
loaded = 1
except:
time.sleep(0.5)
```

But this just hangs, as apparently `time.sleep()` halts the execution of all 
threads, so the plugin won't ever be loaded.

Thanks,
Jared

--
Jared Sampson
Columbia University

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[PyMOL] How to tell from within a script if a plugin is loaded?

[Sampson, Jared M.]

Hi PyMOLers -

Maybe some more experienced users/developers can help me out here.  I'm trying 
to write some automated test scripts for the plugin I'm writing, but the test 
functions end up running before the plugin is loaded.  Is there a way to tell 
if a plugin has been loaded from within a .pml or .py script?  For example, if 
the plugin makes commands available via `cmd.extend('my_func', my_func)`, how 
can I run `cmd.myfunc()` from a script and not have it execute before the 
plugin finishes loading?

I've tried something like this:

```
import time
from pymol import cmd
loaded = 0
while not loaded:
try:
cmd.my_func()  # if it's loaded no exception will be raised
loaded = 1
except:
time.sleep(0.5)
```

But this just hangs, as apparently `time.sleep()` halts the execution of all 
threads, so the plugin won't ever be loaded.

Thanks,
Jared

--
Jared Sampson
Columbia University

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Re: [PyMOL] PyMOL-users Digest, Vol 116, Issue 15

[Sampson, Jared M.]

Hi Annemarie -

Fun problem.  It looks like cmd.transform_selection() only works with 
"molecule" type objects, not with CGOs. You could try doing something like 
what's in the 3rd example in http://www.pymolwiki.org/index.php/Axes, 
calculating the new object matrix itself by transforming the current one, then 
applying it to the object using cmd.set_object_ttt().

Alternatively, if you can reproducibly identify any vector that should be 
perpendicular to the membrane, you could use those points as the start and end 
points for your initial load_cgo command.  For example, if your receptor 
happens to have a symmetric channel, something like this might work.

```
# create pseudoatoms at the average positions of residues at the top and bottom 
of the chain
pseudoatom top,  and n. CA and chain A+B+C+D
pseudoatom bot,  and n. CA and chain A+B+C+D

# Orient to the pseudoatoms and fine tune the positions along the viewport Y 
axis.
# (Make sure you don't move the view until you're done positioning the 
pseudoatoms.)
orient (top or bot)
turn z, 90  # assuming `orient` put them along X and you want them along Y
translate [0, 2, 0], top
translate [0, -1.5, 0], bot

# Get the coordinates of the two end points
from pymol import stored
stored.start = []
stored.end = []
iterate_state 1, top, stored.start = (x,y,z)
iterate_state 1, bot, stored.end = (x,y,z)

# Create the CGO cylinder (I made it semitransparent)
from pymol.cgo import ALPHA, CYLINDER
x1,y1,z1 = stored.start
x2,y2,z2 = stored.end
r1,g1,b1 = 1, 1, 0
r2,g2,b2 = 1, 1, 0
radius = 100
cmd.load_cgo([ ALPHA, 0.5, CYLINDER, x1, y1, z1, x2, y2, z2, radius, r1, g1, 
b1, r2, g2, b2 ], "membrane")

```

Not sure if that will be applicable to your use case, but hopefully it will at 
least give you an idea of one approach that could work.

Hope that helps.

Cheers,
Jared

--
Jared Sampson
Columbia University


On Jan 29, 2016, at 4:33 PM, Honegger Annemarie 
mailto:honeg...@bioc.uzh.ch>> wrote:

I am trying to show some cell surface receptors and to indicate their position 
relative to the membrane.

I thought to indicate the plane of the membrane by a flat disk, a ago cylinder.

x1,y1,z1 = 0, -1, 0 # start point
r1,g1,b1 = 1, 1, 0 # color (yellow)
x2,y2,z2 = 0, -2, 0 # end point
r2,g2,b2 = 1, 1, 0 # color (yellow)
radius = 100
cmd.load_cgo( [ 9.0, x1, y1, z1, x2, y2, z2, radius, r1, g1, b1, r2, g2, b2 ], 
"membrane" )

When I try to move this cylinder into the correct position with 
cmd.transform_selection,
using the transformation parameters extracted from get_view (reordering them as 
needed)
I get the error message "Selector-Error: Invalid selection name “membrane” “

The same transform command works fine if I apply it to a pseudo atom originally 
generated with coordinates 0,0,0.

Any suggestion how else I could indicate the membrane, or how I could place my 
ego object parallel
to the screen yz plane? I have to be able to do this in a reproducible fashion, 
as I have to  do this
for a large number of constructs that bend my receptors relative to the 
membrane in various ways.

Thanks for your help
Annemarie
___

Dr. Annemarie Honegger PhD
Department
of Biochemistry
Zürich University
Winterthurerstrasse 190
CH-8057 Zürich
Switzerland

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Re: [PyMOL] iterate names in group

[Sampson, Jared M.]

Hi Jordan - 

Grouped object names use dots to indicate group inheritance ("groupA.obj1"), so 
maybe try something like this:

```
from pymol import stored

stored.group_names = []
group_name = "groupA"
for obj in cmd.get_names():
if obj[0:len(group_name)] == group_name:
# either add them to a list to use later
stored.group_names.append(obj)
# or run your `iterate` command here
#cmd.iterate(...)
print sorted(stored.group_names)

```

For me the printed dummy output looks like:
['groupA', 'groupA.obj1', 'groupA.obj2', ... ]

Hope that helps.

Cheers,
Jared

> On Jan 25, 2016, at 2:34 PM, Jordan Willis  wrote:
> 
> Hi,
> 
> Is there a way to iterate through the names that have been grouped? 
> 
> iterate 
> 
> doesn’t seem to do it because it kills my pymol app.
> 
> Jordan
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Re: [PyMOL] surface accuracy

[Sampson, Jared M.]

Hi "Someone Else" -

The `rotate` command (http://pymolwiki.org/index.php/Rotate) actually 
transforms the atomic coordinates of the object in model space, which I believe 
are only stored to 3 decimal places (as in PDB files), so there will probably 
be some slight changes in how the surface is rendered between frames.  What 
should work better for you is the `turn` command 
(http://pymolwiki.org/index.php/Turn), which achieves a similar result, but 
instead moves the camera, so the atomic coordinates (and therefore the surface) 
will remain the same for each frame.

Also, you can generate these kinds of movies directly in PyMOL without having 
to write a .pml script for each frame, using e.g. the `mset` command.   Check 
out http://pymolwiki.org/index.php/MovieSchool, which has a good introduction.

Hope that helps.

Cheers,
Jared

On Jan 16, 2016, at 6:42 PM, Someone Else 
mailto:tno...@gmail.com>> wrote:

Hi,

I made a movie with rotating protein structure:
https://vid.me/Y4Nb
The structure itself is static, so the surface should also stay the same. But 
it clearly changes during the movie. Any round-off errors? Is there any  fix 
for this problem?

I rendered frames for the movie by generating a set of PML files like:

load 2gb1.pdb
rotate x, angleX
rotate y, angleY
ray 800,600
png frame_i.png


Thanks for your help,

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Re: [PyMOL] using "bymol" in combination with "within"

[Sampson, Jared M.]

Hi Andrew -

If you're just looking to expand the selection from atoms in water molecules to 
entire water molecules, I would actually use `byres` instead of `bymol`.  The 
`bymolecule` selector is apparently dependent on how PyMOL sees the bonds (e.g. 
try `fetch 3ghe, async=0; select test, bymol chain H and resi 30` -- you only 
select up to the gap at resi 127).  `Byres` should get the entire HOH residue 
as defined by the residue name and number, as long as they are unique for each 
of your water molecules.

So, in short, this should work:

select closewats, byres (wats within 3 of solute)

Or as Spencer mentioned, using the built-in keywords:

select closewats, byres (solvent within 3 of organic)

Or, if you have multiple organic components and only one of them is your 
ligand, which has the residue name DRG:

select closewats, byres (solvent within 3 of resn DRG)

Hope that helps.

Cheers,
Jared

—
Jared Sampson
Graduate Student
Department of Biochemistry and Molecular Biophysics
Columbia University

On Dec 2, 2015, at 2:57 PM, Andrew Kalenkiewicz 
mailto:ajkalenkiew...@gmail.com>> wrote:

Hi Spencer,

Thanks for your response! I was also originally under the impression that my 
selection #2 should be a superset of selection #1, but that is definitely not 
the case. There are atoms in selection #1 that are not included in selection #2.

What I want to do is select all the water molecules that have at least one of 
their atoms within 3 angstroms of my protein-ligand complex (the solute). Based 
on the above discrepancy, I know that selection #2 does not give me this. This 
is corroborated by an independent calculation I did in a different program (the 
Bio3D pacakge in R).

All best,
Andrew

On Wed, Dec 2, 2015 at 10:53 AM, Spencer Bliven 
mailto:spencer.bli...@gmail.com>> wrote:
Andrew,

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

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

select wats within 3 of (bymolecule solute)

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

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

-Spencer

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

On Wed, Dec 2, 2015 at 3:32 PM Andrew Kalenkiewicz 
mailto: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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University of Michigan, Ann Arbor
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Re: [PyMOL] on axis of the subunit

[Sampson, Jared M.]

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 
mailto:smith_liu...@163.com>> 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." 
mailto:jms2...@cumc.columbia.edu>> 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 
mailto:smith_liu...@163.com>> 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 axis of the subunit

[Sampson, Jared M.]

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 
mailto:smith_liu...@163.com>> 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 async

[Sampson, Jared M.]

Hi Smith -

I assume you’re referring to something like `fetch 1xyz, async=0`.  This means 
that the PyMOL interpreter should wait until the PDB file is downloaded and 
loaded before continuing with the next step.

Normally, the commands will be issued one immediately after the other and the 
next one may start before the current one finishes.  So multiple commands may 
be running at the same time, or asynchronously.

For example, if you were to run a script containing the following:

fetch 1xyz
as cartoon
color blue, chain A

Depending on the speed of the download, the protein would likely end up looking 
just like if you only called `fetch 1xyz`, as the other two commands will have 
started (and finished) before the `fetch` is complete.

Cheers,
Jared


On Nov 21, 2015, at 6:11 AM, Smith Liu 
mailto:smith_liu...@163.com>> wrote:

Dear All,

Will you please tell me the meaning of "async"in pymol script?

Smith



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Re: [PyMOL] .pdb files and rendering software

[Sampson, Jared]

Hi again, Joe -

Try saving in COLLADA format with 
`save myfile.dae` (in PyMOL v1.7.3.2 or later).

If you're using Blender, you'll need to `set collada_geometry_mode, 1`, because 
Blender only supports polylists for COLLADA import, and not the more efficient 
structures like triangles, tristrips, trifans, etc.  I've never used Maya, so 
I'm not sure if it has any peculiarities in its COLLADA support.

There is also VRML2, which you can get with `save myfile.wrl`, but I'm partial 
to the COLLADA exporter, since I wrote it.  ;)

Cheers,
Jared

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On Aug 15, 2015, at 1:42 PM, Joseph Georgeson 
mailto:joseph.george...@weizmann.ac.il>> wrote:

Hi all,

I was wondering the best options for importing .pdb files into rendering 
programs like Maya or Blender. Right now I'm trying mMaya with Maya2014 but 
seem to have many issues. Any suggestions?

Thanks,
JoeG
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Re: [PyMOL] How does PyMOL create .obj file?

[Sampson, Jared]

Hi Joe -

The coordinate system in the .obj file is in camera space, where (0,0,0) is the 
center of the viewport, positive x to the right, positive y up, and positive z 
out of the screen toward the viewer.  If you want to correlate them, you would 
need to transform the model coordinates using the view matrix or, probably more 
easily, set the view to coincide with model space, as specified under "Space 
and File saving" 
here.

FYI, there is a bug in .obj output 
of spheres, which are output as a single triangle face with identical 
coordinates for all three points.  Needless to say, you can't see them, unless 
you zoom in really close.  Also, cylinders and cones are not yet implemented in 
.obj output, so, basically the only representation fully supported is surfaces, 
which are made entirely of triangle meshes.

Hope that helps.

Cheers,
Jared

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Xiangpeng Kong Lab
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On Aug 15, 2015, at 1:34 PM, Joseph Georgeson 
mailto:joseph.george...@weizmann.ac.il>> wrote:

Hi all,

I'm trying to correlate an .obj file created in PyMOL to the actual molecular 
coordinates of a protein from the .pdb file. Is this possible? Does anyone know 
how PyMOL creates the .obj file?

Thanks,
JoeG
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Re: [PyMOL] How to get TTT matrix in PyMOL 1.7.6?

[Sampson, Jared]

Hi Paweł -

Honestly, if you prefer to use matrices, I'd say just go ahead and use 
get_object_matrix; I doubt it's going away any time soon.  You may want to use 
this in combination with 
transform_selection.

Also maybe check out Christoph Gohlke's transformations.py 
script.  It offers several 
tools for manipulating quaternions, matrices, and angle/axis operations.  I 
think there's also a newer version on his website, which is linked from the 
wiki page.

Cheers,
Jared

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On Aug 6, 2015, at 4:04 AM, Paweł Tomaszewski 
mailto:croov...@gmail.com>> wrote:

Hello,
I've created a CGO in pymol script (a cone) and I need to make some 
transformations on it. I've found that it is easier for me to modify a TTT 
matrix rather than using translate/rotate functions.

Documentation says [http://www.pymolwiki.org/index.php/Get_object_matrix] 
get_object_matrix is unsupported operation. So how to get/set TTT?

The problem is, that I get (from external source) position in quaternions and 
now I need to make my CGO position equal to those quaternion. How can I make it 
work?

Thanks
Paweł Tomaszewski
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Re: [PyMOL] secondary structure disappears

[Sampson, Jared]

I'm posting the following solution on behalf of Thomas Holder (whose 
sourceforge.net email address is currently down due to 
SF server issues), to ensure it is added to this thread in the archive:

This is due to chain identifier conflict. He's merging 6 models with identical 
identifiers. A simple fix would be:

fetch 3ow9, type=pdb1, async=0
split_states 3ow9
alter 3ow9_000*, segi=model[-1]
create combined, 3ow9_000*

Changing the chain IDs as Rob suggested would also work.

Cheers,

Jared

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On Jul 23, 2015, at 2:42 PM, Robert Campbell 
mailto:robert.campb...@queensu.ca>> wrote:

Hi Adam,

I think you also want to make sure that each strand as a distinct chain
ID if you want the cartoon representation to work correctly.

Unfortunately that means you have to use "alter" but to change the
chain IDs on the objects created by the split_states command before
merging them all into one object.

It worked for me when I tried that with 3ow9.

Cheers,
Rob

On Thu, 2015-07-23 09:23 EDT, "H. Adam Steinberg"
mailto:h.adam.steinb...@gmail.com>> wrote:

Hi All,

If you fetch 3ow9 in PyMOL,
split_states to get all six of the strands,
select all, then copy to object,
You only get the two strands, not all six, I need all six to be
duplicated into one object so I can make a long amyloid fibril.

If I open the pdb file for 3ow9 in text edit and remove all the text
for the individual models (and the waters), then open that file in
PyMOL I get all six strands, but all the cartoon secondary structure
is missing except for the two original strands. I tired running the
alter command in PyMOL, it changes the secondary structure in the
other objects I have open but not in this pdb.

I see the Sheet entry in the pdb file but I don’t know how to
duplicate and change the sheet entry so it applies to the other four
strands in the file.

Could someone point me to a place on the web that explains how to
change the sheet entry (I’d like to learn how to do it)? or tell me
how to fix this pdb file?

Thanks!



H. Adam Steinberg
7904 Bowman Rd
Lodi, WI 53555
608/592-2366





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Re: [PyMOL] how to measure the angle between two protein complexes

[Sampson, Jared]

Hi Yeping -

To calculate such an angle, you will need two vectors, which you can create 
with some pseudoatoms and the 
orient command.  Before you start, 
you should create named selections for the ring and filament.

Step 1: Generate a vector perpendicular to the ring.  This method assumes it is 
fairly symmetrical.

orient ring_selection# should end up with the view centered on the ring
pseudoatom ring1# create a pseudoatom at the center of the viewport
translate [0, 0, 10], ring1# move that pseudoatom 10Å along the viewport 
z-axis
pseudoatom ring2# also at the center of the viewport
distance ring_vector, ring1, ring2# for display only--make sure it looks 
right!

Step 2: Generate a vector parallel to the filament.  Assuming the filament is 
fairly linear, you can use the same approach.  `Orient` should place it along 
the viewport X axis.  Then place a pair of pseudoatoms and move them left and 
right.

orient filament_selection# this should end up being horizontal on the screen
pseudoatom fil1
translate [-10, 0, 0], fil1
pseudoatom fil2
translate [10, 0, 0], fil2
distance filament_vector, fil1, fil2

You could also create pseudoatoms at average positions of a selection at each 
end of the filament instead of using `orient`.

Step 3: From the 4 pseudoatoms, you can get 2 vectors by subtracting the 
coordinates.  Check out Iterate_state for using coordinates in a script.

Step 4: Calculate the angle.  I'll also leave it up to you to calculate the 
angle once you have the two vectors, but have a look at 
http://www.pymolwiki.org/index.php/AngleBetweenHelices or 
http://www.pymolwiki.org/index.php/Elbow_angle for some clues.

With all that said, if you don't want to do all of that, you could always just 
hold a protractor up to your computer monitor!  :)

Cheers,

Jared
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Xiangpeng Kong Lab
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On Jul 8, 2015, at 10:40 PM, sunyeping 
mailto:sunyep...@aliyun.com>> wrote:

Dear all,

 I have a protein complex which has a ring-like shape; and another protein 
complex which forms a long filament. Is there a way in Pymol to measure the 
angle between the ring plane and the filament?

Best regards.


