pymol-users Mailing List for PyMOL Molecular Graphics System

On 5/29/2010 8:21 AM, J. Fleming wrote:
> Hello,
>
> I've been using 'super' to align the C-alphas within one domain of two
> different models of the same protein while leaving the second domain
> to move freely.  I can do this using:
>
> super (A and resid 1-100 and name ca), (B and resid 1-100 and name ca)
>
> What I would like to do is determine the rotation and translation of
> model B's second domain as it moves away from A's second domain.
>
> I can output a matrix after running super using:
>
> print cmd.get_object_matrix("A")
>
> How do I go from the matrix to an angle and distance?
>
> Thanks for any thoughts,
> Jon
>


To extract Euler rotation angles from the superimposition matrix you can 
use the euler_from_matrix function of the transformations.py module at 
<." rel="nofollow">http://www.lfd.uci.edu/~gohlke/code/transformations.py.html>. If you 
rather have a rotation angle and axis use the rotation_from_matrix 
function. You might have to use the transpose of the matrix returned by 
PyMOL, not sure. The extraction of the translation vector has already 
been explained.

To find how domain #2 is translated and rotated in molecule B relative 
to A when the domains #1 of A and B are superimposed, you can write a 
Python script outside of PyMOL. The following untested (!) script 
assumes that you have (1) the C-alpha coordinates of molecule A and B as 
homogeneous coordinate numpy arrays of shape (4, *), and (2) the C-alpha 
atom indices that belong to domain 1 and 2 as Python sequences or slices:


import numpy
import transformations

# transform B such that domain1 of A and B overlap
S0 = transformations.superimposition_matrix(
          B[:, domain1], A[:, domain1])
B = numpy.dot(S0, B)

# calculate matrix to transform domain2 of A to B
S1 = transformations.superimposition_matrix(
          A[:, domain2], B[:, domain2])

# extract translation vector and Euler rotation angles from S1
translation = S1[:3, 3].copy()
eulerangles = transformations.euler_from_matrix(S1)


--
Christoph

Hello,

I've been using 'super' to align the C-alphas within one domain of two
different models of the same protein while leaving the second domain
to move freely.  I can do this using:

super (A and resid 1-100 and name ca), (B and resid 1-100 and name ca)

What I would like to do is determine the rotation and translation of
model B's second domain as it moves away from A's second domain.

I can output a matrix after running super using:

print cmd.get_object_matrix("A")

How do I go from the matrix to an angle and distance?

Thanks for any thoughts,
Jon

Hi all,

Before I go out an buy an ATI video card to test/debug this, can
anyone else verify that this error occurs on the 965G or other desktop
card?  The 965GM, I think is a mobile-only card.  If someone is
experiencing issues on a desktop box, please provide me with the exact
setup.

Cheers,

-- Jason

On Fri, May 28, 2010 at 11:37 AM, Jason Vertrees
<jas...@sc...> wrote:
> Hi Bernhard,
>
> After re-reading Timothy's original email, this very much sounds like
> a driver issue.  Timothy reports proper functionality using the same
> laptop, but in Windows.  Regardless, here's how I responded to
> Timothy's question (offline) about the coloring problems:
>
> """
> Hi Tim,
>
> There are quite a few details here.
>
> First, we prefer working with NVidia cards, because they have better
> performance and support across the various platforms.  But, as you
> already have an ATI card, that's moot, and we can move on to the next
> point.
>
> VMD's rendermode set to GLSL means it's using what's called the
> "openGL Shader Language" which is a variant of how we draw stuff on
> the screen.  PyMOL only has openGL shaders for spheres at this point
> (set sphere_mode, 5).  I will soon be making improvements to PyMOL to
> allow for vertex buffer objects and GPU shading (GLSL).
>
> Things look great after clicking the 'ray' button b/c you're then
> looking at a PNG file.  (That is, when you normally use PyMOL you're
> looking at an openGL screen.  When you click 'ray' or type 'ray' PyMOL
> will ray trace the screen and display the resulting PNG file.  Once
> you touch the screen after ray tracing, PyMOL immediately trashes the
> PNG file so you can keep working.)
>
> Sadly, I don't have any answers for you at this point, but I've CC'd
> my main technical support guru to see what he knows.  I need to get an
> ATI card to more testing.
> """
>
> I cannot be more helpful at this time because my Linux boxes only run
> NVidia cards.  I will either find a machine or go buy an ATI card for
> my Linux box and let you know the results.
>
> Cheers,
>
> -- Jason
>
> --
> Jason Vertrees, PhD
> PyMOL Product Manager
> Schrodinger, LLC
>
> (e) Jas...@sc...
> (o) +1 (603) 374-7120
>



