pymol-users Mailing List for PyMOL Molecular Graphics System (Page 3)

Hello all,
I have generated a movie of 300 snapshots (MD simulation trajectory).
How can i calculate dihedral angles for same four atoms across the
trajectory (or a movie)??
I mean "get_dihedral 58/n,58/c,58/ca,58/cb "values 300 times for each
snapshot.
Regards
Tasneem

Hi Abhinav,
Does this setting help:
set cylinder_shader_ff_workaround, 1
If not, can you please send me a screenshot showing the problem?
Cheers,
-- Jason
On Wed, Jan 9, 2013 at 5:40 PM, Abhinav Kumar
<abh...@sl...> wrote:
> Hi,
> I recently upgraded my desktop to Ubuntu 12.10.
>
> When I load a pdb in pymol, it comes up with line rendering as usual, but if
> I try to do a stick or ribbon rendering, it does not do it. In fact the
> stick operation hides the residue.
>
> These are the graphics specifics written by pymol.
> OpenGL graphics engine:
> GL_VENDOR: nouveau
> GL_RENDERER: Gallium 0.4 on NV84
> GL_VERSION: 3.0 Mesa 9.0
> Detected 4 CPU cores. Enabled multithreaded rendering.
>
> Any help please.
>
> --
> Thanks,
> Abhinav
>
> JCSG@SSRL, SLAC
> (650) 926-2992
>
>
> ------------------------------------------------------------------------------
> Master Java SE, Java EE, Eclipse, Spring, Hibernate, JavaScript, jQuery
> and much more. Keep your Java skills current with LearnJavaNow -
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> _______________________________________________
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--
Jason Vertrees, PhD
Director of Core Modeling Product Management
Schrödinger, Inc.
(e) Jas...@sc...
(o) +1 (603) 374-7120

Hi Amna,
> DNA molecule has internal HBONDS too.. how can i see the hbonds made
> between just ligand and DNA, ???
If there is nothing else than DNA and ligand, this should probably work
(otherwise, be more precise with the selections...):
PyMOL> distance hbonds, (polymer), (organic), mode=2
> how can i show just interacting residues of DNA with ligand
> i am unable to create this presentation..
PyMOL> show sticks, (polymer) within 5 of (organic)
Again, if "polymer" and "organic" are ambiguous, replace them with more
explicit selections like (chain A and resi 34).
http://pymolwiki.org/index.php/Single-word_Selectors
http://pymolwiki.org/index.php/Selection_Algebra
http://pymolwiki.org/index.php/Property_Selectors
Cheers,
 Thomas
-- 
Thomas Holder
PyMOL Developer
Schrödinger Contractor

Hi Robert,
you again need to set the "surface_color" for the selected residues,
instead of using the color command. That these two are not synced makes
sense, you can for example have a half-transparent surface in one color
and a stick representation below in another color.
PyMOL> set surface_color, red, (sele)
By the way: you can omit the "selection" argument in your ramp_new call,
this would be for automatic ranging.
Cheers,
 Thomas
Muench, Robert wrote, On 01/09/13 21:00:
> Dear pymol-user,
> 
> we are currently facing problems with the coloring of molecules. We
> color our molecule using a color ramp as follows:
> 
> pseudoatom pOrig, pos=(0,0,0), label=origin
> fetch XXX, async=0, type=pdb1
> as surface
> ramp_new proximityRamp, pOrig, selection=(XX*), range=[110,160], color=ocean
> set surface_color, proximityRamp, (XX*)
> 
> After that we would like to color defined residues for example in red
> using the selection tool. Although the color is changed in the sequence
> pane, the color is not applied to the molecule.
> 
> Any suggestions?
> 
> Best
> 
> Robert
-- 
Thomas Holder
PyMOL Developer
Schrödinger Contractor

Hi,
I recently upgraded my desktop to Ubuntu 12.10.
When I load a pdb in pymol, it comes up with line rendering as usual, 
but if I try to do a stick or ribbon rendering, it does not do it. In 
fact the stick operation hides the residue.
These are the graphics specifics written by pymol.
OpenGL graphics engine:
 GL_VENDOR: nouveau
 GL_RENDERER: Gallium 0.4 on NV84
 GL_VERSION: 3.0 Mesa 9.0
 Detected 4 CPU cores. Enabled multithreaded rendering.
Any help please.
-- 
Thanks,
Abhinav
JCSG@SSRL, SLAC
(650) 926-2992