Yeping Sun


Institute of Microbiology, Chinese Academy of Sciences

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Re: [PyMOL] how to measure the distance of 2 hydrophobic residues

[Sampson, Jared]

Hi Smith -

This won't tell you anything about the hydrophobic interaction itself, but if 
you want to get the distance between the average positions (like center of 
mass, but without mass) of two groups of atoms to use as an "approximate" 
distance between the two residues/sidechains/etc., you can try something like 
this:

pseudoatom ps1, resi 1 and sidechain
pseudoatom ps2, resi 2 and sidechain
show nb_spheres, ps*
distance d1, ps1, ps2

This will create a pseudoatom at 
the geometric center of each side chain and use that for the distance 
measurement.

This is particularly useful with things like pi-cation stacking, where you want 
to measure the distance between approximately parallel planar groups like 
arginine guanidinium groups and aromatic rings.

Hope that helps.

Cheers,
Jared

Jared Sampson
Xiangpeng Kong Lab
NYU Langone Medical Center
http://kong.med.nyu.edu/






On Jul 8, 2015, at 9:20 PM, Osvaldo Martin 
mailto:aloctavo...@gmail.com>> wrote:


Hi Smith,

Distances are generally defined for two points (although it is possible to 
generalize the idea to higher dimensions). Since residues are 3D objects, there 
is not such a thing as THE distance between 2 residues. Being said that, as we 
generally model residues as a collection of spheres (atoms) you can define 
several distances, for example:

  *   The distance between the centroids of each residue
  *   The minimum distance between any two atoms of each residue
  *   The average distance over all atoms of each residue
  *   The distance between Ca
  *   etc…

Depending on your problem one of those distance could be a reasonable proxy for 
“hydrophobic interaction”, but maybe you will need to use a more complex model 
to solve your problem may be some energy scoring function (AKA forcefield).

I hope this helps.

Cheers,
Osvaldo.

On Wed, Jul 8, 2015 at 9:48 PM, Smith Liu 
mailto:smith_liu...@163.com>> wrote:



Dear Osvaldo,

I want to know whether hydrophobic interactions between 2 residues exist, thus 
I want know the distance between the 2 residues, rather than the distance 
between the atom of each of the 2 residues.

Is any sense and method we measure the distance between 2 residues?

Best regards.

Smith





At 2015-07-09 00:52:32, "Osvaldo Martin" 
mailto:aloctavo...@gmail.com>> wrote:
Hi Smith,


If you want to measure the distance between two residues (hydrophobic or not) 
you could choose and atom from each residue and measure the distance between 
those two atoms. Is this what you want to do, or something more complex?  Could 
you provide more details about your problem?

Cheers,
Osvaldo.

On Wed, Jul 8, 2015 at 12:33 PM, Smith Liu 
mailto:smith_liu...@163.com>> wrote:
Dear All,

Pymol has the function to measure the distance betweeen 2 atoms. In addition, 
if 2 hydrophobic residues are close enough, there will be hydrophobic 
interactions betweem them. But will you please tell me how to measure the 
distance between 2 hydrophobic residues by pymol?

Best regards.

Smith



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Re: [PyMOL] efficiency assigning b-factors

[Sampson, Jared]

Hi Jordan -

I think you're doing it exactly the way I would, given an existing dict 
containing the values.  Note, however, that if you have multiple loaded, or 
multiple chains with the same residue numbers, you may wish to be more specific 
with your selection string; your current script will alter every residue with 
the given resi # in all chains of all loaded objects.

If you're having to do this multiple times with the same structure and it's 
slow each time (e.g. while creating a figure from a script), maybe consider 
saving a new PDB file with the modified B-factors using PyMOL's `save` command, 
so you can just load it directly.

# After your `alter` script
save myfile_mod_b.pdb, myfile

# Then next time load the new version with the same name
# as before to avoid breaking the rest of the script. Now you can
# remove the `alter` for-loop from the script.
load myfile_mod_b.pdb, myfile

Hope that helps.

Cheers,
Jared

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On Jun 16, 2015, at 2:15 AM, Jordan Willis 
mailto:jwillis0...@gmail.com>> wrote:

Hi,

I have a dictionary that has a bunch of values I want to assign to b-factors in 
order to color by. In my script:

for residue in data:
   cmd.alter(“resi 
{}”.format(residue[‘resnum’]),”b={}”.format(residue[‘value’]))

This executes the alter command for each residue. For some reason, its taking 
forever in my script. Is there something inherently inefficient about alter? 
And is there anyway to fix it? Perhaps, assign a bunch of b-factors at once.

Jordan
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Re: [PyMOL] MacPyMOL in command line mode

[Sampson, Jared]

Hi CY -

If you're using the -c flag, you shouldn't need a windowing system at all.  The 
following works for me between a MacBook Air and an iMac, both running 10.9.5, 
with MacPyMOL 1.7.6.0 installed on the iMac.

### begin shell ###
(macbook-air)~ › ssh jared@imac
Password:
Last login: Fri May 29 10:37:12 2015 from macbook-air
(imac)~ › /Applications/MacPyMOL.app/Contents/MacOS/MacPyMOL -cqkd "fetch 3opl, 
async=0; save tmp.png"
PyMOL>fetch 3opl, async=0; save tmp.png
HEADERHYDROLASE   01-SEP-10   3OPL
TITLE ESBL R164H MUTANT SHV-1 BETA-LACTAMASE
COMPNDMOL_ID: 1;
COMPND   2 MOLECULE: BETA-LACTAMASE SHV-1;
COMPND   3 CHAIN: A;
COMPND   4 SYNONYM: PIT-2;
COMPND   5 EC: 3.5.2.6;
COMPND   6 ENGINEERED: YES;
COMPND   7 MUTATION: YES
 ObjectMolecule: Read secondary structure assignments.
 ObjectMolecule: Read crystal symmetry information.
 Symmetry: Found 4 symmetry operators.
 CmdLoad: "./3opl.pdb" loaded as "3opl".
 Ray: render time: 0.99 sec. = 3622.2 frames/hour (0.99 sec. accum.).
 ScenePNG: wrote 640x480 pixel image to file "tmp.png".
(imac)~ › exit
logout
Connection to imac closed.
(macbook-air)~ ›
### end shell ###

The file ~/tmp.png is created on the iMac.  I also used -k to prevent PyMOL 
from reading my ~/.pymolrc; and -d to pass the string of PyMOL commands.  If 
you're running a .pml script, you don't need to include -d, just the path to 
the script (which must be on the remote machine).  As you noted, when it runs I 
see the MacPyMOL application icon pop into the Dock on the iMac and then 
disappear as soon as the script finishes.

Hope that helps.

Cheers,
Jared

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On May 28, 2015, at 11:28 AM, Yu Chen mailto:che...@umbc.edu>> 
wrote:

Hello,

I am trying to run MacPyMOL in command line mode with "-c -q" option. While 
directly logged in to the computer, it works. But if I ssh into the computer 
(even with X11 forwarding enabled), it fails with some errors about connecting 
to WindowServer  And I can tell it actually tried to launch the GUI very 
briefly, then returned to the command line to process the scripts. Is this 
right? Can I run it remotely on another computer just from pure command line.

Thanks.

CY
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[PyMOL] Bug report: cmd.fab() with existing object name produces unexpected results and downstream segfault

[Sampson, Jared]

In the process of investigating Ben Bobay's 
question about 
keyboard shortcuts for adding a methyl group, I may have found a bug, or at 
least unexpected behavior, in cmd.fab().

When first creating a peptide, it works fine:

fab , pep

However, if I call it again with a different (or the same) sequence,

fab , pep

The new residues are overlaid right on top of the initial ones, and 
interspersed in the sequence order (overlapping sticks, 
Screenshot1).
  This breaks cartoon representation, as Ala1 and Ala2 are no longer contiguous 
in the sequence (`as cartoon` leaves nothing drawn, 
Screenshot2).

Also, something happens when switching representations (e.g. from cartoon to 
sticks) that segfaults with certain sequences.  I can semi-reproducibly produce 
a segfault (perhaps 2/3 of the time) with the following commands in Open Source 
PyMOL (1.7.4.0), PyMOLX11Hybrid (1.7.6.0), and MacPyMOL (1.7.6.0).

reinitialize
fab , pep
fab ADAA, pep
as cartoon
as sticks
# sometimes it takes an extra line or two
#fab AADA, pep
#as sticks

I believe this happens specifically when some residues are the same and some 
are different: I haven't been able to produce a segfault using "" as the 
second sequence, but adding the third sequence (second to last line) 
reintroduces the segfault.

I would expect calling `fab` with an existing object name to perform one of the 
following actions (from most to least preferable):

1. Append the residues to the C-terminus of the existing object with sensible 
geometry, similar to `editor.attach_fragment()`.
2. Add a new state to the object with the new sequence, as with 
`cmd.load(state=0)`.
3. Overwrite the existing object (probably not a good idea).

It may also be helpful to have additional arguments to fab, such as append=1 or 
state=0, depending on which of the above options might be implemented.

I'm adding this as a bug report on SourceForge as well.

Cheers,
Jared
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Re: [PyMOL] Add fragment

[Sampson, Jared]

Hi Ben -

Try this:

editor.attach_fragment("pk1", "methane", 1, 0)

Here's how I tracked this down, not having known about this function before 
your email.  cmd._alt() and likewise cmd._ctrl() are functions (you can see for 
yourself in the source code in pymol/modules/pymol/cmd.py), and they are 
basically wrappers (via internal.py and back through cmd.py again) for 
functions in keyboard.py called keyboard.get_alt() and keyboard.get_ctrl(), 
which each return a dictionary list of commands to run for each shortcut key.  
For example:

def get_alt(self_cmd=cmd):
return {
'1' : [ editor.attach_fragment  , ("pk1","formamide",5,0), {}],
'2' : [ editor.attach_fragment  , ("pk1","formamide",4,0), {}],
'3' : [ editor.attach_fragment  , ("pk1","sulfone",3,1), {}],
'4' : [ editor.attach_fragment  , ("pk1","cyclobutane",4,0), {}],
'5' : [ editor.attach_fragment  , ("pk1","cyclopentane",5,0), {}],
'6' : [ editor.attach_fragment  , ("pk1","cyclohexane",7,0), {}],
'7' : [ editor.attach_fragment  , ("pk1","cycloheptane",8,0), {}],
'8' : [ editor.attach_fragment  , ("pk1","cyclopentadiene",5,0), {}],
'9' : [ editor.attach_fragment  , ("pk1","benzene",6,0), {}],
'0' : [ editor.attach_fragment  , ("pk1","formaldehyde",2,0), {}],
'a' : [ editor.attach_amino_acid, ("pk1","ala"), {}],
'b' : [ editor.attach_amino_acid, ("pk1","ace"), {}],
'c' : [ editor.attach_amino_acid, ("pk1","cys"), {}],
'd' : [ editor.attach_amino_acid, ("pk1","asp"), {}],
'e' : [ editor.attach_amino_acid, ("pk1","glu"), {}],
'f' : [ editor.attach_amino_acid, ("pk1","phe"), {}],
...etc
}

So to add a methyl group, just model it after the cyclobutane example, and just 
run the editor.attach_fragment command (which you can explore in 
pymol/modules/pymol/editor.py) for methane.  A little more info from the 
editor.attach_fragment() docstring:

def attach_fragment(selection,fragment,hydrogen,anchor,_self=cmd):
'''
ARGUMENTS

selection = str: must be "pk1"

fragment = str: fragment name to load from fragment library

hydrogen = int: hydrogen atom ID in fragment to fuse

anchor = int: none-hydrogen atom ID in fragment to fuse
'''

You can also define custom 
fragments.

Also, in case you didn't know about it, an easier way to create your peptide 
might be the `fab` function (so long as you don't need to continue editing it 
afterward):

fab GTHYRD, my_peptide

Hope that helps!

Cheers,
Jared

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On May 20, 2015, at 8:43 AM, Benjamin Bobay 
mailto:bgbo...@ncsu.edu>> wrote:

H
​i All,

I was wondering if someone could point me to the correct notation for something.

When making a peptide from the command line one could type:

for aa in "GTHYRD":cmd._alt(string.lower(aa))

Let's say that I want to add a methane. The key code is CTRL+SHIFT+M

I was wondering how to alter the "cmd.​
_
​alt" to be CTRL-SHIFT.

I've tried ​
​"cmd._ctrl+_shift"
"cmd._ctrl and _shift"
"cmd.(_ctrl and _shift)"​
"cmd._ctrl._shift"

Nothing has worked. I searched the list serve but came up empty on how to 
combine two keys to the "cmd'.

Any help would be greatly appreciated!

Thanks
Ben

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Re: [PyMOL] Load very similar molecules into distinct objects?

[Sampson, Jared]

Hi Jorge -

As long as the filenames are different, the molecules should end up in separate 
objects. If the filenames are in fact the same (e.g. same filename but in 
different folders), try explicitly naming the objects using the PyMOL command 
line:

load path/to/the/first/mol1.pdb, first_mol
load path/to/another/mol1.pdb, second_mol

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

Hope that helps.

Cheers,
Jared

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On May 5, 2015, at 2:16 PM, Jorge Fernandez de Cossio Diaz 
mailto:cos...@cim.sld.cu>> wrote:

When I load two molecules into pymol which are very similar, they automatically 
get clumped into the same object as different states.
How can I circumvent this behavior? I want to load two molecules which are very 
similar into different objects. I know about the "split_states" command, but I 
am looking at a bunch of pairs of molecules and running "split_states" every 
time I load a pair is a pain.

Is there a command I can use instead of load or a way to call "pymol mol1.pdb 
mol2.pdb" so that PyMol knows that mol1.pdb and mol2.pdb should go to two 
different objects?
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Re: [PyMOL] moving objects

[Sampson, Jared]

Hi Marcelo -

Is Object 2 actually a pseudoatom?  Or, if not, can it be placed separately 
from Object 1?  If either of those are the case, it would be much easier to 
place the pseudoatom at a point equidistant from the two ends of Object 1 than 
mess with rotation matrices, etc.  Here’s what I worked out.


# get a long protein, e.g. collagen
fetch 1bkv, async=0
as cartoon

# place a couple helper pseudoatoms at the "ends" of the collagen 
(approximately)
pseudoatom nterm, resi 2+31+61, vdw=2
pseudoatom cterm, resi 30+60+90, vdw=2
select ends, nterm or cterm
show spheres, ends

# orient the helper pseudoatoms along one of the display axes (usually ends up 
being x)
orient ends

# place another helper pseudoatom at the "midpoint" of the object
pseudoatom obj_b, ends, vdw=4
show spheres, obj_b

# move it (e.g.) 50Å away
translate [0,0,-50], obj_b

# make sure it looks right
orient ends or obj_b


You could then load your “real” Object 2 (if necessary) and move it to the 
obj_2 pseudoatom using a combination of `origin` and the COM script 
(http://www.pymolwiki.org/index.php/Com), for example.  Haven’t tested that, 
but it should be possible.

Hope that helps!

Cheers,
Jared

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On Apr 28, 2015, at 1:57 PM, Marcelo Marcet 
mailto:mmar...@nait.ca>> wrote:

Hi Pymol Users,

I have 2 objects (objects 1 and 2) and I would like to re-orient object 1 so 
that the distance from either end of object 1 becomes the same to object 2 (see 
image). Is there a way to achieve this in PyMol?

I have tried using the mouse in edit mode and I have tried using the 
rotate/translate commands. Neither method can move object 1 without altering 
the position of the lower end of object 1.

Regards,
Marcelo


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Re: [PyMOL] MacPyMol working dir

[Sampson, Jared]

Hi Luigi -

To get the right working directory, you can use the full path to the binary 
followed by the `-d` flag to run a command (`cd $PWD`) once PyMOL opens.  
Personally, I'd alias it in ~/.profile like this:

alias macpymol='/Applications/MacPyMOL.app/Contents/MacOS/MacPyMOL -d "cd $PWD"'

Alternatively, you could install the open source version, e.g. using 
Homebrew,
 which opens properly in the working directory as well.

Cheers,
Jared

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On Apr 15, 2015, at 4:20 PM, Luigi Cavallo 
mailto:lcava...@unisa.it>> wrote:

Hi,

I just started to use MacPyMol from standard unix like Pymol, and I would like 
to start MacPyMol from a specific working directory, to have pdb and pse files 
I am working on right at hand.  However, I can’t understand how to get this 
done.  I can start by command line

open -a MacPyMol   or
/Applications/MacPyMOL.app/Contents/MacOS/MacPyMOL

and it works, but as I try the “open” option, it starts from my home directory, 
so I have to go down the folders tree. Annoying.  I’ve seen that I can start as

/Applications/MacPyMOL.app/Contents/MacOS/MacPyMOL -m

I have a less fancy graphics, but if I try to “open” a file, it starts looking 
in the directory I started from. Cool. However, according to the manual I loose 
plugin control.
Just wondering if there is a way to have the “open” file starting from the 
working directory with the fancy interface of MacPyMol, rather than the basic 
Unix interface.

Thanks,
gg-kawa


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Re: [PyMOL] cartoon putty present in pymol

[Sampson, Jared]

Hi Wenfu -

Cartoon putty representation varies the diameter of the putty tube based on the 
B-factor column in the loaded PDB file.  In your example file, all the 
B-factors are 0.00.  Perhaps you could use `cartoon tube` instead, which is 
similar to putty, but uses a single cartoon_tube_radius setting to specify the 
size of the tube.

Cheers,
Jared

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On Apr 13, 2015, at 11:39 AM, m...@mskcc.org wrote:

Hi pymol users,

I have a pdb file, which is from the result of a molecular dynamics simulation. 
I want to present the structure with cartoon putty in pymol.
But I can only make it cartoon putty in Macpymol 0.99 version. When I use 
pymol1.7 or 1.3 version, the error is like this: Extrude-Warning: invalid putty 
settings (division by zero)
I attach part of the pdb file and hope to get your suggestions.