-- 
Jason Vertrees, PhD
PyMOL Product Manager
Schrodinger, LLC

(e) Jas...@sc...
(o) +1 (603) 374-7120

On Fri, May 28, 2010 at 10:49 AM, Thomas Juettemann <jue...@gm...>wrote:

> Hi Chris,
>
> the emails are only sent to you because you subscribed to the pymol-users
> list.
> If you don't want them anymore you need to unsubscribe.
>
> Click on "Show details" at the top of this email. Click then on:
> unsubscribe     Unsubscribe from this mailing-list
>
> That will do the magic.


Or click on the link at the bottom of *every email sent to the list*:


> > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
>

Hi Chris,

the emails are only sent to you because you subscribed to the pymol-users list.
If you don't want them anymore you need to unsubscribe.

Click on "Show details" at the top of this email. Click then on:
unsubscribe	Unsubscribe from this mailing-list

That will do the magic.


On Fri, May 28, 2010 at 10:42, Christian De Ford <cde...@gm...> wrote:
> Please stop sending me daily emails.... its very annoying, i would
> appreciate if you erase me from the list
> Thank you!
> ------------------------------------------------------------------------------
>
>
> _______________________________________________
> PyMOL-users mailing list (PyM...@li...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pym...@li...
>

Please stop sending me daily emails.... its very annoying, i would
appreciate if you erase me from the list
Thank you!

Hi All,

I have re-written the center-of-mass script found on the Wiki (which was actually only calculating center-of-geometry).  This script provides three improvements to the previous script: 1) The real center-of-mass can be calculated based on a table of atomic masses, 2) pseudoatoms are used to represent the center-of-mass which, unlike CGO spheres, can be used to measure distances, angles, dihedral etc, 3) The COM/COG calculator is written as an independent function which can be called as "get_com".

Hope you find this useful.

Sean
 		 	   		  
_________________________________________________________________
30 days of prizes: Hotmail makes your day easier! Enter Now.
http://go.microsoft.com/?linkid=9729710

Hi Bernhard,

After re-reading Timothy's original email, this very much sounds like
a driver issue.  Timothy reports proper functionality using the same
laptop, but in Windows.  Regardless, here's how I responded to
Timothy's question (offline) about the coloring problems:

"""
Hi Tim,

There are quite a few details here.

First, we prefer working with NVidia cards, because they have better
performance and support across the various platforms.  But, as you
already have an ATI card, that's moot, and we can move on to the next
point.

VMD's rendermode set to GLSL means it's using what's called the
"openGL Shader Language" which is a variant of how we draw stuff on
the screen.  PyMOL only has openGL shaders for spheres at this point
(set sphere_mode, 5).  I will soon be making improvements to PyMOL to
allow for vertex buffer objects and GPU shading (GLSL).

Things look great after clicking the 'ray' button b/c you're then
looking at a PNG file.  (That is, when you normally use PyMOL you're
looking at an openGL screen.  When you click 'ray' or type 'ray' PyMOL
will ray trace the screen and display the resulting PNG file.  Once
you touch the screen after ray tracing, PyMOL immediately trashes the
PNG file so you can keep working.)

Sadly, I don't have any answers for you at this point, but I've CC'd
my main technical support guru to see what he knows.  I need to get an
ATI card to more testing.
"""

I cannot be more helpful at this time because my Linux boxes only run
NVidia cards.  I will either find a machine or go buy an ATI card for
my Linux box and let you know the results.

Cheers,

-- Jason

-- 
Jason Vertrees, PhD
PyMOL Product Manager
Schrodinger, LLC

(e) Jas...@sc...
(o) +1 (603) 374-7120

Hello,

I have the same problem as Timothy described a few days ago ('Problem
with display on Intel graphics card').

I tried Pymol 1.2r1 and 0.99rc6 on Ubuntu 10.04 and had the problem with
both versions. However, after ray tracing the view with the command
'ray' the color is right, until I change back to the normal view.