Dear pymol-user,
we are currently facing problems with the coloring of molecules. We color our molecule using a color ramp as follows:
pseudoatom pOrig, pos=(0,0,0), label=origin
fetch XXX, async=0, type=pdb1
as surface
ramp_new proximityRamp, pOrig, selection=(XX*), range=[110,160], color=ocean
set surface_color, proximityRamp, (XX*)
After that we would like to color defined residues for example in red using the selection tool. Although the color is changed in the sequence pane, the color is not applied to the molecule.
Any suggestions?
Best
Robert

Hi,
I have a model of DNA-Ligand, defualt both ligand and DNA are represented
as sticks.... i make DNA as cartoon and ligand as stick, this is general
presentation ....
DNA molecule has internal HBONDS too.. how can i see the hbonds made
between just ligand and DNA, ???
how can i show just interacting residues of DNA with ligand
i am unable to create this presentation..
Thanku
regards
amna khan

The handling of density maps changed with (I believe) version 1.5 - 
earlier versions would just load the map as given, later ones appear to 
try to do symmetry expansion (even if the map isn't covering the ASU). 
I've seen this result in a similar error message when loading session 
files (with electron density, created in 1.4) with 1.5. My solution has 
been to stick with 1.4.
However, I don't generally use multi-state session files, so I don't 
know if the electron density problem is related to the multi-state 
problem or not.
Pete
Mike Feldkamp wrote:
> I created a session file with Pymol Version 1.5.0.4 that I am unable to open up on my laptop which is running 1.2r5pre. I am able to see the first state but all of the other remaining states are lost. I haven't had opening session files with saved states in the past so I do not suspect it is a issue of compatibility between versions. The one difference that I think is causing the problem is that the session contains an electron density map that does not appear to save along with the session. Below is the message that I receive from when I go to the state containing the density map. Has anyone else had this issue and been able to resolve it? If so how? 
> This Executable Build integrates and extends Open-Source PyMOL 1.2r3pre.Warning: This session was created with a newer version of PyMOL (15.04).Warning: Some content may not load completely.ExectiveSetSession-Error: after names.ExectiveSetSession-Warning: restore may be incomplete.ObjectMeshUpdate-Error: map 'Density' has been deleted.
> Thanks,Michael
> 		 	 		 
> 
> 
> ------------------------------------------------------------------------
> 
> ------------------------------------------------------------------------------
> Master SQL Server Development, Administration, T-SQL, SSAS, SSIS, SSRS
> and more. Get SQL Server skills now (including 2012) with LearnDevNow -
> 200+ hours of step-by-step video tutorials by Microsoft MVPs and experts.
> SALE 99ドル.99 this month only - learn more at:
> http://p.sf.net/sfu/learnmore_122512
> 
> 
> ------------------------------------------------------------------------
> 
> _______________________________________________
> PyMOL-users mailing list (PyM...@li...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pym...@li...

I created a session file with Pymol Version 1.5.0.4 that I am unable to open up on my laptop which is running 1.2r5pre. I am able to see the first state but all of the other remaining states are lost. I haven't had opening session files with saved states in the past so I do not suspect it is a issue of compatibility between versions. The one difference that I think is causing the problem is that the session contains an electron density map that does not appear to save along with the session. Below is the message that I receive from when I go to the state containing the density map. Has anyone else had this issue and been able to resolve it? If so how? 
 This Executable Build integrates and extends Open-Source PyMOL 1.2r3pre.Warning: This session was created with a newer version of PyMOL (15.04).Warning: Some content may not load completely.ExectiveSetSession-Error: after names.ExectiveSetSession-Warning: restore may be incomplete.ObjectMeshUpdate-Error: map 'Density' has been deleted.
Thanks,Michael
 		 	 		 