Thanks,
Wenfu
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Re: [PyMOL] Pymol molecular visualisation

[Sampson, Jared]

Hi James -

Here is how I would label your objects in grid_mode:

# For each object, create a pseudoatom at its center of geometry to position 
the label
pseudoatom myobj_label, myobj

# Set the label text for the pseudoatom
label myobj_label, "My Object"

# To show the label and the object in the same grid, combine them in a group
# (Alternatively, you can use the 
grid_slot setting for more 
fine-grained control.)
group myobj_grp, myobj*

# Adjust the size and position of the label.  Label position can also be 
adjusted per-object.
set label_size, 10
set label_position, [10, 10, 0]
set label_position, [-10,-10,0], myobj_label

Hope that helps.

Cheers,
Jared

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On Apr 12, 2015, at 9:44 AM, James Starlight 
mailto:jmsstarli...@gmail.com>> wrote:

Thanks !
still have not found solution for grid-mode display:
1- I need to show names of each opened object near its cartoon

2- I need to increase spacing of grid border (m.b like just empty
space)- to better discriminate between opened objects in case of its
high zooming

J

2015-04-11 14:51 GMT+02:00 João M. Damas 
mailto:jmda...@itqb.unl.pt>>:
1- See http://www.pymolwiki.org/index.php/Ray_Trace_Gain. However, from my
experience, I don't think the setting works too well, so what I usually do
is to increase the resolution of the raytrace, which makes the black outline
thinner.

On Fri, Apr 10, 2015 at 4:48 PM, James Starlight 
mailto:jmsstarli...@gmail.com>>
wrote:

Dear Pymol users!

Here I will ask some question regarding visualization issues in pymol.

1- Using ray_trace_mode, 1 I need to decrease at least twisty width of
black countour line (especially in the loop segments).

2- Being in the split mode (visualization of the several objects on
one screen) I need to show title of each of the objects somewhere near
of its cartoon area (e,g in right upper corner)- just to know on the
produced picture names of the corresponded cartoon.

3- Also please have a look on my another topic regarding visualization
of B-factor gradients: actually I need to revert its existing color
pattern and select residues according to it's actual B-factor values
(E.g with B-factor=0, with negative and/or positive) for its
subsequent selective visualization.

Thanks a lot for the advises!


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Re: [PyMOL] Colouring nucleic acids, without changing the colouring of amino acids

[Sampson, Jared]

Hi Brenton -

To avoid coloring e.g. Glycine when you only want to color e.g. guanine, prefix 
the residue name with “D” (as the residues are shown in the Sequence viewer) 
for DNA.  I believe RNA works the same way with “R” as well.

set cartoon_color, green, resn DG

To color the DNA backbone, you could try:

color pink, resn DA+DC+DG+DT and bb.

or, if you know the chain IDs,

color pink, 2XCT and chain A+B+C+D+E and bb.

Hope that helps.

Cheers,
Jared

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On Mar 24, 2015, at 11:47 PM, Brenton Horne 
mailto:brentonho...@ymail.com>> wrote:

Hi,

I've seen this (Example 1 on 3DNA) and 
I noticed to colour each nucleic acid differently they used something like:

set cartoon_color, green, resn G

for each of the four different nucleic acids. When I ran this for 2XCT bio 
assembly 1 it coloured amino acids with the same single letter codes as the 
four nucleic acids (e.g., G for guanine [nucleic acid] and glycine [amino]) and 
I wanted to know how to run it just for nucleic acids. I thought that something 
like this for each chain containing nucleic acids:

set cartoon_color, green, /2XCT//E and resn G

would do the trick but that would take forever seeing how 8 separate chains 
contain nucleic acids. While we're on this topic I'd also like to know how to 
colour the backbone and sugars via a more efficient method than doing something 
like this:

color pink, /2XCT//E and bb.


for each chain containing nucleic acids.

Thanks for your time,
Brenton
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Re: [PyMOL] Chain Selection doesn't work (MacPymolEdu)

[Sampson, Jared]

Hi Simon -

It looks like your default Python is now 3.x rather than 2.x.  The built-in 
function reduce() was moved to functools.reduce() as of version 3.0.  You can 
confirm whether this is the case via “python --version” on the command line.

One solution might be to make 2.7 the default again, perhaps via symlink to 
/usr/bin/python2.7 or adjusting your $PATH, although honestly I'm not sure 
about which Python is actually used by the precompiled Edu binaries.  Maybe 
others can chime in on that.

Hope that helps.

Cheers,
Jared

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On Feb 16, 2015, at 8:24 AM, Simon Fortier 
mailto:simon.fortie...@umontreal.ca>> wrote:

Hi,
I'm trying to select specific chains with the following command, which used to 
work.

select , /3J3A//D

However, under Yosemite 10.10.2 (latest update), I keep receiving the following 
error msg and can't select chains anymore...very annoying...any ideas?

Traceback (most recent call last):
  File "/Users/Simon/Downloads/MacPyMOLEdu.app/pymol/modules/pymol/parser.py", 
line 254, in parse
self.result=apply(layer.kw[0],layer.args,layer.kw_args)
  File 
"/Users/Simon/Downloads/MacPyMOLEdu.app/pymol/modules/pymol/selecting.py", line 
103, in select
selection = selector.process(selection)
  File 
"/Users/Simon/Downloads/MacPyMOLEdu.app/pymol/modules/pymol/selector.py", line 
113, in process
st = reduce(lambda x,y:x+"&"+y,lst)
AttributeError: 'module' object has no attribute 'reduce'

Thanks

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Re: [PyMOL] unable to export obj

[Sampson, Jared]

Hi Albert -

Surface mode 2 outlines the mesh edges with thin cylinders, but if I remember 
correctly, I think PyMOL’s OBJ export doesn’t do cylinders (or spheres or 
cones), only triangle meshes.  You could try exporting to VRML2 (.wrl) or 
COLLADA (.dae) format and using something like, e.g. Blender to convert to OBJ 
if that’s what you really need.

Hope that helps,
Jared

P.S. Albert - sorry for the duplicate email, I forgot to CC the list last time…

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On Jan 21, 2015, at 5:50 AM, Albert Solernou 
mailto:a.soler...@leeds.ac.uk>> wrote:

Hi,
I am trying to get a .obj file, but fail when setting up surface_type to
2. More explicitly:
load 1ppe.pdb, 1ppe
set surface_type, 2
hide everything
show surface
shows a nice triangulated surface. However,
save myscene.obj
saves an empty file.

I've tried pymol versions 1.7.4 and 1.6.0. Saving into an obj file works
well when surface_type is set to 0, or 1. Any help?

Best,
Albert


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Re: [PyMOL] raytracing a transparant surface, with reflections only on the cofactors inside

[Sampson, Jared]

Thanks for the correction, Thomas.  I saw the following in the terminal window 
and thought it meant the setting was applied as I intended:

PyMOL>set spec_reflect, 0, all and not org
 Setting: spec_reflect set for 2105 atoms in object "1shv".
PyMOL>set spec_reflect, 1, org
 Setting: spec_reflect set for 35 atoms in object “1shv”.

(You’d think I’d know better after having worked with lighting in my COLLADA 
export project...)

Perhaps it would be helpful for cmd.set() to output some kind of warning if a 
selection argument is given, but the setting can only be applied globally?

Cheers,
Jared

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On Jan 14, 2015, at 1:18 PM, Tsjerk Wassenaar 
mailto:tsje...@gmail.com>> wrote:

Hi Thomas,

Thanks for chiming in. I guess this would be a step towards textures/finishes. 
I would really like to see more extended support for those in Pymol. Of course 
that would mostly serve artistic purposes, but I'd gladly raise the suggestion 
that it can do wonders for highlighting :)

Floris, I can join you in the lab tomorrow afternoon (~15pm?), and we can have 
a look what we can do. Maybe a POV-Ray session, like in the old days :) Maybe I 
can even find my finish settings somewhere :)

Cheers,

Tsjerk

On Wed, Jan 14, 2015 at 7:03 PM, Thomas Holder 
mailto:thomas.hol...@schrodinger.com>> wrote:
Hi Floris, Tsjerk, Jared,

all lighting settings in PyMOL are only global, so setting them on objects or 
selections will have no effect. This is not a bug, bug of course can be 
considered a missing feature. We will check how difficult this would be to 
implement on the object or atom level.

Cheers,
  Thomas

On 14 Jan 2015, at 12:07, Floris van Eerden 
mailto:f.j.van.eer...@rug.nl>> wrote:

> Hello Jared and Tsjerk,
>
> I tried your suggestion, but unfortunately it does not work on my computer.
> When I type the command
> set spec_reflect, 0, all
> Pymol gives the following output:
> -->Setting: spec_reflect set to 0.0 in 8 objects.
>
> So it seems okay. But however when I raytrace, I still get all reflections.
> When I subsequently type
> set spec_reflect, 0
> and then raytrace, the reflections are really turned off.
>
> Could this be a bug, or do I forget something?
>
> Thanks
>
> Floris
>
> On 09-01-15 16:55, Sampson, Jared wrote:
>> set spec_reflect, 0, all and not organic

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Re: [PyMOL] raytracing a transparant surface, with reflections only on the cofactors inside

[Sampson, Jared]

Hi Floris -

Tsjerk is correct.  You can set spec_reflect for a selection. Something like:

set spec_reflect, 0, all and not organic

This would turn of specular reflection on anything that’s not a “ligand” atom.

Cheers,
Jared

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On Jan 9, 2015, at 10:42 AM, Tsjerk Wassenaar 
mailto:tsje...@gmail.com>> wrote:


Hi Floris,

I'm not entirely sure whether these are object/selection or global properties. 
But have you tried specifying the selection?

set spec_reflect, 0, protein

Haven't tried it myself, though.

Cheers,

Tsjerk

On Jan 9, 2015 4:07 PM, "Floris van Eerden" 
mailto:f.j.van.eer...@rug.nl>> wrote:
Dear all,

My question is if I can set for different molecules in my system, how much they 
reflect light during ray-tracing

My current system is a protein which contains some cofactors.
The cofactors are coloured according to their B value and the protein is shown 
as a transparant grey surface.
When I start Ray-tracing, I get a quite nice picture. The problem is however 
that the transparant surface is reflecting the light, and becomes therefore at 
some places not transparant, which makes it kinda difficult to see the 
cofactors in the protein (which are the most important). I played around with 
all the spec_reflect, spec_direct settings. When I set spec_reflect to 0, there 
are no reflections anymore, but the image becomes rather dull.
I was wondering if it is possible to select somehow to make only the cofactors 
inside the protein reflect the light, but not the protein surface. In VMD you 
can do this for example by making molecules from different ‘materials’, e.g. 
you can make your cofactors from a reflective material, and your protein 
surface from a non reflective, transparant material. Is something similar 
possible in Pymol???

Thanks for your suggestions,

Floris
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Re: [PyMOL] Dot representation

[Sampson, Jared]

Hi Yarrow -

1. Yes, according to the wiki, the 
dots are located on the vdW surface unless the `dot_solvent` setting is turned 
on (in which case they’re on the solvent accessible surface).

2. Based on the settings listed with “dot” in their names, it doesn’t look like 
dot_transparency is currently available.

Hope that helps.

Cheers,
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On Dec 30, 2014, at 6:48 PM, Yarrow Madrona 
mailto:acacia.madr...@ucsf.edu>> wrote:

Hell Pymolers,

1. Does anyone know what the dot representation for a residue represents? Is it 
the van der waals radii?

2. Is there a way to draw transparency for the dots?

-Yarrow


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Re: [PyMOL] selection of a set of amino acids

[Sampson, Jared]

Hi Alireza -

For renumbering a chain, the program PDBSET in the CCP4 suite is my tool of 
choice.  If your protein is chain A, the command would look something like this:

pdbset xyzin my_protein.pdb xyzout my_protein_renumbered.pdb > wrote:

Thanks for your prompt answer,
numbers resets in every chain - and there is a lot of nucleobases in the 
beginning (A,C,U,G) and MG at the end and these atoms mess up the residues 
number additionally !

can I remove them via pymol ? Thank you


On Sat, Dec 13, 2014 at 5:45 PM, Andreas Warnecke 
<4ndreas.warne...@gmail.com> wrote:

Hi,

There is a script available on the pymol wiki called "zero_residues". This will 
allow you to easily renumber any AA sequence.
As far as other heteroatoms are concerned you could consider removing them 
(remove hetatm), or extract them into a second object.
Another alternative is to simply adjust the coloring command according to the 
pdb.

Hope that helps,

Andreas

On Dec 13, 2014 4:41 PM, "Alireza Kashani" 
mailto:alireza.kashanip...@gmail.com>> wrote:
Dear All,

I would like to colour different regions of a protein in different colour; say 
region one, amino acid number 1 to 100 and region two amino acid 101 to 150; 
However, when I look into a pdb file using pymol; by displaying the residuals, 
I see the residue number 1, does not correspond to the first amino acid; I 
assume, because of other atoms (metals, ions and etc).

I was wondering if I should filter the pdb file, beforehand to be free from 
these metals, or is there any command that I can put them away and make a 
selection based on set of amino acids ?

I appreciate your help,

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Re: [PyMOL] homebrew pymol

[Sampson, Jared]

Hi Ryan -

Have a look at this post, 
which may also help you in creating an app out of your Homebrewed PyMOL.  I’d 
recommend using a symlink within the app bundle to /usr/local/bin/pymol, so 
when you update with homebrew, you don’t have to change anything in the app.

Cheers,
Jared

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On Dec 10, 2014, at 1:13 PM, Walker, Ryan (walker3) 
mailto:walk...@mail.uc.edu>> wrote:

Hi All,

Sorry if this has been asked before. Is there a way to set up it so that you 
can click the pdb file to launch pymol that was installed using home-brew? As 
of right now, when you click the ‘open with’ tab, there is no way to select the 
pymol app that was installed using home-brew of course.  Is there a work around 
for this? Using Mac OS 10.10.

Thanks!

Ryan
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Re: [PyMOL] Super, algorithm

[Sampson, Jared]

Hi Spencer -

If you need a superposition algorithm with a published reference, try 
CEAlign.  Some references are 
listed on the page for the former CEAlign 
Plugin  from 
before it was incorporated into PyMOL (in version 1.3).

Just be careful to note that the order of the first two arguments (target, 
mobile) is switched compared to the `super` and `align` commands (mobile, 
target).

Cheers,
Jared

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On Nov 26, 2014, at 7:13 AM, Spencer Bliven 
mailto:sbli...@ucsd.edu>> wrote:

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 
mailto:aloctavo...@gmail.com>> wrote:
Hi,

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

Thanks.

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Re: [PyMOL] View Matrix operation

[Sampson, Jared]

Hi Louris -

If your view is centered on the atom from which you would like to draw the 
line, and oriented the way you want it, you can achieve something similar to 
what it sounds like you want with the following commands.

center myAtom
move x, -4   # `move` works in camera space
pseudoatom myMarker  # creates a pseudoatom called “marker” at the center of 
the screen
move x, 4# move it back
distance myLine, myAtom, myMarker

To customize the line, have a look at the dash_* settings.  You can show the 
pseudoatom as a sphere as well.  If you want to draw something else (triangle, 
square, etc.) rather than a sphere, you’ll have to do it as a CGO, and the 
“axes.py" script Takanori suggested will be helpful.  You can get the 
coordinates of the pseudoatom using 
iterate_state.

Hope that helps.

Cheers,
Jared

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Xiangpeng Kong Lab
NYU Langone Medical Center
http://kong.med.nyu.edu/






On Nov 19, 2014, at 7:14 AM, Feitsma, L.J. 
mailto:l.j.feit...@uu.nl>> wrote:

Hi all,

I have a small question about transformations with the view matrix in pymol, 
since I’m not very familiar with the architecture of the matrix.

E.g. I take some coordinates [x1,y1,z1], and using cgo objects, I want to draw 
a line/triangle/square to a point distance 4 to the right on the screen (so not 
4 in object x-coördinates!).
How can I use the information in [0:8] of the view matrix to calculate object 
coordinates [x2, y2, z2] needed to draw the line between [x1, y1, z1] and [x2, 
y2, z2]?

Does anyone has an example script, or link about which matrix operation I need 
for this?

Kind regards,

Louris Feitsma

Crystal and Structural Chemistry

Utrecht University

Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539182

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Re: [PyMOL] Access API without the GUI

[Sampson, Jared]

Hi Doug -

You can launch PyMOL with the -c flag for command line only (no GUI).  See 
http://www.pymolwiki.org/index.php/Command_Line_Options for more details.

Cheers,
Jared

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Xiangpeng Kong Lab
NYU Langone Medical Center
http://kong.med.nyu.edu/






On Nov 11, 2014, at 2:56 PM, Douglas Houston 
mailto:douglasr.hous...@ed.ac.uk>> wrote:

Hi all,

Does anyone know if there's a way of accessing Pymol's API without the
GUI? There are some useful functions in there and my loops would
iterate a lot faster if the GUI didn't fire up every time.

cheers,
Doug
_
Dr. Douglas R. Houston
Lecturer
Institute of Structural and Molecular Biology
Room 3.23, Michael Swann Building
King's Buildings
University of Edinburgh
Edinburgh, EH9 3JR, UK
Tel. 0131 650 7358
http://tinyurl.com/douglasrhouston

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Re: [PyMOL] ligand binding site visualisation

[Sampson, Jared]

Hi James -

You could put in a feature 
request to ask that 
non-canonical residues be included in the preset.

In the meantime, the Property 
Selectors, Single-Word 
Selectors, and 
Selection Algebra 
operators and are going to be your friends here.  For dashes, use the 
distance command.

For example, the following lines will show your ligand(s) as sticks and 
residues with any atom near the ligand as lines, and draw dashes for the polar 
contacts between them:

###

select ligand, organic
as sticks, ligand

select binding_site, br. all within 4 of ligand
show lines, binding_site
as nb_spheres, binding_site and solvent

distance ligand_polar_conts, binding_site, ligand, cutoff=3.5, mode=2

###

Using combinations of these selectors, you can come very close to re-creating 
whichever preset you wanted to use.  Hope that helps.