I didn't note the problem on the same computer with Ubuntu 8.04 and
Pymol 0.99.

I hope this additional information helps with the problem.

Bernhard

Hi Sean,

PyMOL statically allocates space for I/O.  I think the current line
length is 1024.  I ran into the problem a few years ago myself,
reported it to Warren and he just bumped the line length from 512 to
1024 or something like that.  So, until I come up with a better
solution, we're stuck with the fixed line length.

Cheers,

-- Jason

On Wed, May 26, 2010 at 10:08 AM, Sean Law <mag...@ho...> wrote:
> Hi All,
>
> I noticed that when I write a script that prints something in PyMOL that
> there appears to be a limitation to the continuous length that can be
> printed to the external GUI.  Here is an example script:
>
> #####################################
> from pymol import cmd
>
> def testing ():
>
>     out=""
>
>     for i in range (300):
>         out+=str(i)+" "
>
>     print out
>
>     return
>
> cmd.extend("testing", testing)
>
> ##################################
>
> In this example, my GUI is only able to print the value of "281" before it
> inserts a newline character and continues printing.  I should note that the
> terminal (from where I opened PyMOL) prints everything out correctly.
>
> Anybody know how to resolve this?
>
> Thanks.
>
> Sean
>
> ________________________________
> MSN Dating: Find someone special. Start now. Start now!
> ------------------------------------------------------------------------------
>
>
> _______________________________________________
> PyMOL-users mailing list (PyM...@li...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pym...@li...
>



-- 
Jason Vertrees, PhD
PyMOL Product Manager
Schrodinger, LLC

(e) Jas...@sc...
(o) +1 (603) 374-7120

Hi Thomas,

> To address your question, it is not possible to my knowledge to upload
> a sequence only to PyMOL. Keep in mind that PyMOL is a molecular
> viewer, not a sequence viewer.  If you want to see your sequence, you
> probably would have to create a 3D model of your sequence (e.g. using
> MODELLER).

You can load FASTA files into PyMOL.  Good luck understanding the
results though.  For example:

# fetch a protein and save its sequence
fetch 1cll, async=0
save 1cll.fasta, 1cll

# delete everything & load the FASTA file
dele *
load 1cll.fasta

Cheers,

-- Jason

-- 
Jason Vertrees, PhD
PyMOL Product Manager
Schrodinger, LLC

(e) Jas...@sc...
(o) +1 (603) 374-7120

A multiple sequence viewer incorporating structural information would be 
incredibly helpful, as then I wouldn't have to generate models for 
everything I want to compare substitutions in.

It might be too much to ask of PyMOL to be good at everything, however. 
Perhaps adding the ability to read in alignments from an external 
program (e.g. in aligned fasta format) containing the sequence of the 
structure (or model) to be aligned to would be sufficient?

Jed


Thomas Juettemann wrote:
> Hi Ashok,
>
> there are several ways to visualise alignments. Here is a nice overview:
>
> Visualization of multiple alignments, phylogenies and gene family evolution
> James B Procter, Julie Thompson, Ivica Letunic, Chris Creevey, Fabrice
> Jossinet & Geoffrey J Barton
> Nature Methods 7, S16 - S25 (2010)
> http://dx.doi.org/doi:10.1038/nmeth.1434
>
> To address your question, it is not possible to my knowledge to upload
> a sequence only to PyMOL. Keep in mind that PyMOL is a molecular
> viewer, not a sequence viewer.  If you want to see your sequence, you
> probably would have to create a 3D model of your sequence (e.g. using
> MODELLER).
>
> However, I think you have an interesting idea. It would be handy to
> sometimes see a given sequence aligned to the structure I am looking
> at.
>
> Question to Jason (and the community for feedback):
> Would it be possible to write a module that takes one or more
> sequences, aligns  them to a given structure (or set) that is opened
> in PyMOL and shows the aligned sequences in the sequence viewer? This
> feature would be very handy for me when evaluating alignments before I
> run MODELLER.
>
> Cheers,
> Thomas
>
> On Tue, May 25, 2010 at 23:13, Ashok Adhikari
> <ash...@st...> wrote:
>   
>> hi,
>>
>> do u know how to upload a sequence which is not in PDB. we dnt know the name
>> of the sequence and we have only 250 residues ....we can align with the
>> other file. we did that and we can upload those sequences from PDB but now
>> we need to upload the original sequence.
>>
>> thanks...in advance.
>>
>> ashok
>> from UNSW
>>
>> ------------------------------------------------------------------------------
>>
>>
>> _______________________________________________
>> PyMOL-users mailing list (PyM...@li...)
>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
>> Archives: http://www.mail-archive.com/pym...@li...
>>
>>     
>
> ------------------------------------------------------------------------------
>
> _______________________________________________
> PyMOL-users mailing list (PyM...@li...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pym...@li...
>
>   