Hi Abida,
thanks for the PDB file that you sent me off-list.
It is a naming conflict, you have more than one chain A which have
overlapping residue numbers and even IDs. You can still load them like this:
PyMOL> set retain_order
PyMOL> load complex.1.pdb
PyMOL> as cartoon
I also suggest to fix the chain identifier:
PyMOL> alter complex.1 and rank 3578-9999, chain="B"
PyMOL> util.cbc
And for the second file:
PyMOL> set retain_order
PyMOL> load complex.5.pdb
PyMOL> as cartoon
PyMOL> alter complex.5 and chain A and rank 1322-9999, chain="C"
PyMOL> util.cbc
Hope that helps.
Cheers,
 Thomas
Abida Siddiqa wrote, On 01/08/13 16:58:
> 
> Thomas and Martin I have tried both suggestions. Still it did not work out.
> Regards
> Abida
> ------------------------------------------------------------------------
> From: abi...@ho...
> To: pym...@li...
> Subject: Pymol visualization problem
> Date: Tue, 8 Jan 2013 10:12:46 +0500
> 
> Hello, 
> 
> I have docked one protein named 'L1'( 450 amino acid) with another protein
> named 'E2'(68 amino acid, Chain A) and used pymol-v1.3r1-edu-Win32.msi to visualize
> the complex. my system is windows 7 , 64 bit. The problem is, i am unable
> to see the sequence of 'E2' protein and so as its structure. In order to
> confirm, if it is docking problem or visualization problem, i have used
> swiss pdb viewer. it has shown me sequence and structure of both proteins. i
> wonder why can not i see it in pymol.
> secondly, i docked L1 and E2 ( this time used chain A and B of it), and
> visualized the complex in pymol. i was only able to see L1, and chain A of
> E2 (both chain A and B are alike). Then in order to see if it is docking
> error or visualization error, i rendered the complex in swiss pdb viwer and
> saw the L1 and E2 (both chain A and B).
> Thirdly, i changed the docking software and generated a complex using
> another software, this time i still was unable to visualize complete complex
> in pymol.
> Any help will be much appreciated.
> Kind regards
> Abida
-- 
Thomas Holder
PyMOL Developer
Schrödinger Contractor

Thomas and Martin I have tried both suggestions. Still it did not work out.RegardsAbida
From: abi...@ho...
To: pym...@li...
Subject: Pymol visualization problem
Date: Tue, 8 Jan 2013 10:12:46 +0500
Hello, 
I have docked one protein named 'L1'( 450 amino acid) with another protein
named 'E2'(68 amino acid, Chain A) and used pymol-v1.3r1-edu-Win32.msi to visualize
the complex. my system is windows 7 , 64 bit. The problem is, i am unable
to see the sequence of 'E2' protein and so as its structure. In order to
confirm, if it is docking problem or visualization problem, i have used
 swiss pdb viewer. it has shown me sequence and structure of both proteins. i
wonder why can not i see it in pymol.
secondly, i docked L1 and E2 ( this time used chain A and B of it), and
visualized the complex in pymol. i was only able to see L1, and chain A of
E2 (both chain A and B are alike). Then in order to see if it is docking
error or visualization error, i rendered the complex in swiss pdb viwer and
 saw the L1 and E2 (both chain A and B).
Thirdly, i changed the docking software and generated a complex using
another software, this time i still was unable to visualize complete complex
in pymol.
Any help will be much appreciated.
Kind regards
Abida 		 	 		 		 	 		 