Cheers,
Jared

--
Jared Sampson
Xiangpeng Kong Lab
NYU Langone Medical Center
http://kong.med.nyu.edu/






On Nov 6, 2014, at 3:50 AM, James Starlight 
mailto:jmsstarli...@gmail.com>> wrote:

Dear Pymol users!

Typically when I'm looking at the ligand binding sites (present->show of the 
receptor-ligand.pdb complexes all receptors non-canonical residues or the 
different titrable forms of the standard ones (e.g HIP-protonated HIS or ASH- 
protonated ASN) are recognized as the ligands as well and pymol try to find 
hydrogen bonds or vdv contacts of these residues with its surroundings. How I 
could prevent it to see only on the ligand surrounding within such pdbs? What 
another pymol options will be useful for the ligand sites visualization?


Thanks for help,

James
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Re: [PyMOL] How to calculate Hinge angle

[Sampson, Jared]

Hi Shoeib -

It’s hard to say exactly what you need, because it will vary depending on your 
specific case.

If you’re looking for the change in a hinge angle between two structures of 
multi-domain proteins A and B, you can first superimpose domain 1 of B to 
domain 1 of A, get the matrix of B, superimpose domain 2 of B to domain 2 of A, 
get the second matrix, then use 
transformation.py to 
calculate the axis and angle of that transformation.  Also see this thread 
http://sourceforge.net/p/pymol/mailman/message/25398209/ for more info.

If it has a standard hinge definition, perhaps something like the elbow 
angle of antibody Fab 
fragments, you may be able to calculate it directly from one structure, but, 
again, the details of that calculation will depend on your specific protein.

Hope that helps.

Cheers,
Jared

--
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Xiangpeng Kong Lab
NYU Langone Medical Center
http://kong.med.nyu.edu/






On Nov 2, 2014, at 10:02 PM, Shoeib Moradi 
mailto:shoeib.mor...@monash.edu>> wrote:

Dear All

I am wondering if you know how to calculate "Hinge Angle" between 2 domains of 
a protein?

I am not quite sure how to calculate "Center of mass" of protein and then 
calculating the hinge angle.

Any help is appreciated.

Regards

Shoeib


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Re: [PyMOL] PyMOLWiki Update

[Sampson, Jared]

Hi Justin -

I see this same “weirdness" using the https protocol.  If you remove the ’s’ 
from ‘https’ in your URL, however, it will load properly.  It must be on a 
shared server that has something goofy happening with the handling of https 
traffic.  I think Jason is still the admin for the wiki, so maybe he can 
comment.

Cheers,
Jared

--
Jared Sampson
Xiangpeng Kong Lab
NYU Langone Medical Center
http://kong.med.nyu.edu/






On Oct 20, 2014, at 3:28 AM, Justin Lecher 
mailto:j.lec...@fz-juelich.de>> wrote:

On 20/06/14 17:45, Jason Vertrees wrote:
Hi Suzanne,

Everything should look and act exactly like it has in the past, including the
address.

Cheers,

-- Jason


Hi,

I just saw some weirdness when I try to access

https://www.pymolwiki.org/

That doesn't look like pymol stuff.

Cheers,
Justin

--
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Institute of Complex Systems
ICS-6 Structural Biochemistry
Research Centre Juelich
52425 Juelich, Germany
phone: +49 2461 61 2117


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Re: [PyMOL] Show all residues forming H-bonds

[Sampson, Jared]

Hi Markus -

First, you need to run the python script from the wiki page (save it as, e.g. 
polarpairs.py).  Then, to run pure Python code within a pml file, you’ll need 
to enclose those lines in a python block 
(http://www.pymolwiki.org/index.php/Python) using ‘python’ and ‘python end’.  
For example, to list all the H bonds between chains A and B:

###

run path/to/polarpairs.py

python

# the example from http://www.pymolwiki.org/index.php/Polarpairs
pairs = polarpairs('chain A', 'chain B')
for p in pairs:
dist = cmd.get_distance('(%s`%s)' % p[0], '(%s`%s)' % p[1])
print p, 'Distance: %.2f' % (dist)

python end

###

Hope that helps.

Cheers,
Jared

--
Jared Sampson
Xiangpeng Kong Lab
NYU Langone Medical Center
http://kong.med.nyu.edu/






On Oct 15, 2014, at 6:17 PM, Markus Heller 
mailto:mhel...@cdrd.ca>> wrote:

Jared,

I'm a newbie to pythom/PyMOL; how do I get this to work in a pml script?  A 
pointer to an example script would be enough .

Thanks
Markus

From: Sampson, Jared [mailto:jared.samp...@nyumc.org]
Sent: Friday, October 10, 2014 4:17 PM
To: Markus Heller
Cc: pymol-users@lists.sourceforge.net<mailto:pymol-users@lists.sourceforge.net>
Subject: Re: [PyMOL] Show all residues forming H-bonds

Actually, an even better option is Thomas' polarpairs.py script: 
http://www.pymolwiki.org/index.php/Polarpairs, which considers the H-bond angle 
as well as distance.

Apologies for the multiple emails, but I hope that is closer to what you're 
looking for.

Cheers,
Jared


On Oct 10, 2014, at 7:10 PM, Sampson, Jared 
mailto:jared.samp...@nyumc.org>> wrote:


Hi Markus -

Ah, sorry, I misunderstood your request at first.

What about the "acceptors" and "donors" selectors?  
http://www.pymolwiki.org/index.php/Single-word_Selectors

e.g.
select hbond_residues, byres ((acceptors within 3.5 of donors) or (donors 
within 3.5 of acceptors))

Cheers,
Jared

--
Jared Sampson
Xiangpeng Kong Lab
NYU Langone Medical Center
http://kong.med.nyu.edu/





On Oct 10, 2014, at 6:41 PM, Markus Heller  wrote:


Hi Jared,

Thanks for the reply.

This is NOT what I'm looking for.  As you stated, distance mode 2 yields the 
*distances* as dashes, but not the actual residues.  I don't want the dashes, 
but I want the residues (i.e. the donors and acceptors) in selectable objects.

I hope it's clearer now what I'm after .

Cheers
M

From: Sampson, Jared [mailto:jared.samp...@nyumc.org]
Sent: Friday, October 10, 2014 3:33 PM
To: Markus Heller
Subject: Re: [PyMOL] Show all residues forming H-bonds

Hi Markus -

Under the GUI "action" menu A > find > polar contacts, you'll find several 
options which will create a new object with all the specified distances as 
dashes.

This is also available with `distance` command.  
http://www.pymolwiki.org/index.php/Distance

Hope that helps.

Cheers,
Jared

--
Jared Sampson
Xiangpeng Kong Lab
NYU Langone Medical Center
http://kong.med.nyu.edu/






On Oct 10, 2014, at 2:45 AM, Markus Heller  wrote:



Hello list,

subject says it all.  The 2 options I came across search the www are:

http://sourceforge.net/p/pymol/mailman/message/7562444/http://sourceforge.net/p/pymol/mailman/message/7562444/

and DistancesRH 
(http://www.pymolwiki.org/index.php/DistancesRH)http://www.pymolwiki.org/index.php/DistancesRH

Is this current state-of-the-art, true-and-tried, or is there something more 
powerful hiding out there?

Thanks
Markus
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Re: [PyMOL] colour surface meshes

[Sampson, Jared]

Hi David -

Yes, indeed, PyMOL can save VRML2 (.wrl) files, although it outputs vertex 
colors rather than face colors.

Cheers,
Jared

--
Jared Sampson
Xiangpeng Kong Lab
NYU Langone Medical Center
http://kong.med.nyu.edu/






On Oct 13, 2014, at 11:18 AM, David Pattinson 
mailto:dj...@cam.ac.uk>> wrote:

Hi all

Is pymol able to save surface mesh files (.obj or .wrl) which include face 
colours?

Many thanks
David

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PhD Student in the Centre for Pathogen Evolution
Department of Zoology
University of Cambridge

dj...@cam.ac.uk

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Re: [PyMOL] Show all residues forming H-bonds

[Sampson, Jared]

Actually, an even better option is Thomas’ polarpairs.py script: 
http://www.pymolwiki.org/index.php/Polarpairs, which considers the H-bond angle 
as well as distance.

Apologies for the multiple emails, but I hope that is closer to what you’re 
looking for.

Cheers,
Jared


On Oct 10, 2014, at 7:10 PM, Sampson, Jared 
mailto:jared.samp...@nyumc.org>> wrote:

Hi Markus -

Ah, sorry, I misunderstood your request at first.

What about the “acceptors” and “donors” selectors?  
http://www.pymolwiki.org/index.php/Single-word_Selectors

e.g.
select hbond_residues, byres ((acceptors within 3.5 of donors) or (donors 
within 3.5 of acceptors))

Cheers,
Jared

--
Jared Sampson
Xiangpeng Kong Lab
NYU Langone Medical Center
http://kong.med.nyu.edu/






On Oct 10, 2014, at 6:41 PM, Markus Heller 
mailto:mhel...@cdrd.ca>> wrote:

Hi Jared,

Thanks for the reply.

This is NOT what I’m looking for.  As you stated, distance mode 2 yields the 
*distances* as dashes, but not the actual residues.  I don’t want the dashes, 
but I want the residues (i.e. the donors and acceptors) in selectable objects.

I hope it’s clearer now what I’m after …

Cheers
M

From: Sampson, Jared [mailto:jared.samp...@nyumc.org]
Sent: Friday, October 10, 2014 3:33 PM
To: Markus Heller
Subject: Re: [PyMOL] Show all residues forming H-bonds

Hi Markus -

Under the GUI “action” menu A > find > polar contacts, you’ll find several 
options which will create a new object with all the specified distances as 
dashes.

This is also available with `distance` command.  
http://www.pymolwiki.org/index.php/Distance

Hope that helps.

Cheers,
Jared

--
Jared Sampson
Xiangpeng Kong Lab
NYU Langone Medical Center
http://kong.med.nyu.edu/





On Oct 10, 2014, at 2:45 AM, Markus Heller 
mailto:mhel...@cdrd.ca>> wrote:


Hello list,

subject says it all.  The 2 options I came across search the www are:

http://sourceforge.net/p/pymol/mailman/message/7562444/http://sourceforge.net/p/pymol/mailman/message/7562444/

and DistancesRH 
(http://www.pymolwiki.org/index.php/DistancesRH)http://www.pymolwiki.org/index.php/DistancesRH

Is this current state-of-the-art, true-and-tried, or is there something more 
powerful hiding out there?

Thanks
Markus
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Re: [PyMOL] Show all residues forming H-bonds

[Sampson, Jared]

Hi Markus -

Ah, sorry, I misunderstood your request at first.

What about the “acceptors” and “donors” selectors?  
http://www.pymolwiki.org/index.php/Single-word_Selectors

e.g.
select hbond_residues, byres ((acceptors within 3.5 of donors) or (donors 
within 3.5 of acceptors))

Cheers,
Jared

--
Jared Sampson
Xiangpeng Kong Lab
NYU Langone Medical Center
http://kong.med.nyu.edu/






On Oct 10, 2014, at 6:41 PM, Markus Heller 
mailto:mhel...@cdrd.ca>> wrote:

Hi Jared,

Thanks for the reply.

This is NOT what I’m looking for.  As you stated, distance mode 2 yields the 
*distances* as dashes, but not the actual residues.  I don’t want the dashes, 
but I want the residues (i.e. the donors and acceptors) in selectable objects.

I hope it’s clearer now what I’m after …

Cheers
M

From: Sampson, Jared [mailto:jared.samp...@nyumc.org]
Sent: Friday, October 10, 2014 3:33 PM
To: Markus Heller
Subject: Re: [PyMOL] Show all residues forming H-bonds

Hi Markus -

Under the GUI “action” menu A > find > polar contacts, you’ll find several 
options which will create a new object with all the specified distances as 
dashes.

This is also available with `distance` command.  
http://www.pymolwiki.org/index.php/Distance

Hope that helps.

Cheers,
Jared

--
Jared Sampson
Xiangpeng Kong Lab
NYU Langone Medical Center
http://kong.med.nyu.edu/





On Oct 10, 2014, at 2:45 AM, Markus Heller 
mailto:mhel...@cdrd.ca>> wrote:


Hello list,

subject says it all.  The 2 options I came across search the www are:

http://sourceforge.net/p/pymol/mailman/message/7562444/http://sourceforge.net/p/pymol/mailman/message/7562444/

and DistancesRH 
(http://www.pymolwiki.org/index.php/DistancesRH)http://www.pymolwiki.org/index.php/DistancesRH

Is this current state-of-the-art, true-and-tried, or is there something more 
powerful hiding out there?

Thanks
Markus
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Re: [PyMOL] measure angles in programming

[Sampson, Jared]

Hi Lei -

The `get_angle` command needs an atom selection for your “tunnel" atoms, which, 
like the B-factor as Matt mentioned, you can also get using `iterate`:

###

# create a list
stored.centers = []

# get the macro selection string for each atom in tunnel
cmd.iterate("tunnel", 'stored.centers.append("/%s/%s/%s/%s`%s/%s" % (model, 
segi, chain, resn, resi, name))')

# loop through the list of centers and print each angle
for s in stored.centers:
angle = cmd.get_angle('start_point', 'end_point', s)
print "%s: %3.2f" % (s, angle)

###

Hope that helps.

Cheers,
Jared

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Jared Sampson
Xiangpeng Kong Lab
NYU Langone Medical Center
http://kong.med.nyu.edu/






On Sep 24, 2014, at 6:52 PM, Matthew Baumgartner 
mailto:mp...@pitt.edu>> wrote:

Hi,
you can just use the 'angle' command.

cmd.angle('angle1', 'start_point', 'end_point', a)

To print the b-factor you can use the iterate command
(http://www.pymolwiki.org/index.php/Iterate)
cmd.iterate('(a)', 'print b')

HTH,
Matt Baumgartner

On 09/24/2014 06:35 PM, rainfieldcn wrote:
Hi all,
I generate two pseudoatoms "start_point" and "end_point" by
center_of_mass.py. I load an object "tunnel" which has a sets of atoms
in one chain.
I want to measure the angle from each atoms in "tunnel" to "end_point"
to "start_point". at the same time, I want to print the B-factor of
atoms in "tunnel".
To measure the angle, I programmed like this，but it doesn't work.
I guess it's because get_angle function needs some particular variable
format.
By the way, how can I print the b factor of atom?
Thanks,
Lei

from pymol import cmd, stored
def vertical_distance( start_point, end_point, tunnel ):
centers = cmd.get_model(tunnel,1)
for a in centers.atom:
angle= cmd.get_angle(start_point, end_point,a)
print angle
return (start_point, end_point, tunnel)
cmd.extend( "vertical_distance", vertical_distance );






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

[Sampson, Jared]

Hi James -

On Sep 22, 2014, at 4:30 AM, James Starlight 
mailto:jmsstarli...@gmail.com>> wrote:

Hi Jared,


many thanks for the suggestion!
your method works perfect (i only slightly modified dir for input file)

# dock each model to the ligand
for pdb in $receptors/*.pdb; do
  filename=$(basename "$pdb")
  M=${filename/.pdb/}
  echo "Processing of ${M} is initiated..."
  #remove water and ions; change EMD to TER
  grep -v "ATOM.*\(WAT\|NA+\|Cl-\)" $pdb | sed -e 's/^END/TER/g' > 
${dirr}/temp/${M}_clean.pdb
  #superimsoposition using pymol against reference
  pymol $ref ${dirr}/temp/${M}_clean.pdb -c -q -d "super $M, $R and resi 2-280; 
save ./superimposed/${M}_aligned.pdb, $M" > ./superimposed/pymol_${M}.log
  cp $ref ./superimposed
done


Glad it worked for you.

two additional questions:

1) will it possible to use more flexibility in case of the selection of region 
for alignment in reference structure?
super $M, $R and resi 2-280
For instance I'd like to select all residues which are part of the alpha 
helixes of the reference. how it should be done?

Try `$R and resi 2-280 and ss h`.  See 
http://www.pymolwiki.org/index.php/Property_Selectors for more info.  (That 
page comes up as the very first result for me on Google with “pymol select 
secondary structure” as the search term.)

2) what advantages could give me tmalign method for the superimposition in 
comparison to super and ce programs? does the coordinates of the reference will 
not changed after alignment of each mobile on it (like fitting in case of 
super) ?

>From the description here (http://www.pymolwiki.org/index.php/TMalign) that 
>TMalign, like CEalign, can be useful for structures in the “twilight zone,” 
>where sequence alignment by `align` or structural alignment by `super` may not 
>provide a good fit.  For any of the programs, though, only the mobile 
>structures should move; the target/reference coordinates should always remain 
>unchanged.

Cheers,
Jared



James

2014-09-22 10:21 GMT+02:00 James Starlight 
mailto:jmsstarli...@gmail.com>>:
Hi Jared,


many thanks for the suggestion!
your method works perfect (i only slightly modified dir for input file)


2014-09-19 20:19 GMT+02:00 Sampson, Jared 
mailto:jared.samp...@nyumc.org>>:

Hi James -

I don’t have any experience with Profit.  However, instead of using "something 
like” PyMOL’s `super` command as you asked, you could actually use `super` in 
your shell session by launching PyMOL in command line 
mode<http://www.pymolwiki.org/index.php/Command_Line_Options>.  Of course, you 
would need to modify it according to your file naming scheme, but here’s a 
working example.