-- 
------------------------
Jed Goldstone
Research Specialist
Woods Hole Oceanographic Institution
Redfield 3-52 MS#32
Woods Hole, MA 02543
http://www.whoi.edu/hpb/Site.do?id=481
Phone: 508-289-4823

Hi Ashok,

there are several ways to visualise alignments. Here is a nice overview:

Visualization of multiple alignments, phylogenies and gene family evolution
James B Procter, Julie Thompson, Ivica Letunic, Chris Creevey, Fabrice
Jossinet & Geoffrey J Barton
Nature Methods 7, S16 - S25 (2010)
http://dx.doi.org/doi:10.1038/nmeth.1434

To address your question, it is not possible to my knowledge to upload
a sequence only to PyMOL. Keep in mind that PyMOL is a molecular
viewer, not a sequence viewer.  If you want to see your sequence, you
probably would have to create a 3D model of your sequence (e.g. using
MODELLER).

However, I think you have an interesting idea. It would be handy to
sometimes see a given sequence aligned to the structure I am looking
at.

Question to Jason (and the community for feedback):
Would it be possible to write a module that takes one or more
sequences, aligns  them to a given structure (or set) that is opened
in PyMOL and shows the aligned sequences in the sequence viewer? This
feature would be very handy for me when evaluating alignments before I
run MODELLER.

Cheers,
Thomas

On Tue, May 25, 2010 at 23:13, Ashok Adhikari
<ash...@st...> wrote:
> hi,
>
> do u know how to upload a sequence which is not in PDB. we dnt know the name
> of the sequence and we have only 250 residues ....we can align with the
> other file. we did that and we can upload those sequences from PDB but now
> we need to upload the original sequence.
>
> thanks...in advance.
>
> ashok
> from UNSW
>
> ------------------------------------------------------------------------------
>
>
> _______________________________________________
> PyMOL-users mailing list (PyM...@li...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pym...@li...
>

Hi Timothy,

Can you please send me the screenshots.

Adaptation to the vagaries of vendor-specific hardware is always an
issue.  I'm happy to look into the problem.

Thanks,

-- Jason

On Tue, May 25, 2010 at 6:31 PM, Tim Travers <tst...@gm...> wrote:
>
> Good afternoon,
>
> Sorry for posting twice, just in case the previous one with attached
> screenshots
> is too large to be posted.
> I've been having problems with color rendering when using PyMOL on a laptop
> with an Intel graphics card. This only occurs when used with linux (I've
> tested
> Fedora 11, Fedora 12, and Ubuntu 10.04), but not when using Windows Vista
> on the same laptop. The main problem is that the color rendering for the
> stick
> drawing method does not work right.
>
> I can send screenshots if needed. These screenshots use the stick drawing
> with
> coloring supposed to be by element. But the coloring is not at all done by
> element,
> instead some regions get clustered by different colors. Just to note, the
> coloring
> for drawing by line does seem to work fine.
> I've googled this for some time now, and couldn't find any resolution. Just
> to note,
> I also have this problem with VMD's licorice rendering (its version of
> stick). Again,
> both work fine on Windows but not on the linux distros I've tested so far.
> I'm not sure
> if this'll be helpful, but here's the output of glxinfo | grep -i opengl:
>
> OpenGL vendor string: Tungsten Graphics, Inc
> OpenGL renderer string: Mesa DRI Intel(R) 965GM GEM 20091221 2009Q4
> OpenGL version string: 2.1 Mesa 7.7.1
> OpenGL shading language version string: 1.20
>
> As an aside, I used to have a problem with a flickering display, but this
> was fixed by
> turning off desktop effects like compiz. For this coloring problem, is there
> some
> X setting that needs to be maybe tweaked for Intel graphics cards?
>
> Thanks for any help on this.
>
> Thanks again,
> Timothy
>
>
>
> ------------------------------------------------------------------------------
>
>
> _______________________________________________
> PyMOL-users mailing list (PyM...@li...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pym...@li...
>