Hi Briony,
this sounds like a very cool project!
Regarding question 1: If your PDB DNA model is long enough, you can use
"cafit_orientation" from the "psico" module (a PyMOL extension) to draw
the axis. It determines the axis by least-square linear fit on the
backbone atoms. This requires a recent PyMOL version and numpy.
If the helix is not long enough, cafit_orientation will most likely
result in a slightly skewed axis, but I think you need a perfect axis,
right? If you are interested, I could customize the script to take the
bases orientations into account when interpolating the axis. Just let me
know.
http://www.pymolwiki.org/index.php/psico
Cheers,
 Thomas
Briony Marshall (Personal) wrote, On 01/07/13 17:43:
> Apologies - Slightly off topic request for collaboration from a
> sculptor, but it does relate to how Pymol works
> 
> Dear all, 
> 
> I am a sculptor working on an ambitious bronze sculpture of DNA and I am
> looking to find out some more detailed measurements of ideal B-DNA which
> I am having difficulty getting from Pymol.
> 
> You can see my previous work on my website:
> http://www.briony.com
> 
> The sculpture I am making represents a single turn of ideal B-DNA at a
> scale of 500 million times life size, i.e. it will be 1m wide by 1.66m
> tall. Each atom is represented by a small human figure made of bronze,
> with the bonds between them represented by the arms and legs of the figures.
> (this is a much more complicated version of this sculpture I did
> previously based on the structure of
> diamond: http://www.briony.com/works/dream-II_1.html)
> 
> I studied biochemistry at Oxford in the mid-90s and did a specialisation
> in DNA dynamics so I am not altogether wet behind the ears, but as I
> spend most of my time now with plaster and clay, my in depth DNA
> knowledge is a bit weak and I'm new to Pymol. I have been working from
> the ideal B-DNA PDB file for all my measurements.
> 
> I am at the stage that I have made all 20 bases, and 20 sections of
> sugar phosphate backbone in bronze, and I am about to start constructing
> my double helix around a stainless steel central access.
> 
> 1. I haven't worked out how to get the central axis of B-DNA to appear
> on Pymol. Is there a way to do this? 
> 
> If not, I would need a scale drawings of both base pairs with the
> central axis point (of B-DNA) marked. This would allow me to make
> various measurements to ensure I put the bases and sugar phospate
> sections together accurately.
> 
> (In particular I need to know the distance between the central axis and
> the N of each base pair that attaches to the backbone, and the angle
> between these two lines within each base pair 'rung')
> 
> 2. I was looking for advice on whether I can safely ignore the base pair
> axis inclination (as this is only 1.2° I think so) and the propelor
> twist of the base pairs (I was less sure about this). I think I can
> straightening up the base pairs but ensure that where they attach to the
> backbone stays in the same place. I'm hoping the only effect might be on
> the length and orientation of the hydrogen bonds.
> 
> 3. Final question for now - is there a standard colour convention for
> representation of bases like there is for atoms? FYI, I had contemplated
> doing the patina (colouring) of the sculpture according to the atomic
> colour code, but with about 1000 atoms, this would be a very fiddly long
> job. I am now considering colouring each base a different colour and was
> wondering if there was a standard, such as Adenine is always represented
> blue, etc..
> 
> Many thanks in advance for any help you can give.
> Regards
> Briony
> 
> Briony Marshall - Sculptor
> www.briony.com <http://www.briony.com/>
> <http://www.briony.com/>join my mailing
> list: www.briony.com/subscribe.html <http://www.briony.com/subscribe.html>
> or like me on facebook: www.facebook.com/brionymarshallsculptor
> <http://www.facebook.com/brionymarshallsculptor>
> UK mobile: +44 (0)7956 107 893
> 
> Pangolin London Sculptor in Residence
> blog:
> www.a-n.co.uk/link/creative-year <http://www.a-n.co.uk/link/creative-year>
-- 
Thomas Holder
PyMOL Developer
Schrödinger Contractor

Hi Abida,
if the PDB has multible models, you can also enable the "all_states"
setting instead of modifying the file.
PyMOL> set all_states
If this doesn't solve the issue, I guess it's a chain naming conflict
with duplicate chain identifiers. Feel free to send me the PDB file
off-list and I'll have a look at it.
Cheers,
 Thomas
Martin Hediger wrote, On 01/08/13 09:08:
> Hi Abida
> Is it possible that you have multiple states in your PDB file? Try
> clicking the ">" arrow in the bottom right corner of PyMOL and see if
> you can display the other protein. If so, you probably need to delete
> the "MODEL" and "END" from your PDB file. Then all should appear at once.
> 
> Martin
> 
> On 08.01.13 06:12, Abida Siddiqa wrote:
>> Hello, 
>>
>> I have docked one protein named 'L1'( 450 amino acid) with another protein
>> named 'E2'(68 amino acid, Chain A) and used pymol-v1.3r1-edu-Win32.msi to visualize
>> the complex. my system is windows 7 , 64 bit. The problem is, i am unable
>> to see the sequence of 'E2' protein and so as its structure. In order to
>> confirm, if it is docking problem or visualization problem, i have used
>> swiss pdb viewer. it has shown me sequence and structure of both proteins. i
>> wonder why can not i see it in pymol.
>> secondly, i docked L1 and E2 ( this time used chain A and B of it), and
>> visualized the complex in pymol. i was only able to see L1, and chain A of
>> E2 (both chain A and B are alike). Then in order to see if it is docking
>> error or visualization error, i rendered the complex in swiss pdb viwer and
>> saw the L1 and E2 (both chain A and B).
>> Thirdly, i changed the docking software and generated a complex using
>> another software, this time i still was unable to visualize complete complex
>> in pymol.
>> Any help will be much appreciated.
>> Kind regards
>> Abida
-- 
Thomas Holder
PyMOL Developer
Schrödinger Contractor

