Re: [PyMOL] Pymol wrl output

[Hurt, Darrell (NIH/NIAID) [E]]

Hi everyone,

We are developing a new NIH web portal for freely preparing 3D print files from 
molecular, microscopy, and medical imaging data. The website is in public beta, 
so you may see some changes in the final release, but this email thread seemed 
like a good opportunity to make you aware of it. Anyone can browse and download 
files, but only registered users can create and upload 3D printable files to 
share.

If you have the PDB code, you can simply type it in (under "Create") and our 
tools will generate several different representations of the protein(s) that 
should be directly printable. Alternatively, if you have a custom PDB, you can 
simply upload it and get the same kind of output.

Please give it a try and let us know what you think!  http://3dprint.nih.gov

Thanks,
Darrell

--
Darrell Hurt, Ph.D.
Section Head, Computational Biology
Bioinformatics and Computational Biosciences Branch (BCBB)
OCICB/OSMO/OD/NIAID/NIH

31 Center Drive, Room 3B62B, MSC 2135
Bethesda, MD 20892-2135
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From: David Hall mailto:li...@cowsandmilk.net>>
Date: Sunday, May 4, 2014 8:48 AM
To: Grateful Frog mailto:gratefulf...@gmail.com>>
Cc: 
"pymol-users@lists.sourceforge.net" 
mailto:pymol-users@lists.sourceforge.net>>
Subject: Re: [PyMOL] Pymol wrl output

if you're just typing the command, you can type "as surface" (or "show_as 
surface") and it will only use the surface representation. The menu I'm talking 
about is the letter [S] next to each object on the RHS of the screen. The first 
line under Show: is as, which pops out another menu where you can choose 
representations.

-David


On Sun, May 4, 2014 at 8:40 AM, Grateful Frog 
mailto:gratefulf...@gmail.com>> wrote:
HI David,

Thanks for that tip.  I didn't understand where the menu show > as > surface is?

But, I did "Hide everything", then "Show Suface" and Shapeways liked it!

So I now have a working solution!

Thanks EVERYONE!

This is a great support mailing list!

Ciao,
Bob


On Sun, May 4, 2014 at 2:08 PM, David Hall 
mailto:li...@cowsandmilk.net>> wrote:
Have you tried doing show > as > surface

It appears the wrl file has a bunch of extra information from the cartoon 
representation, which could confuse shapeways?

-David


On Sun, May 4, 2014 at 4:49 AM, Grateful Frog 
mailto:gratefulf...@gmail.com>> wrote:
Hi Jared &  everyone,

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

I am using the Pymol GUI (1.7).

I've created a shared 
folder
 with all my files so you can test with them if you like.

The important files are:

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

My process is:

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

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

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

Thanks again for any help!

Ciao, Bob.




On Sun, May 4, 2014 at 1:29 AM, Sampson, Jared 
mailto:jared.samp...@nyumc.org>> wrote:
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 p

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

--
Jared Sampson
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

[M. Faridounnia]

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 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  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
>
> --
> "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."
>
> http://p.sf.net/sfu/SauceLabs___
> PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net)
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