-- 
Jason Vertrees, PhD
PyMOL Product Manager
Schrodinger, LLC

(e) Jas...@sc...
(o) +1 (603) 374-7120

Hi All,

I noticed that when I write a script that prints something in PyMOL that there appears to be a limitation to the continuous length that can be printed to the external GUI.  Here is an example script:

#####################################
from pymol import cmd

def testing ():

    out=""
    
    for i in range (300):
        out+=str(i)+" "

    print out

    return
    
cmd.extend("testing", testing)

##################################

In this example, my GUI is only able to print the value of "281" before it inserts a newline character and continues printing.  I should note that the terminal (from where I opened PyMOL) prints everything out correctly.

Anybody know how to resolve this?

Thanks.

Sean
 		 	   		  
_________________________________________________________________
MSN Dating: Find someone special. Start now.
http://go.microsoft.com/?linkid=9729707

hi,

do u know how to upload a sequence which is not in PDB. we dnt know the name of the sequence and we have only 250 residues ....we can align with the other file. we did that and we can upload those sequences from PDB but now we need to upload the original sequence.

thanks...in advance.

ashok
from UNSW

Good afternoon,

Sorry for posting twice, just in case the previous one with attached
screenshots
is too large to be posted.

I've been having problems with color rendering when using PyMOL on a laptop
with an Intel graphics card. This only occurs when used with linux (I've
tested
Fedora 11, Fedora 12, and Ubuntu 10.04), but not when using Windows Vista
on the same laptop. The main problem is that the color rendering for the
stick
drawing method does not work right.

I can send screenshots if needed. These screenshots use the stick drawing
with
coloring supposed to be by element. But the coloring is not at all done by
element,
instead some regions get clustered by different colors. Just to note, the
coloring
for drawing by line does seem to work fine.

I've googled this for some time now, and couldn't find any resolution. Just
to note,
I also have this problem with VMD's licorice rendering (its version of
stick). Again,
both work fine on Windows but not on the linux distros I've tested so far.
I'm not sure
if this'll be helpful, but here's the output of glxinfo | grep -i opengl:

OpenGL vendor string: Tungsten Graphics, Inc
OpenGL renderer string: Mesa DRI Intel(R) 965GM GEM 20091221 2009Q4
OpenGL version string: 2.1 Mesa 7.7.1
OpenGL shading language version string: 1.20

As an aside, I used to have a problem with a flickering display, but this
was fixed by
turning off desktop effects like compiz. For this coloring problem, is there
some
X setting that needs to be maybe tweaked for Intel graphics cards?

Thanks for any help on this.

Thanks again,
Timothy

Thanks a lot! That helped!

Carsten Siebenhaar

-
Am 24.05.2010 um 21:50 schrieb Folmer Fredslund:

> Dear Carsten,
> 
> On 17 May 2010 14:39, Carsten Siebenhaar <cs...@gw...> wrote:
>> Hello, I'm new to this board.
>> I came across a certain problem with the mutagenesis tool. I got a pdb-file with amino acids that are partly displayed as 2 rotamers (so one amino acid displayed in two different ways in the Viewer).
>> Usually, the mutagenesis tool works fine, but if you try to mutate this amino acid it won't accept it, but will just mention in the external GUI that it selected the corresponding atoms:
>>> You clicked /11//A/HIS`509/CD2`A
>>  Selector: selection "sele" defined with 20 atoms.<
>> PyMol keeps on asking me to pick a residue.
>> 
>> Is there a way to easily avoid this problem or could this be considered a real bug?
>> Thanks a lot!
>> Carsten
> 
> 
> Do you want to retain the double conformations? If not, then you could
> use PyMOL to delete the alternate conformations thus, just retaining
> one of them.
> 
> # select & remove all non A altlocs
> remove not (alt ''+A)
> # reset the PDB information
> alter all, alt=''
> 
> taken from:
> http://pymolwiki.org/index.php/Property_Selectors#Alternate_Locations
> 
> 
> I hope this helps.
> Folmer Fredslund
> 
> 
>> 
>> 
>> ------------------------------------------------------------------------------
>> 
>> _______________________________________________
>> PyMOL-users mailing list (PyM...@li...)
>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
>> Archives: http://www.mail-archive.com/pym...@li...
>> 