###
#!/bin/bash

REF=reference.pdb

# grab some related pdb files to use and make one of them the reference
# (obviously you won’t have to do this)
i=0
for pdb in 1bbd 7fab 1dba 1plg 1nl0; do
pymol -c -d "fetch ${pdb}, mobile${i}, async=0; save mobile${i}.pdb"
i=$((i+1))
done
mv mobile0.pdb $REF

# align all the mobile files to a selection in the reference file
i=1
for MOB in mobile*.pdb; do
# strip the extensions
R=$(echo $REF | sed 's/\.pdb$//')
M=$(echo $MOB | sed 's/\.pdb$//')

# superimpose and save aligned mobile coordinates
pymol $REF $MOB -c -q -d "super $M, $R and resi 1-110; save 
${M}_aligned.pdb"
done

pymol mobile*_aligned.pdb
###

You could also use CEalign if you need something citable, just switch the order 
of the arguments to it: `cealign $R and resi 1-110, $M`.

Hope that helps.

Cheers,
Jared

--
Jared Sampson
Xiangpeng Kong Lab
NYU Langone Medical Center
http://kong.med.nyu.edu/






On Sep 19, 2014, at 6:03 AM, James Starlight 
mailto:jmsstarli...@gmail.com>> wrote:

Dear all,

I still need some help regarding some algorithm for structural superimposition 
of my mobile structures regarding one specified reference using some fitting 
method (to avoid changing in the position of the reference.pdb which is very 
important for me!)=>something like super command in pymol. Using ProFit I have 
faced with some errors during superimposition regarding the chosing reference 
(in case where there were some differences in the positions of ref and mob 
structures its alignment was not perfect (the mob had not been fully aligned on 
the ref) obtaining very big RMSD (20 A!) as the result although its actual 
value should be in range of 2-5 A. I'll be thankful for possible sollutions of 
this problem using Profit is there are users experienced with this software (mb 
it should to define fitting zones or atom subsets more accurately but I have no 
ideas here ) or any other alternatives which could be used as parts of the 
shell script.

James





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

[Sampson, Jared]

Hi James -

I don’t have any experience with Profit.  However, instead of using "something 
like” PyMOL’s `super` command as you asked, you could actually use `super` in 
your shell session by launching PyMOL in command line 
mode.  Of course, you 
would need to modify it according to your file naming scheme, but here’s a 
working example.

###
#!/bin/bash

REF=reference.pdb

# grab some related pdb files to use and make one of them the reference
# (obviously you won’t have to do this)
i=0
for pdb in 1bbd 7fab 1dba 1plg 1nl0; do
pymol -c -d "fetch ${pdb}, mobile${i}, async=0; save mobile${i}.pdb"
i=$((i+1))
done
mv mobile0.pdb $REF

# align all the mobile files to a selection in the reference file
i=1
for MOB in mobile*.pdb; do
# strip the extensions
R=$(echo $REF | sed 's/\.pdb$//')
M=$(echo $MOB | sed 's/\.pdb$//')

# superimpose and save aligned mobile coordinates
pymol $REF $MOB -c -q -d "super $M, $R and resi 1-110; save 
${M}_aligned.pdb"
done

pymol mobile*_aligned.pdb
###

You could also use CEalign if you need something citable, just switch the order 
of the arguments to it: `cealign $R and resi 1-110, $M`.

Hope that helps.

Cheers,
Jared

--
Jared Sampson
Xiangpeng Kong Lab
NYU Langone Medical Center
http://kong.med.nyu.edu/






On Sep 19, 2014, at 6:03 AM, James Starlight 
mailto:jmsstarli...@gmail.com>> wrote:

Dear all,

I still need some help regarding some algorithm for structural superimposition 
of my mobile structures regarding one specified reference using some fitting 
method (to avoid changing in the position of the reference.pdb which is very 
important for me!)=>something like super command in pymol. Using ProFit I have 
faced with some errors during superimposition regarding the chosing reference 
(in case where there were some differences in the positions of ref and mob 
structures its alignment was not perfect (the mob had not been fully aligned on 
the ref) obtaining very big RMSD (20 A!) as the result although its actual 
value should be in range of 2-5 A. I'll be thankful for possible sollutions of 
this problem using Profit is there are users experienced with this software (mb 
it should to define fitting zones or atom subsets more accurately but I have no 
ideas here ) or any other alternatives which could be used as parts of the 
shell script.

James


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

[Sampson, Jared]

Hi James -

What version of PyMOL are you using?  For me, using Open Source PyMOL 1.7.2.0, 
a typical PDB file I tested ends up with more information in that column, not 
less, after saving from PyMOL:

Before:
ATOM   1312  NH1 ARG A 198   0.544  14.093  19.655  1.00 34.61   N

After:
ATOM   1312  NH1 ARG A 198   0.544  14.093  19.655  1.00 34.61   N1+

Are you sure the column is there in your input file, and hasn’t been removed 
before loading into PyMOL?

Cheers,
Jared

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Xiangpeng Kong Lab
NYU Langone Medical Center
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On Sep 11, 2014, at 5:36 AM, James Starlight 
mailto:jmsstarli...@gmail.com>> wrote:

I guess I've passed superimpoition- it works great - with the one exception- 
after fitting to ref.pdb the last colum (consisted of the atom names like C, N, 
O etc) from the each fitted mobile.pdb has been removed. I need to keep this 
column on the resulted pdb because I'll use this pdb as the initial structure 
for the autodock docking (actually I do superimposition because I have had all 
input docking parameters including XYZ of the cavity for the ref structure). If 
the last column is missed I have promblems with the pdb2pdbqt conversion of the 
mobile_fit.pdb using babel. I'll thankful to everyone who have faced with the 
same problem and could provide me with some suggestions.


Thank for help,

James

2014-09-09 12:35 GMT+04:00 James Starlight 
mailto:jmsstarli...@gmail.com>>:
Thanks Markus, I'll try to examine it!

Jed,

the main problem with the profit is that I need to superimpose structures in 
loop which are not always has the same sequence length. Is it possible to 
superimpose each structure based on some common criterium found for each mobile 
and reference automatically?

Kind regards,

James

2014-09-08 20:32 GMT+04:00 Markus Heller 
mailto:mhel...@cdrd.ca>>:
Shot in the dark, based on reading “ensemble of the structures” and “ProFit”:

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2828896/

CARON – Average RMSD of NMR structure ensemble

Hope that helps!

Markus

From: James Starlight 
[mailto:jmsstarli...@gmail.com]
Sent: Monday, September 08, 2014 6:52 AM
To: pymol-users
Subject: Re: [PyMOL] Access to pymol commands from the terminal

Ok, ProFit has been passed :D
Now I'm looking for some software which could do the same least-square fitting 
for the ensemble of the structures taken it as the separate pdbs from the work 
dir (I'm not sure if the mustang software could be useful for this task)=> 
because looping using ProFit might be not good for me because each time I need 
to provide new atom selection for the superimposition  for each model in the 
ProFit's script file.
James

2014-09-07 11:11 GMT+02:00 Maciek Dziubiński 
mailto:pona...@gmail.com>>:

Boo
7 wrz 2014 09:26 "Jamesno Starligois ht" 
mailto:jmsstarli...@gmail.com>>napisał napisał(a):

>
> Thomas,thanks for help- I'll try to test your script!
>
> Jed, many thanks too!
>
> if I understood correctly align.profit should contain thefollowing lines:
>
> # using ProFIT to align the model to 2hi4
> open $PROFIT, "> align.profit" or die "Cannot open file align.profit\n";
> print $PROFIT "ATOMS CA\n";
> print $PROFIT "ZONE 34-513:1-480\n";
> print $PROFIT "FIT\n";
> print $PROFIT "WRITE $folder/$dir/$pdbnew\n";
> close $PROFIT;
>
> shouldn't it?
>
> that that file is provided to 1 command line
> `profit -f align.profit -h /home/jedgold/modelling/NAMD/2hi4.pdb 
> $folder/$dir/$pdbnew`;
> where 2hi4.pdb is my ref
> $pdbnew variable assosiated with the target pdb
>
> one question about align.profit: will the output aligned mobile.pdb consist 
> of all atoms? I've found that only CA atoms are used for the superimposition
> print $PROFIT "ATOMS CA\n";
>
>
> James
>
>
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7 wrz 2014 09:26 "James Starlight" 
mailto:jmsstarli...@gmail.com>> napisał(a):
Thomas,thanks for help- I'll try to test your script!

Jed, many thanks too!

if I understood correctly align.profit should contain thefollowing lines:

# using ProFIT to align the model to 2hi4
open $PROFIT, "> align.profit" or die "Cannot open file align.profit\n";
print $PROFIT "ATOMS CA\n";
print $PROFIT "ZONE 34-513:1-480\n";
print $PROFIT "FIT\n";
print $PROFIT "WRITE $folder/$dir/$pdbnew\n";
close $PROFIT;

shouldn't it?

that that file is provided to 1 command line
`profit -f align.profit -h /home/jedgold/modelling/NAMD/2hi4.pdb 
$folder/$dir/$pdbnew`;
where 2hi4.pdb is my ref
$pdbnew

Re: [PyMOL] Residue-residue contacts from PDB

[Sampson, Jared]

Hi Bhumika -

Have a look at the CCP4 program NCONT: http://www.ccp4.ac.uk/html/ncont.html.

You can run it within the CCP4 GUI or from the command line.  For example, for 
contacts between helices 1 and 2, type these lines at the prompt (or copy and 
paste), substituting the correct path to the PDB file and ranges you want to 
examine.

ncont  xyzin 2rh1.pdb <
  360 contacts found:

  SOURCE ATOMS   TARGET ATOMS DISTANCE

 /1/A/  32(TRP). / CE3[ C]:  /1/A/  95(LEU). / CD2[ C]:   5.16
 /1/A/  32(TRP). / CZ3[ C]:  /1/A/  95(LEU). / CD2[ C]:   4.43
 /1/A/  32(TRP). / CH2[ C]:  /1/A/  94(ILE). / CG2[ C]:   5.39
 /1/A/  95(LEU). / CD2[ C]:   4.78
 /1/A/  33(VAL). / CA [ C]:  /1/A/  95(LEU). / CD2[ C]:   4.23
 /1/A/  33(VAL). / C  [ C]:  /1/A/  95(LEU). / CD2[ C]:   4.35
 /1/A/  95(LEU). / CG [ C]:   5.49
 /1/A/  33(VAL). / O  [ O]:  /1/A/  95(LEU). / CD1[ C]:   4.56
 /1/A/  95(LEU). / CD2[ C]:   3.64
 /1/A/  95(LEU). / CB [ C]:   5.41
 /1/A/  95(LEU). / CG [ C]:   4.69
 /1/A/  33(VAL). / CB [ C]:  /1/A/  95(LEU). / CB [ C]:   5.44
 /1/A/  95(LEU). / O  [ O]:   5.24
 /1/A/  95(LEU). / CD2[ C]:   4.50
 /1/A/  33(VAL). / CG1[ C]:  /1/A/  95(LEU). / C  [ C]:   4.92
 /1/A/  95(LEU). / CG [ C]:   4.47
 /1/A/  95(LEU). / CD1[ C]:   4.89
 /1/A/  95(LEU). / CD2[ C]:   3.74
 /1/A/  95(LEU). / CA [ C]:   4.80
 /1/A/  95(LEU). / O  [ O]:   4.36
 /1/A/  95(LEU). / CB [ C]:   4.20



You can also visualize contact residues in PyMOL using selection 
algebra.  A simple 
version might look like:

fetch 2rh1, async=0
as cartoon

# create helix selections
select helix1, chain A and resi 29-60
select helix2, chain A and resi 67-96

# create contact selection for the helix pair
select cont_1_2, (helix2 within 5.5 of helix1) or (helix1 within 5.5 of helix2)

# visualize contacts
show sticks, cont_1_2


Hope that helps.

Cheers,
Jared

--
Jared Sampson
Xiangpeng Kong Lab
NYU Langone Medical Center
http://kong.med.nyu.edu/






On Sep 7, 2014, at 8:03 PM, bhumika arora 
mailto:bhumikar...@gmail.com>> wrote:

Dear Pymol users,

I wish to know how to calculate residue-residue contacts from a PDB file. 
Where, contact definition is : two residues are considered to be in contact if 
the
minimal distance of their side chain or backbone heavy atoms is < 5.5A ˚ .

Specifically, I want to calculate inter-helical (helix-helix) contacts from a 
PDB; when two residues from different helices (transmembrane helixes) are 
considered to be in contact if the minimal distance of their side chain or 
backbone heavy atoms is < 5.5A ˚

For example, I want to calculate the inter-helical residue contacts of the PDB  
 "2RH1"

Please advise.

Regards,
Bhumika.
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Re: [PyMOL] re： cartoon and line representation

[Sampson, Jared]

Hi Yeping -

Yes, I can.  But there is one additional requirement:  to save all the states, 
you must add a `state=0` keyword argument to the save command to include all 
states.  Otherwise, the default is `state=-1`, which includes only the current 
state.

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

Cheers,
Jared

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On Sep 2, 2014, at 2:09 PM, sunyeping 
mailto:sunyep...@aliyun.com>> wrote:


Dear Jared,

I am using  Open Source PyMOL 1.6.0.0. If you save the whole virus structure as 
a single pdb file, and reload it into pymol and then show it as cartoon, can 
you still display the whole structure? As for me, it can display only one chain 
shown as cartoon_loop.

Best regards.

Yeping Sun

Institute of Microbiology, Chinese Academy of Sciences

--
发件人：Sampson, Jared mailto:jared.samp...@nyumc.org>>
发送时间：2014年9月2日(星期二) 22:23
收件人：孙业平 mailto:sunyep...@aliyun.com>>
抄　送：pymol-users 
mailto:pymol-users@lists.sourceforge.net>>
主　题：Re: [PyMOL] cartoon and line representation

Hi Yeping -

I’m unable to reproduce the behavior you’re seeing—using your commands in Open 
Source PyMOL 1.7.2.0, I get the whole capsid displayed properly as a cartoon.  
What version of PyMOL are you using?

You could also try using the `all_states` setting instead:

fetch 3j2v, type=pdb1, async=0
set all_states, 1
orient
as cartoon

I am using  Open Source PyMOL 1.6.0.0.


Cheers,
Jared

--
Jared Sampson
Xiangpeng Kong Lab
NYU Langone Medical Center
http://kong.med.nyu.edu/






On Sep 2, 2014, at 6:20 AM, sunyeping 
mailto:sunyep...@aliyun.com>> wrote:

Dear all

I want to display structures which contains numerous chains such as viruses in 
pymol. I find these sturctures can be displayed normally as line 
representation. However, when I show them as cartoon, usually only one chain 
can be displayed, and usually it is cartoon loop rather than the normal 
cartoon. It there any way to display the whole structute as cartoon?

For example, I display the HBV capsid in pymol by the follow commands:

fetch 3j2v, type=pdb1, async=0

split_states 3j2v

delete 3j2v

orient

The whole virus capsid appeared as line representation. Then I type:

Hide everything
show cartoon

Only one chain shown as cartoon loop in pymol


Thanks in advance.



Yeping Sun

Institute of Microbiology, Chinese Academy of Sciences

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Re: [PyMOL] cartoon and line representation

[Sampson, Jared]

Hi Yeping -

I’m unable to reproduce the behavior you’re seeing—using your commands in Open 
Source PyMOL 1.7.2.0, I get the whole capsid displayed properly as a cartoon.  
What version of PyMOL are you using?

You could also try using the `all_states` setting instead:

fetch 3j2v, type=pdb1, async=0
set all_states, 1
orient
as cartoon

Cheers,
Jared

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On Sep 2, 2014, at 6:20 AM, sunyeping 
mailto:sunyep...@aliyun.com>> wrote:

Dear all

I want to display structures which contains numerous chains such as viruses in 
pymol. I find these sturctures can be displayed normally as line 
representation. However, when I show them as cartoon, usually only one chain 
can be displayed, and usually it is cartoon loop rather than the normal 
cartoon. It there any way to display the whole structute as cartoon?

For example, I display the HBV capsid in pymol by the follow commands:

fetch 3j2v, type=pdb1, async=0

split_states 3j2v

delete 3j2v

orient

The whole virus capsid appeared as line representation. Then I type:

Hide everything
show cartoon

Only one chain shown as cartoon loop in pymol


Thanks in advance.



Yeping Sun

Institute of Microbiology, Chinese Academy of Sciences

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Re: [PyMOL] Other coloring strategies based on user-provided properties

[Sampson, Jared]

Hi Chen -

As you guessed, this is commonly done by modifying the B-factor column 
directly.  You can do this with data available to you in PyMOL (e.g. distances, 
charges, and so forth) using alter and 
iterate  and a few other related 
commands.  There are examples on the wiki to help as well.

For other types of information, you can modify the B-factor column values 
directly in a text editor or other program.

In either case, your last step will likely include the 
spectrum command.

Good luck!

Cheers,
Jared

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Xiangpeng Kong Lab
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On Aug 29, 2014, at 12:25 PM, Chen Zhao 
mailto:chenzhaoh...@gmail.com>> wrote:

Dear all,

I am thinking whether it is possible to color a molecule by a specific property 
residue-wise or atom-wise like generally be done on B-factor? This property 
could be provided as numbers in a column. An obvious way might just be to 
change the B-factor column to the user-provided column and "color by B-factor". 
But I am wondering whether there are some direct ways of doing this.

Best,
Chen
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Re: [PyMOL] Show cation-pi/pi-pi interactions

[Sampson, Jared]

Hi Markus -

It’s already possible to highlight polar interactions using the `distance` 
command with mode=2.  http://www.pymolwiki.org/index.php/Distance

For pi-cation stacking, it might be useful to create pseudo atoms at the 
average position of the atoms in each charged group or ring in question (e.g. 
`pseudoatom ring_Y102, resi 102 and name CG+CD1+CD2+CE1+CE2+CZ`) and use them 
to create sensibly positioned distance dashes between them.