Dear Carsten,

On 17 May 2010 14:39, Carsten Siebenhaar <cs...@gw...> wrote:
> Hello, I'm new to this board.
> I came across a certain problem with the mutagenesis tool. I got a pdb-file with amino acids that are partly displayed as 2 rotamers (so one amino acid displayed in two different ways in the Viewer).
> Usually, the mutagenesis tool works fine, but if you try to mutate this amino acid it won't accept it, but will just mention in the external GUI that it selected the corresponding atoms:
>>You clicked /11//A/HIS`509/CD2`A
>  Selector: selection "sele" defined with 20 atoms.<
> PyMol keeps on asking me to pick a residue.
>
> Is there a way to easily avoid this problem or could this be considered a real bug?
> Thanks a lot!
> Carsten


Do you want to retain the double conformations? If not, then you could
use PyMOL to delete the alternate conformations thus, just retaining
one of them.

# select & remove all non A altlocs
remove not (alt ''+A)
# reset the PDB information
alter all, alt=''

taken from:
http://pymolwiki.org/index.php/Property_Selectors#Alternate_Locations


I hope this helps.
Folmer Fredslund


>
>
> ------------------------------------------------------------------------------
>
> _______________________________________________
> PyMOL-users mailing list (PyM...@li...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pym...@li...
>

Hi All,

I have written a quick little script to jump through various frames from an MD simulation loaded into PyMOL:

###################################################
from pymol import cmd
import time

def jump (*args, **kwargs):

    #Example: jump 1, 10, 20
    #This will jump from frame 1 to frame 10 to frame 20
    #for a total of 10 times (default) while pausing in 
    #between frames for 0.1 seconds (default)

    #Example: jump 1, 50, 100, 1000, x=5, sleep=0.01
    #This will jump from frame 1 to frame 10 to frame 100 to frame 1000
    #for a total of 5 times while pausing in between frames for 0.01 seconds

    #Notice that I am using *args in order to allow a variable number of 
    #frames to be specified

    x=10
    sleep=0.1

    for key in kwargs:
        if (key == "x"):
            x=kwargs["x"]
            x=int(x)
        elif (key == "sleep"):
            sleep=kwargs["sleep"]
            sleep=float(sleep)
        else:
            continue

    args=list(args)

    for i in range (x):
        #This loop runs through all of the selected frames "x" times
        #Need some way to recognize input from user to exit loop/return
        for j in range (len(args)):
            #This loop runs through each of the selected frames one time
            #Need some way to recognize input from user to exit loop/return
            cmd.frame(int(args[j]))
            #This skips to the specified frame
            cmd.refresh()
            #This refreshes the display
            time.sleep(sleep)
            #This "pauses" the loop for a period of time, acts like frame rate

    return

cmd.extend("jump", jump)

#################################################


I have two questions:

1) Is there some way that I can tell PyMOL to exit either of the "for loops" by pressing the keyboard/stdin?   The purpose of jumping through various frames is to look for conformational changes in the structure but with the current script, it is necessary to run through both "for loops" before it stops.  However, I would like a way to stop the script at any time by simply pressing a user defined button on the keyboard.  I've marked the places above where the script would be required to look for user input and move on if no input is provided.  Alternatively, I could have the user hold down a keyboard key in order to run through the loops and once the key is released have it automatically exit/return.  Either would be fine.  FYI, I did try to play with "raw_input" command but it didn't seem to work/help.

2) In this case, since I'm using "*args" and "**kwargs", how do I specify the usage?  Right now, when I do "jump ?" in PyMOL, it just spits out "Usage: jump" without any of the usual usage information.  Is there some explicit way of telling PyMOL exactly what usage information to print out??



Any suggestions would be greatly appreciated! 

Thanks.

Sean
 		 	   		  
_________________________________________________________________
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Hi all,

Thanks a lot. It worked great.