Cheers,
Jared

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On Aug 13, 2014, at 4:59 PM, Markus Heller 
mailto:mhel...@cdrd.ca>> wrote:

Hello,

There's a thread in the PyMol Wiki (http://www.pymolwiki.org/index.php/Ideas) 
that mentions the possible implementation of functionality to highlight 
H-bonds, salt bridges, Pi-stacking, Pi-cations.  Has such a thing been 
implemented yet, and if not, what's the current status?

Thanks and Cheers
Markus

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Re: [PyMOL] RMSD for selected residues

[Sampson, Jared]

Hi Nidhi -

The “Align” feature in the GUI uses PyMOL's `align` command, which performs a 
sequence alignment to use as the basis for structural alignment.  It only uses 
those residues which match exactly, which can throw off the RMSD.  Try using 
`super` or `cealign` instead, which are structural alignments.  For example, 
assuming you have named selections for your active site residues:

super active_site_1, active_site_2

With `super`, the first selection is mobile, and is superimposed onto the 
second selection.  For `cealign`, switch the order of the arguments.

http://www.pymolwiki.org/index.php/Super
http://www.pymolwiki.org/index.php/Cealign

Cheers,
Jared

(Also, sorry for the duplicate message—I forgot to Reply All the first time.)
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Xiangpeng Kong Lab
NYU Langone Medical Center
http://kong.med.nyu.edu/






On Aug 9, 2014, at 6:12 AM, Nidhi Jatana 
mailto:nidhijat...@bic-svc.ac.in>> wrote:

Dear Sir/Madam

I have generated five models for a protein and I wanted to check the RMSD of 
only the binding site residues. I have the list of binding site residues. I 
tried using this through graphics by selecting the residues and then aligning 
by selection but somehow its giving me a higher RMSD than the entire structure 
but this should not happen. What is the other way to align specific residues?


Thanking you

Regards

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Senior Research Fellow
Bioinformatics Center
Sri Venkateswara College
(University of Delhi)
Dhaula Kuan
New Delhi-110021.
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Re: [PyMOL] Problems with superposing small molecules and transformation

[Sampson, Jared]

Hi German -

I’m not sure I follow exactly what you’re asking, but `align` does its 
superimposition based on sequence alignment, which isn’t really meaningful for 
small molecule ligands.  I would suggest using `fit`, `super`, or `cealign` 
instead, which all use just the coordinates, although it’s possible these also 
won’t work.

For a more sophisticated approach, maybe check out LigAlign, which comes with a 
tutorial: http://www.pymolwiki.org/index.php/LigAlign.

Cheers,
Jared

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On Aug 5, 2014, at 10:04 AM, German Erlenkamp 
mailto:erlenk...@uni-duesseldorf.de>> wrote:

Hi all,

I have two sets of ligands, the first are the crystal structures, the second
one are the same compounds, but aligned by a flexible ligand alignment, where
I used one of the crystal structures as a template. Unfortunately the
coordinates of the templates changed during the alignment.
Now I want to calculate the RMSD-values between these structures, and for this
I want to superpose the group of aligned ligands to the template ligand.
I started with 'align Aligned_1, Start_1' but after this command, all atoms of
'Aligned_1' vanished and I can only represent this as a sphere. This will be
Ok for me, because the RMSD between 'Aligned_1' and 'Start_1' is 0.
But after this I want to move 'Aligned_2' the same way as I moved 'Aligned_1'.
I thought 'matrix_copy Alinged_1, Start_1' should do the job, but after this
all atoms of 'Aligned_2' are gone. I still have this object, but nothing more.

My questions are: Am I using the correct commands for this task, or not? And, if
I am using the right commands, what is going wrong? And - for the case my way
is not correct - what would be the proper way to solve my problem?

Thanks in advance,

German
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Heinrich-Heine-Universität Düsseldorf
Institut für Pharmazeutische und Medizinische Chemie
Universitätsstr. 1
40225 Düsseldorf
Germany

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E-Mail: erlenk...@uni-duesseldorf.de
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Re: [PyMOL] How to show the surface border of a specific residue?

[Sampson, Jared]

Hi Ooker -

As I understand it, you want to overlay a line to show which part of the 
surface belongs to which residue.  There is currently no way to do this 
directly within PyMOL.  However, is possible to achieve something similar using 
multiple layers in a composite image.  See this previous thread: 
https://www.mail-archive.com/pymol-users@lists.sourceforge.net/msg12281.html

I’ve also just created a page on the PyMOL Wiki with an example:  
http://www.pymolwiki.org/index.php/Outline

Hope that helps.

Cheers,
Jared

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On Jul 24, 2014, at 10:15 AM, Ooker 
mailto:ganuongp...@gmail.com>> wrote:

I have a potential map of a protein and I would like to have a border
between a specific residue while the map keeps unchanged.

I have thought about making a new object of the residue and tried to
find a command similar to:

set label_outline_color, black

but I can't find one.

Do you have any ideas? Thank you so much.

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Re: [PyMOL] Faster installation of plugins during development

[Sampson, Jared]

Hi Matt -

Does your plugin require a GUI, or can you rely on scripted commands and output 
files for your tests?

For any tests that don’t need the GUI, you might consider running them with 
something like `pymol -ckq my_test.pml`.

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

Cheers,
Jared

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On Jul 18, 2014, at 1:47 PM, Matthew Baumgartner 
mailto:mp...@pitt.edu>> wrote:

Hi,
Thank you for you suggestions.
However, I was looking for a way to do it without restarting pymol if possible. 
Currently, restarting is the fastest solution, but it still takes up about 
10-15 seconds to close pymol, restart it, and have it load the structures I 
need to test my script.

One question that I have is that when pymol starts up, does it load the scripts 
in the plugin menu into memory? Or when you click on the plugin in the menu, 
does that read from a file on the disk somewhere?
My testing indicates the former, because launching pymol and then editing the 
script in the ~/.pymol/startup folder does not change the plugin.

Ideally, what I would like to be able to do is launch pymol once, then open my 
plugin. Then if I make some changes to the code in the appropriate folder, if I 
simply close the tk window and open the plugin from the menu again, it would 
reopen the plugin with the new changes.

Short of that, running some commands in the command line window would also be 
acceptable. I tried using the execfile command you suggested, but that doesn't 
seem to do what I want. Did I do something wrong?

Thanks again for your help,
Matt


On 07/18/2014 01:23 PM, Andreas Warnecke wrote:
Hej Matthew,

1. The advantage of using the plugin manager is that it will automatically 
import all the plugin in the 'plugins' folder of the 'pymol-script-repo'. This 
should re-load you plugin if it is located in a folder managed by the plugin 
manager. The loading of plugins located therein occurs automatically.
You can add paths to the plugin manager either manually or using scripts during 
startup as described in the link. This is the way I prefer to do it. Check the 
examples and linked pages:
http://www.pymolwiki.org/index.php/Plugin_manager

Note that deliberate import of these plugins changes:
e.g. to import colorama.py post startup use:
import pmg_tk.startup.colorama
# this is shown in the info dialog of the Plugin manager

A simple restart of PyMOL should re-load your updated plugin with the changes 
made, provided the path is added to its list. It may require a __init__.py file 
if it is a module.

2. if you are testing a plugin you can always have it in a separate folder that 
you add yourself.
I sometime use the following to test scripts (added in the run_on_startup.py):
#
import sys
import os
sys.path.append(os.path.abspath(os.path.join(os.environ['PYMOL_PATH'], 
'plugins_private'))) # contains a folder called private with a (empty)  
__init__.py file
import private
#

3. Another (maybe deprecated?) way of running your code would be to use 
'execfile'. This would correspond to running the python code in PyMOL.

#
import os
PYMOLPATH=os.environ['PYMOL_PATH']
#Append 'plugin' folder # Change to 'Pymol-script-repo' if required
PLUGINPATH=os.path.realpath(os.path.join(PYMOLPATH, 'plugins'))

# Run every script in the folder and max. one sub-folder that is '.py'
PLUGINPATH_LIST=[os.path.realpath(os.path.join(PLUGINPATH, name)) for name in 
os.listdir(PLUGINPATH) if os.path.isdir(os.path.join(PLUGINPATH, name))]
PLUGINPATH_LIST=[PLUGINPATH]+PLUGINPATH_LIST
print 'paths for plugins: '
for p in PLUGINPATH_LIST: print p
print 
'#---'
for d in PLUGINPATH_LIST:
print 'Initiating (sub)-directory: '+d
for f in os.listdir(d):
if f=='__init__.py': continue
if f.endswith('.py'):
print "Executing plugin: "+f
execfile(os.path.realpath(os.path.join(d, f)))
else:
if not os.path.isdir(os.path.join(d,f)):print 'skipping non .py 
file: '+f
#

The drawback in 2 or 3 is that this will not work for true plugins that add 
menus to PyMOL.

4. For simple script or short chunks of code I often copy-paste:
python
#code here
python end

into the pymol mini shell. This is great for testing part of the code.

In conclusion I recommend using option. 1 and restart PyMOL after making 
changes to the script: The plugin manager is a very practical addition to PyMOL 
and I love it. It just needs to be configured correctly, which is something 
that changed in comparison to other PyMOL versions (cf. the link).
Just beware: removing a installed plugin may physically delete the file. So be 
sure to backup your script should you decide to remove scripts or paths that 
were added to the Plugin Manager.

Hope this will relieve som

Re: [PyMOL] Faster installation of plugins during development

[Sampson, Jared]

Hi Matt -

Does your plugin require a GUI, or can you rely on scripted commands and output 
files for your tests?

For any tests that don’t need the GUI, you might consider running them with 
something like `pymol -ckq my_test.pml`.

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

Cheers,
Jared

--
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Xiangpeng Kong Lab
NYU Langone Medical Center
http://kong.med.nyu.edu/






On Jul 18, 2014, at 1:47 PM, Matthew Baumgartner 
mailto:mp...@pitt.edu>> wrote:

Hi,
Thank you for you suggestions.
However, I was looking for a way to do it without restarting pymol if possible. 
Currently, restarting is the fastest solution, but it still takes up about 
10-15 seconds to close pymol, restart it, and have it load the structures I 
need to test my script.

One question that I have is that when pymol starts up, does it load the scripts 
in the plugin menu into memory? Or when you click on the plugin in the menu, 
does that read from a file on the disk somewhere?
My testing indicates the former, because launching pymol and then editing the 
script in the ~/.pymol/startup folder does not change the plugin.

Ideally, what I would like to be able to do is launch pymol once, then open my 
plugin. Then if I make some changes to the code in the appropriate folder, if I 
simply close the tk window and open the plugin from the menu again, it would 
reopen the plugin with the new changes.

Short of that, running some commands in the command line window would also be 
acceptable. I tried using the execfile command you suggested, but that doesn't 
seem to do what I want. Did I do something wrong?

Thanks again for your help,
Matt


On 07/18/2014 01:23 PM, Andreas Warnecke wrote:
Hej Matthew,

1. The advantage of using the plugin manager is that it will automatically 
import all the plugin in the 'plugins' folder of the 'pymol-script-repo'. This 
should re-load you plugin if it is located in a folder managed by the plugin 
manager. The loading of plugins located therein occurs automatically.
You can add paths to the plugin manager either manually or using scripts during 
startup as described in the link. This is the way I prefer to do it. Check the 
examples and linked pages:
http://www.pymolwiki.org/index.php/Plugin_manager

Note that deliberate import of these plugins changes:
e.g. to import colorama.py post startup use:
import pmg_tk.startup.colorama
# this is shown in the info dialog of the Plugin manager

A simple restart of PyMOL should re-load your updated plugin with the changes 
made, provided the path is added to its list. It may require a __init__.py file 
if it is a module.

2. if you are testing a plugin you can always have it in a separate folder that 
you add yourself.
I sometime use the following to test scripts (added in the run_on_startup.py):
#
import sys
import os
sys.path.append(os.path.abspath(os.path.join(os.environ['PYMOL_PATH'], 
'plugins_private'))) # contains a folder called private with a (empty)  
__init__.py file
import private
#

3. Another (maybe deprecated?) way of running your code would be to use 
'execfile'. This would correspond to running the python code in PyMOL.

#
import os
PYMOLPATH=os.environ['PYMOL_PATH']
#Append 'plugin' folder # Change to 'Pymol-script-repo' if required
PLUGINPATH=os.path.realpath(os.path.join(PYMOLPATH, 'plugins'))

# Run every script in the folder and max. one sub-folder that is '.py'
PLUGINPATH_LIST=[os.path.realpath(os.path.join(PLUGINPATH, name)) for name in 
os.listdir(PLUGINPATH) if os.path.isdir(os.path.join(PLUGINPATH, name))]
PLUGINPATH_LIST=[PLUGINPATH]+PLUGINPATH_LIST
print 'paths for plugins: '
for p in PLUGINPATH_LIST: print p
print 
'#---'
for d in PLUGINPATH_LIST:
print 'Initiating (sub)-directory: '+d
for f in os.listdir(d):
if f=='__init__.py': continue
if f.endswith('.py'):
print "Executing plugin: "+f
execfile(os.path.realpath(os.path.join(d, f)))
else:
if not os.path.isdir(os.path.join(d,f)):print 'skipping non .py 
file: '+f
#

The drawback in 2 or 3 is that this will not work for true plugins that add 
menus to PyMOL.

4. For simple script or short chunks of code I often copy-paste:
python
#code here
python end

into the pymol mini shell. This is great for testing part of the code.

In conclusion I recommend using option. 1 and restart PyMOL after making 
changes to the script: The plugin manager is a very practical addition to PyMOL 
and I love it. It just needs to be configured correctly, which is something 
that changed in comparison to other PyMOL versions (cf. the link).
Just beware: removing a installed plugin may physically delete the file. So be 
sure to backup your script should you decide to remove scripts or paths that 
were added to the Plugin Manager.

Hope this will relieve som

Re: [PyMOL] FW： RE： what is the pymol representation in this figure?

[Sampson, Jared]

Hi Yeping -

I followed  Jared's instruction and then show surface, but the surface is still 
an incomplete plane, unlike what I wish as in the sample.

You will probably have to create new objects for those individual residues to 
show their surfaces in whole.  Otherwise, you only get the portion of the whole 
object’s surface belonging to each residue.  Use the 
`create` command to duplicate a 
selection as a new object.

create peptide_surface_residues, chain P and resi 3+5
create protein_surface_residues, chain A and resi 97+114+116+156
show surface, *_surface_residues

There is also `extract`, which does 
the same thing, but removes the selection from the original object.  That’s 
good for separating out ligands.

And I have another question:

I show a residue in a helix of cartoon representation as sticks, and give it a 
color different from the cartoons of the helix, but the new color extented to 
the helix. How chould I prevent this happening? cartoon_discrete_colors seems 
doesn't work.


You picked the wrong cartoon color setting.  :)

`cartoon_discrete_colors`
 controls where and how the color changes if two residues are colored 
differently in a cartoon.  When set to 1 (or `on`), the color changes abruptly 
between two residues.  When 0 (or `off`), there is a smooth gradient between 
the two colors.


To change the color of the cartoon for a selection, use the 
`cartoon_color` setting:

set cartoon_color, blue, resi 1-100

Hope that helps.

Cheers,
Jared


Dear Yeping,
you should check Jared's reponse to your message.
I think he gave you all the hints you need.
:)
Gian


Guess I missed one.  :)

On 7/11/14 8:27 AM, sunyeping wrote:
>
> 发送时间：2014年7月10日(星期四) 21:20
> 收件人：pymol-users 
> mailto:pymol-users@lists.sourceforge.net>>
> 主　题：Re: [PyMOL] what is the pymol representation in this figure?
>
> It should be a solid surface with transparency on,
> if I'm not getting it wrong.
>
> Dear Gianluca,
>
> Thank you for the response, but how to set the side chain of the
> selected residues as solid surface? I used the command
>
> show surface, sele
>
> but the surface appears not like the sample figure in which there seems
> to be a 3D volume around the sticks representations of the side chains,
> instead, the surface shown is just a plane aside the sticks
> representation. So what is the proper way to obtain the effects in the
> sample figure?
>
> Best Regards.
>
> Yeping
>
> On 7/10/14 12:40 PM, sunyeping wrote:
> > Dear all,
> >
> > Could anyone tell me how the figure attached to the following web site
> > or the attach file is drawn? In What pymol repersentation of the
> > residues is shown?
> >
> > http://cashero.lingw.net/
> >
> > Yeping Sun
> >
> >
> >
> >
> >
> >
> --
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> >
>
>
> --
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> Dynamop Group
> Institut de Biologie Structurale
> 6 rue Jules Horowitz
> 38027 Grenoble Cedex 1
> France
> _
> Please avoid sending me Word or PowerPoint attachments.
> See http://www.gnu.org/philosophy/no-word-attachments.html
>
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38027 Grenoble Cedex 1
France
_
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Re: [PyMOL] what is the pymol representation in this figure?

[Sampson, Jared]

Hi Yeping -

Looks like the following settings are in play here:

# different cartoon modes
cartoon automatic, alpha1  # for the alpha1 helix
cartoon tube, chain P   # for the orange, green and blue peptides

# hide backbone sticks/lines where cartoon is shown
set cartoon_side_chain_helper, on

# surface transparency
set transparency, 0.5

# to color the surface a different color from the sticks/lines
set surface_color, orange, chain P and resi 5

Along with showing surface and line representations for the appropriate 
residues, this should get you pretty close.

Cheers,
Jared

--
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Xiangpeng Kong Lab
NYU Langone Medical Center
http://kong.med.nyu.edu/






On Jul 10, 2014, at 6:40 AM, sunyeping 
mailto:sunyep...@aliyun.com>> wrote:

Dear all,

Could anyone tell me how the figure attached to the following web site or the 
attach file is drawn? In What pymol repersentation of the residues is shown?

http://cashero.lingw.net/

Yeping Sun


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Re: [PyMOL] paste pictures

[Sampson, Jared]

Hi Yeping -

The best way is to upload your image to a file sharing website (e.g. Dropbox, 
Box, Google Drive, etc.) and include a link to the image (or folder of images) 
in your message.  That way, people only have to download the image if they want 
to do so.