Cheers,
Ariel



On Sat, 2010-05-22 at 13:45 -0500, Jason Vertrees wrote:
> Hi all,
> 
> Don't worry it's still there, just under a different command.
> Stick_color, stick_transparency, etc are properties of bonds, so it's
> best to now use 'set_bond' intead of 'set'.  For example,
> 
>     set_bond stick_transparency, 0.5, objectName
> 
> Cheers,
> 
> -- Jason
> 
> 
> On Fri, May 21, 2010 at 3:13 PM, Michael Zimmermann
> <mic...@ia...> wrote:
> > Sorry, I didn't mention that I use 1.2r1 on xinXP
> > It could be a version difference if the command does not work correctly for
> > you.
> >
> > On Fri, May 21, 2010 at 11:50 AM, Ariel Talavera <tal...@ci...>
> > wrote:
> >>
> >> Hi again,
> >>
> >> Actually it seems that for some reason the comma after the value (0.5)
> >> invalidate the command line.
> >>
> >> Ariel
> >>
> >> On Fri, 2010-05-21 at 11:40 -0500, Matthew Franklin wrote:
> >> > (I'm putting this back on-list)
> >> >
> >> > That's too bad.  It worked for me: PyMOL 1.2r2, Windows XP.  Can you set
> >> > other properties of this object: color, stick_radius, etc.?
> >> >
> >> > - Matt
> >> >
> >> >
> >> >
> >> > --
> >> > Matthew Franklin , Ph.D.
> >> > Senior Scientist, ImClone Systems,
> >> > a wholly owned subsidiary of Eli Lilly & Company
> >> > 180 Varick Street, 6th floor
> >> > New York, NY 10014
> >> > phone:(917)606-4116   fax:(212)645-2054
> >> >
> >> >
> >> > > -----Original Message-----
> >> > > From: Ariel Talavera [mailto:tal...@ci...]
> >> > > Sent: Friday, May 21, 2010 12:26 PM
> >> > > To: Matthew Franklin
> >> > > Subject: RE: [PyMOL] stick transparency
> >> > >
> >> > > Thanks for the very quick answer, but it didn't succeed.
> >> > >
> >> > > Best,
> >> > > Ariel
> >> > >
> >> > > On Fri, 2010-05-21 at 11:18 -0500, Matthew Franklin wrote:
> >> > > Hi Ariel -
> >> > >
> >> > > Try "set stick_transparency=0.5, peg_1"
> >> > >
> >> > > - Matt
> >> > >
> >> > >
> >> > > --
> >> > > Matthew Franklin , Ph.D.
> >> > > Senior Scientist, ImClone Systems,
> >> > > a wholly owned subsidiary of Eli Lilly & Company
> >> > > 180 Varick Street, 6th floor
> >> > > New York, NY 10014
> >> > > phone:(917)606-4116   fax:(212)645-2054
> >> > >
> >> > > > -----Original Message-----
> >> > > > From: Ariel Talavera [mailto:tal...@ci...]
> >> > > > Sent: Friday, May 21, 2010 12:01 PM
> >> > > > To: pym...@li...
> >> > > > Subject: [PyMOL] stick transparency
> >> > > >
> >> > > > Hi there,
> >> > > >
> >> > > > I am trying to set stick transparency using the following command:
> >> > > > set stick_transparency, 0.5, peg_1, but with no success. The problem
> >> > > > is
> >> > > > with the selection, because if I use instead, set
> >> > > > stick_transparency,
> >> > > > 0.5, then every thing represented with stick get 50% transparent.
> >> > > > Can
> >> > > > you help with this? I am using Pymol 1.2 under Ubuntu 10.04.
> >> > > >
> >> > > > Thanks a lot in advanced,
> >> > > >
> >> > > > Best regards,
> >> > > > Ariel
> >> > > >
> >> > Confidentiality Note:
> >> > This e-mail, and any attachment to it, contains privileged and
> >> > confidential information intended only for the use of the individual(s) or
> >> > entity named on the e-mail. If the reader of this e-mail is not the intended
> >> > recipient, or the employee or agent responsible for delivering it to the
> >> > intended recipient, you are hereby notified that reading it is strictly
> >> > prohibited. If you have received this e-mail in error, please immediately
> >> > return it to the sender and delete it from your system.
> >> >
> >> > Thank you.
> >>
> >>
> >>
> >>
> >> ------------------------------------------------------------------------------
> >>
> >> _______________________________________________
> >> PyMOL-users mailing list (PyM...@li...)
> >> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> >> Archives: http://www.mail-archive.com/pym...@li...
> >
> >
> >
> > --
> > Michael Zimmermann
> > Ph.D. student in Bioinformatics and Computational Biology
> > Department of Biochemistry, Biophysics and Molecular Biology
> > Iowa State University
> >
> > ------------------------------------------------------------------------------
> >
> >
> > _______________________________________________
> > PyMOL-users mailing list (PyM...@li...)
> > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> > Archives: http://www.mail-archive.com/pym...@li...
> >
> 
> 
> 

Vivek,

I know of no way to easily set a dihedral angle in PyMOL.  We should
consider making this easier in the future.

Thanks,

-- Jason

On Sat, May 22, 2010 at 9:25 PM, Vivek Ranjan <vr...@gm...> wrote:
> Helllo,
>
> I am using pymol to change dihedral angles in a polymer chain.
> However, dihedral angles have poor precision. If I want to set them
> to, say 150, it never gets me that. I always get something like 149.5.
> I would like it to be 150.00. At least that precision. I was not able
> to find set_dihedral in the source code. Wondering if someone has some
> idea how a better precision can be achieved. Perhaps a tolerance issue
> that can be fixed easily. Please let me know.
>
> --
> Thank you and Regards,
>
> Vivek Ranjan
>
> ------------------------------------------------------------------------------
>
> _______________________________________________
> PyMOL-users mailing list (PyM...@li...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pym...@li...
>



-- 
Jason Vertrees, PhD
PyMOL Product Manager
Schrodinger, LLC

(e) Jas...@sc...
(o) +1 (603) 374-7120

Hi Carsten,

Welcome and sorry for the delayed response, I was away at a training
camp last week.  Unfortunately, PyMOL cannot handle alternate
conformations in the mutagenesis wizard.  You can pick other atoms,
but not those with alternate locations.

Cheers

-- Jason

On Mon, May 17, 2010 at 8:39 AM, Carsten Siebenhaar <cs...@gw...> wrote:
> Hello, I'm new to this board.
> I came across a certain problem with the mutagenesis tool. I got a pdb-file with amino acids that are partly displayed as 2 rotamers (so one amino acid displayed in two different ways in the Viewer).
> Usually, the mutagenesis tool works fine, but if you try to mutate this amino acid it won't accept it, but will just mention in the external GUI that it selected the corresponding atoms:
>>You clicked /11//A/HIS`509/CD2`A
>  Selector: selection "sele" defined with 20 atoms.<
> PyMol keeps on asking me to pick a residue.
>
> Is there a way to easily avoid this problem or could this be considered a real bug?
> Thanks a lot!
> Carsten
>
>
> ------------------------------------------------------------------------------
>
> _______________________________________________
> PyMOL-users mailing list (PyM...@li...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pym...@li...
>



-- 
Jason Vertrees, PhD
PyMOL Product Manager
Schrodinger, LLC

(e) Jas...@sc...
(o) +1 (603) 374-7120

Thank you for your help. However, I have 4  Mg ions  in the au, so all 
Mg ions (and all coordinated ligands) got connected. I need only 
coordination for one Mg.

Maia

Nathaniel Echols wrote:
> On Sun, May 23, 2010 at 3:55 PM, Maia Cherney <ch...@ua... 
> <mailto:ch...@ua...>> wrote:
>
>     I would like to show coordination bonds between Mg ion and its ligands
>     (oxygens) as broken lines, the distance of Mg-O bond is between
>     1.9-2.2 A.
>
>  
> dist elem mg, (all within 2.2 of elem mg) 
>
> Might need to try a slightly longer length to catch everything.
>
> -Nat
> ------------------------------------------------------------------------
>
> ------------------------------------------------------------------------------
>
>   
> ------------------------------------------------------------------------
>
> _______________________________________________
> PyMOL-users mailing list (PyM...@li...)
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> Archives: http://www.mail-archive.com/pym...@li...

On Sun, May 23, 2010 at 6:33 PM, Maia Cherney <ch...@ua...> wrote:

> Thank you for your help. However, I have 4  Mg ions  in the au, so all Mg
> ions (and all coordinated ligands) got connected. I need only coordination
> for one Mg.
>

Then you need to qualify the selection with the residue number, and repeat
up to 4 times.  Same principle still applies, though:

dist (elem mg and resid 341), (all within 2.2 of (elem mg and resid 341))

this particular example may be unnecessarily verbose if the residue number
is unique.

-Nat