It is also possible to send attached photos to the list, just make sure the 
file size isn’t too big (a 200KB PNG file, for example, shows plenty of 
detail—no need for a 2MB image).  Many (most?) mail programs have options to 
reduce the file size of attached images.

Cheers,
Jared

--
Jared Sampson
Xiangpeng Kong Lab
NYU Langone Medical Center
http://kong.med.nyu.edu/






On Jul 9, 2014, at 11:12 AM, sunyeping 
mailto:sunyep...@aliyun.com>> wrote:

Dear all,

how can I paste pictures on this pymol mail list? Thanks.


Yeping Sun


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

[Sampson, Jared]

Hi Suzanne - The reason you have been getting only one distance in your output 
file is that your script is opening the file in “write” mode:

f=open('distnew.txt','w')

This will overwrite the contents of distnew.txt each time the script is run.  
If you want to keep all the distances without changing the rest of your script, 
you could open the file in “append” mode.

f=open('distnew.txt',’a’)

This way, each line will just get added to the bottom of the script.  Keep in 
mind that if you want to start over with a new list of distances, you’ll need 
either to change the filename that gets opened (as you’ve done with 
“distnew.txt”) or delete the existing file.  For this reason, I would go with 
one of the other approaches mentioned by Andreas, or look into using a list to 
define the atoms to which you’d like to measure the distance from the first 
atom, and loop through that list.  Perhaps something like this (untested) bit 
of script would be useful, especially if you have many different atoms to check:


first_atom = 'B///297/cb'
second_atoms_list = ['A///17/cb', 'A///18/cb', 'A///19/cb']

with open("dist.txt", 'w') as f:
for second_atom in second_atoms_list:
f.write("%8.3f\n" % cmd.distance("tmp", first_atom, second_atom))


Good luck!

Cheers,
Jared

On Jun 17, 2014, at 2:21 PM, Lapolla, Suzanne M (HSC) 
mailto:suzanne-lapo...@ouhsc.edu>> wrote:

Another follow up question to this. I decided to use the measure distance 
python script on the pymol wiki to do this, and I was able to do it 
successfully with a range of residues, but my question is about the output txt 
file. When I run the script I get the correct distances (all 3 of them) to show 
on the GUI but the text file that is generated (distnew.txt) only lists one 
distance--so perhaps the script needs to be modified for this as well for the 
residues measured?

The original script is at the link 
http://www.pymolwiki.org/index.php/Measure_Distance
and my modified version is below. Suggestions appreciated! Thank you.

# This script writes the distance from
# atom mol1///25/ha to atom mol1///26/ha
# out to the file "dist.txt"
# Simply change your selections to see different distances.

# import PyMOL's command namespace
from pymol import cmd

# open dist.txt for writing
f=open('distnew.txt','w')

# calculate the distance and store it in dst
dst=cmd.distance('tmp','B///297/cb','A///17-19/cb')

# write the formatted value of the distance (dst)
# to the output file
f.write("%8.3f\n"%dst)

# close the output file.
f.close()

From: Robert Campbell 
[robert.campb...@queensu.ca]
Sent: Monday, June 09, 2014 10:04 AM
To: pymol-users@lists.sourceforge.net
Subject: Re: [PyMOL] command question RE printing out distances to text file

Hi Suzanne,

You can also get the distance printed in the external GUI or terminal window
by using the "cmd.distance" version of the command.  So either you can
assign the distance to a variable and print it or you can print the result
directly.

Assuming you have two selections, sele1 and sele2 specifying the atoms of
interest you can do:

 d = cmd.distance(sele1,sele2)
 print sele1,sele2,d


Cheers,
Rob

On Mon, 2014-06-09
13:13 EDT, Thomas Holder 
mailto:thomas.hol...@schrodinger.com>> wrote:

Hi Suzanne,

you can use the get_distance command. It doesn't generate a distance
object but prints the distance to the external window.

https://urldefense.proofpoint.com/v1/url?u=http://pymolwiki.org/index.php/Get_Distance&k=7DHVT22D9IhC0F3WohFMBA%3D%3D%0A&r=1ciN0EuZ9XNq3lPnYtgkI5sKPXgKVaywidBN0C981SQ%3D%0A&m=fr2bAoLQoVgp9h2t2fgBvfGVVX7oQ1g14g1AODFz%2FRg%3D%0A&s=921f4dfed39cd38f4ae7a70dfb937844d4e3faf1bc967c2f4d1f2944fa2ea31b

Cheers,
 Thomas

On 06 Jun 2014, at 23:03, Lapolla, Suzanne M (HSC)
mailto:suzanne-lapo...@ouhsc.edu>> wrote:

Fellow Pymol Users:
I may have asked this question before...but if so have forgotten. I am
measuring distances between 2 atoms in 2 different objects using the
distance command, and it is working perfectly, but I wonder if there is
a command I can use/add so that those distances can be printed in the
external gui as well as being shown in the viewer. I will be doing lots
of these at the same time and the screen will get crowded. Thank you in
advance.





--
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Senior Research Associate/Adjunct Assistant Professor
Dept. of Biomedical & Molecular Sciences
Botterell Hall Rm 644
Queen's University,
Kingston, ON K7L 3N6  Canada
Tel: 613-533-6821
mailto:robert.campb...@queensu.ca>>
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Re: [PyMOL] filled rings

[Sampson, Jared]

Hi H. Adam -

Try the cartoon_ring_color setting.  You can do this per-selection as well.

set cartoon_ring_color, blue, my_selection

Hope that helps!

Cheers,
Jared

--
Jared Sampson
Xiangpeng Kong Lab
NYU Langone Medical Center
http://kong.med.nyu.edu/






On Jun 16, 2014, at 4:57 PM, H. Adam Steinberg 
mailto:h.adam.steinb...@gmail.com>> wrote:

Hi All,

Somehow I have turned on or adjusted a setting and cannot figure out what it is 
or how to turn it off.

All of the rings in my nucleic acid structures are filled (and that is okay) 
but they are all filled with green! They are not filled with the same color as 
the rest of the base.

Can anyone help?

Sample image attached…



H. Adam Steinberg
7904 Bowman Rd
Lodi, WI 53555
608/592-2366

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Re: [PyMOL] Visualize Sheets from C-alpha Only Structure

[Sampson, Jared]

Hi Sean -

By “radially symmetric” I mean that a particular representation (e.g. anything 
in cartoon tube or putty modes, or loops in automatic mode) is drawn as a 
series of truncated cylinders or cones, so for PyMOL to draw them, basically 
all it needs for each short section are two end points and a radius (or start 
and end radii, in the case of the cones).  If you zoom in really close, you can 
actually see the boundaries between individual sections.

This differs from sheets in automatic, oval, rectangle, and dumbbell modes, 
because those require extra information to define the orientation of the 
“width” and “height” dimensions of the section with respect to the “length” 
axis (the one along the trace of the cartoon).

Hope that helps.

Cheers,
Jared

--
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Xiangpeng Kong Lab
NYU Langone Medical Center
http://kong.med.nyu.edu/






On Jun 4, 2014, at 4:17 PM, Sean Law 
mailto:magic...@hotmail.com>> wrote:

Jared,

For now, we are using different colors to indicate the SS assignments but it's 
not pretty. We would prefer to show the SS for both sheets and helices.

Can you elaborate on what you mean by "radially symmetric". Are there other 
cartoon modes where I would be able to get both helices and sheets after 
altering the residue's SS assignment by hand? I see what you mean by not being 
able to define the flat plane though.

Best,

Sean


From: jared.samp...@nyumc.org
To: magic...@hotmail.com
CC: pymol-users@lists.sourceforge.net
Subject: Re: [PyMOL] Visualize Sheets from C-alpha Only Structure
Date: Wed, 4 Jun 2014 20:03:54 +

Hi Sean -

I can confirm this behavior, but I’m not sure it’s unintentional on PyMOL’s 
part.  Rather, I think it may have something to do with two facts: 1) unlike 
loops, sheets represented in automatic mode are not radially symmetric; and 2) 
unlike helices, the orientation of the sheet at a particular CA atom cannot be 
determined by its immediate neighbors.  I haven’t had a chance to look at the 
relevant source, so I can’t confirm this at the moment, but it seems likely to 
me that PyMOL uses the other (non-CA) backbone atoms to define the “flat” plane 
of a sheet, and without this information, instead of guessing at its 
orientation, it omits the sheet entirely.  (This also appears to be the case 
for other non-radially symmetric modes, including dumbbell, rectangle, and 
oval.)

Could you get by using different colors to indicate your SS assignments in 
another cartoon mode?

Cheers,
Jared

Jared Sampson
Xiangpeng Kong Lab
NYU Langone Medical Center
http://kong.med.nyu.edu/






On Jun 4, 2014, at 1:50 PM, Sean Law 
mailto:magic...@hotmail.com>> wrote:

Hi PyMOLers,

I have a c-alpha only model and I would like to visualize both helices and 
sheets based on my own custom SS assignments (via "alter"). Altering a 
residue's SS assignment to helix or loop (ss="H" or ss="L") is fine and can be 
visualized. However, altering a residue's SS assignment to sheet (ss="S") 
causes that residue to disappear. Again, this is c-alpha only and I am 
visualizing in "cartoon automatic" mode.

Any suggestions for visualizing the sheets in this case would be greatly 
appreciated.

Best,

Sean
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Re: [PyMOL] Visualize Sheets from C-alpha Only Structure

[Sampson, Jared]

Hi Sean -

I can confirm this behavior, but I’m not sure it’s unintentional on PyMOL’s 
part.  Rather, I think it may have something to do with two facts: 1) unlike 
loops, sheets represented in automatic mode are not radially symmetric; and 2) 
unlike helices, the orientation of the sheet at a particular CA atom cannot be 
determined by its immediate neighbors.  I haven’t had a chance to look at the 
relevant source, so I can’t confirm this at the moment, but it seems likely to 
me that PyMOL uses the other (non-CA) backbone atoms to define the “flat” plane 
of a sheet, and without this information, instead of guessing at its 
orientation, it omits the sheet entirely.  (This also appears to be the case 
for other non-radially symmetric modes, including dumbbell, rectangle, and 
oval.)

Could you get by using different colors to indicate your SS assignments in 
another cartoon mode?

Cheers,
Jared

Jared Sampson
Xiangpeng Kong Lab
NYU Langone Medical Center
http://kong.med.nyu.edu/






On Jun 4, 2014, at 1:50 PM, Sean Law 
mailto:magic...@hotmail.com>> wrote:

Hi PyMOLers,

I have a c-alpha only model and I would like to visualize both helices and 
sheets based on my own custom SS assignments (via "alter"). Altering a 
residue's SS assignment to helix or loop (ss="H" or ss="L") is fine and can be 
visualized. However, altering a residue's SS assignment to sheet (ss="S") 
causes that residue to disappear. Again, this is c-alpha only and I am 
visualizing in "cartoon automatic" mode.

Any suggestions for visualizing the sheets in this case would be greatly 
appreciated.

Best,

Sean
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Re: [PyMOL] align or pair_fit display problem

[Sampson, Jared]

Hi I-Ji -

You say the superimposed atoms are still there; that seems like normal behavior 
to me.  If you disable one of the objects, can you see the other one, and vice 
versa?

If the two structures are nearly identical, you may not be able to 
differentiate them visually after alignment.  If that is the case, you may wish 
to use different representations and/or colors for the two objects.

Cheers,
Jared

--
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Xiangpeng Kong Lab
NYU Langone Medical Center
http://kong.med.nyu.edu/






On May 26, 2014, at 6:58 PM, I-Ji Jung 
mailto:u5205...@anu.edu.au>> wrote:

Hi,

I'm trying to superimpose a small structure to a residue of a protein.
When I use align or pair_fit to do this, the superposition works, but for some 
weird reason I can't see my small structure anymore. Like it's whole structure 
disappears. The superimposed atoms are there - but then those are overlapped by 
the same atoms of the residue, so you can't see them anyway. I've tried 
pair_fit some while ago and I recall using it without a problem. Why am I 
suddenly having this problem?
Can somebody help me?

Thanks,

I-Ji
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Re: [PyMOL] how to count all the Polar contacts

[Sampson, Jared]

Hi Merlin -

Try limiting the distances shown to those between atoms in specific selections 
using the `distance` command.  For example, to show H-bonds to solvent, disable 
the “my_obj_pol_conts” object created by the technical preset and use the 
command:

distance my_dist, my_obj and not solvent, my_obj and solvent, cutoff=3.5

Make sure to specify a cutoff or you’ll get every pair of polar atoms between 
your selections.

Hope that helps.

Cheers,
Jared
--
Jared Sampson
Xiangpeng Kong Lab
NYU Langone Medical Center
http://kong.med.nyu.edu/






On May 27, 2014, at 3:33 AM, 天元 <422294...@qq.com> 
wrote:


Dear PyMol users!


I'm analysing polar contacts by "preset:technical". I got so many yellow bar 
measurements that I can't count the number.

IS there any else way to count the number of all polar contacts ?

Thanks for help,


Merlin

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Re: [PyMOL] Ray trace mode 1 outline thickness

[Sampson, Jared]

Hi Martin -

Try increasing the `ray_trace_gain` setting.  Default value is 0.12, so maybe 
try 1 or 2.  If you go much higher, you’ll start to see additional lines or 
spots.

Cheers,
Jared

--
Jared Sampson
Xiangpeng Kong Lab
NYU Langone Medical Center
http://kong.med.nyu.edu/






On May 14, 2014, at 9:36 AM, Martin Hediger 
mailto:ma@bluewin.ch>> wrote:

Hi guys

I wonder if you could help, I'm rendering this image:

http://qmviews.blogspot.ch/2014/05/illustrating-protein-structures.html

and I wonder if and how I could increase the thickness of the black
outlines?

Thanks for help
Martin

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Re: [PyMOL] using a pseudoatom for distance measurement

[Sampson, Jared]

Hi Mary -

If you already know which state has the conformation you want to use for your 
measurement, or if you want to create a pseudoatom for each state, you can do 
so by passing the `state` keyword to pseudoatom:

set state, 1   # or 2, 3, etc.
pseudoatom test, pdbfile_0001 and chain A and resi 100 and n. 
cg+cd1+ce1+cz+ce2+cd2, color=tv_blue, state=1  # or 2, 3, etc.

You also may be interested in the iterate_state function.

Cheers,
Jared

--
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Xiangpeng Kong Lab
NYU Langone Medical Center
http://kong.med.nyu.edu/






On May 6, 2014, at 9:32 AM, M. Faridounnia 
mailto:faridoun...@gmail.com>> wrote:

Thanks a lot for the tip and explaining the whole thing, Jared. I learned a lot 
from that. It worked but here is why I had a problem at the beginning (and 
tried the command I emailed), still same problem persists.

I had tried similar command on one of the models after splitting the pdb file 
(split_states pdbfile, ) and it was not working.
>split_states pdbfile,
>pseudoatom test, pdbfile_0001 and chain A and resi 100 and n. 
>cg+cd1+ce1+cz+ce2+cd2, color=tv_blue


Now, I tried exactly what you mentioned. After splitting the states it doesn't 
work, but when I don't do split_states, the same command works and creates a 
pseudoatom. The problem is that the NMR structure I have been doing 
split_states on is an average structure of 20 models. So, I need to create the 
pseudoatom on one of the 20 structure models ( the closest to the average or 
the lowest energy). It is not a big deal for now because for these two residues 
all the 20 structure are very similar but I still wonder why isn't it possible!

I mean it would make more sense that the command doesn't work on the average 
structure, because it doesn't refer to a real coordinate in the file and it can 
take any of the twenty models, but when it knows which model to take, it is 
more probable to work because it refers to the right coordinates. Any comments 
on that?

Cheers
Mary


On Mon, May 5, 2014 at 4:17 PM, Sampson, Jared 
mailto:jared.samp...@nyumc.org>> wrote:
Hi Mary -

There are a couple problems here.  First, you’re giving the pseudoatom command 
a positional argument out-of-order (and after keyword parameters).  Keyword 
parameters can appear in any order, but only if you use the keyword.  
Otherwise, you must list them in the order specified by the function.  So, you 
either need to use the keyword and enclose the selection in quotes 
(selection=“n. …”) or simply move it to its proper position, like this:

pseudoatom test, n. cg+cd1+ce1+cz+ce2+cd2, resi=100, color=tv_blue

For the full order of arguments, see 
http://www.pymolwiki.org/index.php/Pseudoatom or type `help pseudoatom` on the 
PyMOL command line.

Second, your current selection is going to use any atom named cg+cd1…etc. in 
the entire session, not just in your single Phe residue.  This is because the 
resi=100 and color=tv_blue are used to determine the properties of the new 
pseudoatom, and not to determine or refine the selection.  If you want to use 
the ring of Phe 100 only, the selection argument needs to include that 
information.  If you have more than one object or chain that includes resi 100, 
you will also need to specify that.

So I’m guessing what you probably want is something along the lines of 
(replacing “myobject” and “A” with appropriate values):

pseudoatom test, myobject and chain A and resi 100 and n. 
cg+cd1+ce1+cz+ce2+cd2, color=tv_blue

which will create a tv_blue-colored pseudoatom in the center of the ring of 
residue 100.

Hope that helps.

Cheers,
Jared

--
Jared Sampson
Xiangpeng Kong Lab
NYU Langone Medical Center
http://kong.med.nyu.edu/



On May 4, 2014, at 2:12 PM, M. Faridounnia 
mailto:faridoun...@gmail.com>> wrote:

Hi there,

I want to measure the distance and angle between an aromatic ring (phenylalanin 
and a residue backbone) like this: 
http://www.pymolwiki.org/index.php/File:Pseu1.png

I learned from here that I need to make a pseudoatom but I cannot make it work.

I tried
pseudoatom test, resi=100, color=tv_blue, n. cg+cd1+ce1+cz+ce2+cd2

and some other ways! I don't know how should I choose the write atoms and make 
the pseudoatom. After this probably distance and angle measurement would be 
straightforward.

Best regards
Mary
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Re: [PyMOL] using a pseudoatom for distance measurement

[Sampson, Jared]

Hi Mary -

There are a couple problems here.  First, you’re giving the pseudoatom command 
a positional argument out-of-order (and after keyword parameters).  Keyword 
parameters can appear in any order, but only if you use the keyword.  
Otherwise, you must list them in the order specified by the function.  So, you 
either need to use the keyword and enclose the selection in quotes 
(selection=“n. …”) or simply move it to its proper position, like this:

pseudoatom test, n. cg+cd1+ce1+cz+ce2+cd2, resi=100, color=tv_blue

For the full order of arguments, see 
http://www.pymolwiki.org/index.php/Pseudoatom or type `help pseudoatom` on the 
PyMOL command line.

Second, your current selection is going to use any atom named cg+cd1…etc. in 
the entire session, not just in your single Phe residue.  This is because the 
resi=100 and color=tv_blue are used to determine the properties of the new 
pseudoatom, and not to determine or refine the selection.  If you want to use 
the ring of Phe 100 only, the selection argument needs to include that 
information.  If you have more than one object or chain that includes resi 100, 
you will also need to specify that.

So I’m guessing what you probably want is something along the lines of 
(replacing “myobject” and “A” with appropriate values):

pseudoatom test, myobject and chain A and resi 100 and n. 
cg+cd1+ce1+cz+ce2+cd2, color=tv_blue

which will create a tv_blue-colored pseudoatom in the center of the ring of 
residue 100.

Hope that helps.

Cheers,
Jared

--
Jared Sampson
Xiangpeng Kong Lab
NYU Langone Medical Center
http://kong.med.nyu.edu/


On May 4, 2014, at 2:12 PM, M. Faridounnia  wrote:

Hi there,

I want to measure the distance and angle between an aromatic ring (phenylalanin 
and a residue backbone) like this: 
http://www.pymolwiki.org/index.php/File:Pseu1.png

I learned from here that I need to make a pseudoatom but I cannot make it work.

I tried
pseudoatom test, resi=100, color=tv_blue, n. cg+cd1+ce1+cz+ce2+cd2

and some other ways! I don't know how should I choose the write atoms and make 
the pseudoatom. After this probably distance and angle measurement would be 
straightforward.

Best regards
Mary
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Re: [PyMOL] Pymol wrl output

[Sampson, Jared]

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

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

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

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

Thanks,
Jared

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

Hi,

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

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

Any help would be great!

Thanks for all this!

Ciao,
Bob


On Sat, May 3, 2014 at 6:44 PM, Sampson, Jared 
mailto:jared.samp...@nyumc.org>> wrote:
Hi Bob -

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

Cheers,
Jared

--
Jared Sampson
Xiangpeng Kong Lab
NYU School of Medicine
kong.med.nyu.edu<http://kong.med.nyu.edu>

From: Grateful Frog [gratefulf...@gmail.com<mailto:gratefulf...@gmail.com>]
Sent: Friday, May 02, 2014 7:07 PM
To: Marcelo Marcet
Cc: pymol-users@lists.sourceforge.net<mailto:pymol-users@lists.sourceforge.net>
Subject: Re: [PyMOL] Pymol wrl output

these are the errors that Shapeways sent back:

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

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

Please visit your 3D model page to update your 
file:http://www.shapeways.com/model/upload-and-buy/1932482<http://www.shapeways.com/model/upload-and-buy/1932482?etId=14290783&utm_source=automated-contact&utm_medium=email&utm_campaign=model-processing-failed>

Our tutorials and 
FAQ<http://www.shapeways.com/support?etId=14290783&utm_source=automated-contact&utm_medium=email&utm_campaign=model-processing-failed>
 can be super helpful for more detailed information, or you can always ask the 
community a specific question on our 
forum<http://www.shapeways.com/forum?etId=14290783&utm_source=automated-contact&utm_medium=email&utm_campaign=model-processing-failed>

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

Additional non-critical errors:

  *   Invalid field, unparsable value, name: Material.diffuseColor , value: 
[-1.0, -1.0, 1.0]. Value ignored.
  *   Invalid field, unparsable value, name: Material.diffuseColor , value: 
[-1.0, -1.0, 1.0]. Value ignored.
  *   Invalid field, unparsable value, name: Material.diffuseColor , value: 
[-1.0, -1.0, 1.0]. Value ignored.

-> this goes on for tons of lines...



On Sat, May 3, 2014 at 12:39 AM, Grateful Frog 
mailto:gratefulf...@gmail.com>> wrote:
Hi Marcelo,

Thanks for your help and suggestion!

I did that and the surface is much nicer.

However, the Pymol rendering in VRML still won't load to Shapeways without 
error.

I have to re-render in VRML in MeshLab.

My goal is to do it all in Pymol.

Any more ideas would be great!

Ciao,
Bob


On Sat, May 3, 2014 at 12:17 AM, Marcelo Marcet 
mailto:mmar...@nait.ca>> wrote:
Hi Bob,

Before you save your file from pymol try increasing the quality to max, then 
save as VRML. This increases the number of polygons in the file and after 
exporting from meshlab the final molecule will look a lot smoother.

Cheers,
Marcelo

On May 2, 2014, at 2:

Re: [PyMOL] Pymol wrl output

[Sampson, Jared]

Hi Bob -

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

Cheers,
Jared

--
Jared Sampson
Xiangpeng Kong Lab
NYU School of Medicine
kong.med.nyu.edu

From: Grateful Frog [gratefulf...@gmail.com]
Sent: Friday, May 02, 2014 7:07 PM
To: Marcelo Marcet
Cc: pymol-users@lists.sourceforge.net
Subject: Re: [PyMOL] Pymol wrl output

these are the errors that Shapeways sent back:

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

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

Please visit your 3D model page to update your 
file:http://www.shapeways.com/model/upload-and-buy/1932482

Our tutorials and 
FAQ
 can be super helpful for more detailed information, or you can always ask the 
community a specific question on our 
forum

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

Additional non-critical errors:

  *   Invalid field, unparsable value, name: Material.diffuseColor , value: 
[-1.0, -1.0, 1.0]. Value ignored.
  *   Invalid field, unparsable value, name: Material.diffuseColor , value: 
[-1.0, -1.0, 1.0]. Value ignored.
  *   Invalid field, unparsable value, name: Material.diffuseColor , value: 
[-1.0, -1.0, 1.0]. Value ignored.

-> this goes on for tons of lines...



On Sat, May 3, 2014 at 12:39 AM, Grateful Frog 
mailto:gratefulf...@gmail.com>> wrote:
Hi Marcelo,

Thanks for your help and suggestion!

I did that and the surface is much nicer.

However, the Pymol rendering in VRML still won't load to Shapeways without 
error.

I have to re-render in VRML in MeshLab.

My goal is to do it all in Pymol.

Any more ideas would be great!

Ciao,
Bob


On Sat, May 3, 2014 at 12:17 AM, Marcelo Marcet 
mailto:mmar...@nait.ca>> wrote:
Hi Bob,

Before you save your file from pymol try increasing the quality to max, then 
save as VRML. This increases the number of polygons in the file and after 
exporting from meshlab the final molecule will look a lot smoother.

Cheers,
Marcelo

On May 2, 2014, at 2:15 PM, Grateful Frog 
mailto:gratefulf...@gmail.com>> wrote:

> Hi all,
>
> I'm new to this list and to this tool.  I have encountered a problem with 
> exporting as wrl in pylolk 1.7 that I compiled on my Ubuntu 12.04 platform.
>
> I load a PDB file and it displays fine.
>
> I then type the command "show surface" and this works fine, too.
>
> I then save image as VRML 2, and write the file to disk.
>
> This file can be visualized fine in MeshLab.
>
> However, it cannot be 3D printed at Shapeways. The error message does not say 
> what is wrong.
>
> The work-around that I have found is to open the wrl file, generated by 
> Pymol, in Meshlab and re-save another copy as wrl, but generated by Meshlab. 
> This new file can be 3D printed at Shapeways.
>
> However, the look of the surface is not as nice when it comes out of Meshlab, 
> as it is in Pymol...
>
> Any thoughts would be great!
>
> Thanks,
> Bob
> --
> "Accelerate Dev Cycles with Automated Cross-Browser Testing - For FREE
> Instantly run your Selenium tests across 300+ browser/OS combos.  Get
> unparalleled scalability from the best Selenium testing platform available.
> Simple to use. Nothing to install. Get started now for free."
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Re: [PyMOL] RE： gradually changed colors with b-factor colum

[Sampson, Jared]

Hi Yeping -

It doesn’t look like Spectrumbar supports additional labeling, but you could 
add labels at each end by using pseudoatoms at the positions where you want the 
labels to appear (see the second example at 
http://pymolwiki.org/index.php/Pseudoatom).

For the 2D gradient box, you can create whatever intermediate labels you like, 
just keep the same scale.  For example, if your bar covers data values from 
-0.3 to +2.3 and you make it 260 pixels wide, then each 10px accounts for 0.1 
unit.  So “0.0” will be 30px from the left side, “+0.5” will be at 80px, and so 
forth.  After you create it at that scale, you can resize it as you wish and 
the relative positions will remain the same.

Hope that helps.

Cheers,
Jared

--
Jared Sampson
Xiangpeng Kong Lab
NYU Langone Medical Center
http://kong.med.nyu.edu/






On Apr 28, 2014, at 10:20 PM, sunyeping 
mailto:sunyep...@aliyun.com>> wrote:

Dear Jared,

Thank you for the reply. But I still have a couple of questions:

 As for the spectrumbar<http://pymolwiki.org/index.php/Spectrumbar> script, 
how could I assign a particular data value to a particular color?  By using the 
command:

spectrumbar blue, white, red

I can get a spectrumbar. If the range of my data is -0.3~2.3, maybe I can label 
two end of the bar with -0.3 and 2.3 manually, respectively. But if I want to 
label more data to the bar? How shold I do?

  As you suggest, I can simplely get a 2D box with a linear gradient fill. 
But the question is the same with above: how could I correctly label the bar 
according my data set?

Best regards,


Yeping

------
发件人：Sampson, Jared mailto:jared.samp...@nyumc.org>>
发送时间：2014年4月29日(星期二) 04:36
收件人：孙业平 mailto:sunyep...@aliyun.com>>
抄　送：pymol-users 
mailto:pymol-users@lists.sourceforge.net>>
主　题：Re: [PyMOL] gradually changed colors with b-factor colum

Hi Yeping -

I was about to suggest Sean Law’s new 
spectrumbar<http://pymolwiki.org/index.php/Spectrumbar> script, but I see he 
beat me to it.  You’ll have to adjust the positioning of the bar with some 
trial and error.  Also, in case you get a “NameError: global name 're' is not 
defined” error, simply change the 4th line from:

from re import *

to

import re

I’ve just submitted a pull 
request<https://github.com/Pymol-Scripts/Pymol-script-repo/pull/55> with this 
fix, but if you download the script before it’s accepted, you'll have to make 
the change yourself.

Alternatively, you could fairly easily create a simple 2D box with a gradient 
fill in e.g. Inkscape or Illustrator with the appropriate colors and add the 
labels manually.  So long as you specify a linear gradient, it should be fairly 
consistent with the PyMOL values.

Hope that helps.

Cheers,
Jared

--
Jared Sampson
Xiangpeng Kong Lab
NYU Langone Medical Center
http://kong.med.nyu.edu/


On Apr 27, 2014, at 8:50 AM, sunyeping 
mailto:sunyep...@aliyun.com>> wrote:

Dear proessor Holder and pymol users,

I previously tried to color a protein structure accord to a set of customer 
data. I replaced the b factor of individual Ca atoms and colored the structure 
with the command:

spectrum b, blue_white_red, byres=1

But I think I need a color scale bar to show the range of the data set. 
According to PymolWiki 
(http://www.pymolwiki.org/index.php/Advanced_Coloring#Creating_a_Color_bar), 
this can be done with the following steps:

  1.  Create a pdb-file which contains CA positions only, whereas the numbers 
correspond to your wanted increments of colors. Make CA's to be separated by 5 
Angstroem.
  2.  Load this new pseudobar-pdb file into PyMOL, make bonds between increment 
1 and increment 2 [increment 2 and increment 3 and so on...], define/assign a 
smooth color for each increment (copy colors definition from automatically 
created colors made by b-factor script) and show the b-factor bar as lines (or 
sticks).

Could you tell me how to assign blue_white_red color for these increment? And 
if the range of my data set is -0.8 to 2.3, how to make the color gradient 
reflect this range? Thank you very much.




Yeping Sun

Institute of Microbiology, Chinese Academy of Sciences

--
发件人：Thomas Holder 
mailto:spel...@users.sourceforge.net>>
发送时间：2013年12月11日(星期三) 12:49
收件人：孙业平 mailto:sunyep...@aliyun.com>>
抄　送：pymol-users 
mailto:pymol-users@lists.sourceforge.net>>
主　题：Re: [PyMOL] 答复： gradually changed colors with flexibility

Hi Yeping,

the spectrum command has a "byres" argument to operate on the residue level:

PyMOL>spectrum b, blue_white_red, byres=1

There is no white_blue color ramp, but there is a script which provides this:
http://pymolwiki.org/index.php/Spectrumany
It doesn't have the byres argument. If you only show cartoon, just limit the 
selection to CA atoms:

PyMOL>run path/to

Re: [PyMOL] gradually changed colors with b-factor colum

[Sampson, Jared]

Hi Yeping -

I was about to suggest Sean Law’s new 
spectrumbar script, but I see he 
beat me to it.  You’ll have to adjust the positioning of the bar with some 
trial and error.  Also, in case you get a “NameError: global name 're' is not 
defined” error, simply change the 4th line from:

from re import *

to

import re

I’ve just submitted a pull 
request with this 
fix, but if you download the script before it’s accepted, you'll have to make 
the change yourself.

Alternatively, you could fairly easily create a simple 2D box with a gradient 
fill in e.g. Inkscape or Illustrator with the appropriate colors and add the 
labels manually.  So long as you specify a linear gradient, it should be fairly 
consistent with the PyMOL values.

Hope that helps.

Cheers,
Jared

--
Jared Sampson
Xiangpeng Kong Lab
NYU Langone Medical Center
http://kong.med.nyu.edu/


On Apr 27, 2014, at 8:50 AM, sunyeping 
mailto:sunyep...@aliyun.com>> wrote:

Dear proessor Holder and pymol users,

I previously tried to color a protein structure accord to a set of customer 
data. I replaced the b factor of individual Ca atoms and colored the structure 
with the command:

spectrum b, blue_white_red, byres=1

But I think I need a color scale bar to show the range of the data set. 
According to PymolWiki 
(http://www.pymolwiki.org/index.php/Advanced_Coloring#Creating_a_Color_bar), 
this can be done with the following steps:

  1.  Create a pdb-file which contains CA positions only, whereas the numbers 
correspond to your wanted increments of colors. Make CA's to be separated by 5 
Angstroem.
  2.  Load this new pseudobar-pdb file into PyMOL, make bonds between increment 
1 and increment 2 [increment 2 and increment 3 and so on...], define/assign a 
smooth color for each increment (copy colors definition from automatically 
created colors made by b-factor script) and show the b-factor bar as lines (or 
sticks).

Could you tell me how to assign blue_white_red color for these increment? And 
if the range of my data set is -0.8 to 2.3, how to make the color gradient 
reflect this range? Thank you very much.




Yeping Sun

Institute of Microbiology, Chinese Academy of Sciences

--
发件人：Thomas Holder 
mailto:spel...@users.sourceforge.net>>
发送时间：2013年12月11日(星期三) 12:49
收件人：孙业平 mailto:sunyep...@aliyun.com>>
抄　送：pymol-users 
mailto:pymol-users@lists.sourceforge.net>>
主　题：Re: [PyMOL] 答复： gradually changed colors with flexibility

Hi Yeping,

the spectrum command has a "byres" argument to operate on the residue level:

PyMOL>spectrum b, blue_white_red, byres=1

There is no white_blue color ramp, but there is a script which provides this:
http://pymolwiki.org/index.php/Spectrumany
It doesn't have the byres argument. If you only show cartoon, just limit the 
selection to CA atoms:

PyMOL>run path/to/spectrumany.py
PyMOL>spectrumany b, white blue, name CA

If you want to show all atoms, you can map the CA atom b-factor to all residue 
atoms with this script:
http://pymolwiki.org/index.php/AlphaToAll

Hope that helps.

Cheers,
Thomas

On 10 Dec 2013, at 01:04, sunyeping  wrote:

> Hi, professor Holder,
>
> Thank you for the reply, but how can I do this on the level of individual 
> amino acids in stead of atom? I have two homolog stuctures and I want to map 
> the difference between the b factors of the corresonding residues of these 
> two stuctures rather than individual atoms. And I want to use gradually 
> deepened color from white to blue. Could you explain more in detail? Thanks.
>
> Yeping Sun
>
> Institute of Microbiology, Chinese Academy of Sciences
>
>
> --
> 发件人：Thomas Holder 
> 发送时间：2013年12月10日(星期二) 04:50
> 收件人：孙业平 
> 抄　送：pymol-users 
> 主　题：Re: [PyMOL] gradually changed colors with flexibility
>
> Hi Yeping,
>
> use the spectrum command:
>
> PyMOL> spectrum b, blue_white_red
>
> http://pymolwiki.org/index.php/Spectrum
>
> Cheers,
> Thomas
>
> On 09 Dec 2013, at 11:30, sunyeping  wrote:
>
> > Dear all,
> >
> > I want to show amino acids in a structure according to their flexibility (B 
> > factor) by gradually changed colors. Can pymol do this? Thanks.
> >
> > Yeping Sun
> >
> > Institute of Microbiology, Chinese Academy of Sciences

--
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