Hi Abida
Is it possible that you have multiple states in your PDB file? Try 
clicking the ">" arrow in the bottom right corner of PyMOL and see if 
you can display the other protein. If so, you probably need to delete 
the "MODEL" and "END" from your PDB file. Then all should appear at once.
Martin
On 08.01.13 06:12, Abida Siddiqa wrote:
> Hello,
>
> I have docked one protein named 'L1'( 450 amino acid) with another protein
> named 'E2'(68 amino acid, Chain A) and used pymol-v1.3r1-edu-Win32.msi to visualize
> the complex. my system is windows 7 , 64 bit. The problem is, i am unable
> to see the sequence of 'E2' protein and so as its structure. In order to
> confirm, if it is docking problem or visualization problem, i have used
> swiss pdb viewer. it has shown me sequence and structure of both proteins. i
> wonder why can not i see it in pymol.
> secondly, i docked L1 and E2 ( this time used chain A and B of it), and
> visualized the complex in pymol. i was only able to see L1, and chain A of
> E2 (both chain A and B are alike). Then in order to see if it is docking
> error or visualization error, i rendered the complex in swiss pdb viwer and
> saw the L1 and E2 (both chain A and B).
> Thirdly, i changed the docking software and generated a complex using
> another software, this time i still was unable to visualize complete complex
> in pymol.
> Any help will be much appreciated.
> Kind regards
> Abida
>
>
> ------------------------------------------------------------------------------
> Master SQL Server Development, Administration, T-SQL, SSAS, SSIS, SSRS
> and more. Get SQL Server skills now (including 2012) with LearnDevNow -
> 200+ hours of step-by-step video tutorials by Microsoft MVPs and experts.
> SALE 99ドル.99 this month only - learn more at:
> http://p.sf.net/sfu/learnmore_122512
>
>
> _______________________________________________
> PyMOL-users mailing list (PyM...@li...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pym...@li...

Hello, 
I have docked one protein named 'L1'( 450 amino acid) with another protein
named 'E2'(68 amino acid, Chain A) and used pymol-v1.3r1-edu-Win32.msi to visualize
the complex. my system is windows 7 , 64 bit. The problem is, i am unable
to see the sequence of 'E2' protein and so as its structure. In order to
confirm, if it is docking problem or visualization problem, i have used
 swiss pdb viewer. it has shown me sequence and structure of both proteins. i
wonder why can not i see it in pymol.
secondly, i docked L1 and E2 ( this time used chain A and B of it), and
visualized the complex in pymol. i was only able to see L1, and chain A of
E2 (both chain A and B are alike). Then in order to see if it is docking
error or visualization error, i rendered the complex in swiss pdb viwer and
 saw the L1 and E2 (both chain A and B).
Thirdly, i changed the docking software and generated a complex using
another software, this time i still was unable to visualize complete complex
in pymol.
Any help will be much appreciated.
Kind regards
Abida 		 	 		 

Apologies - Slightly off topic request for collaboration from a sculptor,
but it does relate to how Pymol works
Dear all,
I am a sculptor working on an ambitious bronze sculpture of DNA and I am
looking to find out some more detailed measurements of ideal B-DNA which I
am having difficulty getting from Pymol.
You can see my previous work on my website:
http://www.briony.com
The sculpture I am making represents a single turn of ideal B-DNA at a
scale of 500 million times life size, i.e. it will be 1m wide by 1.66m
tall. Each atom is represented by a small human figure made of bronze, with
the bonds between them represented by the arms and legs of the figures.
(this is a much more complicated version of this sculpture I did previously
based on the structure of diamond:
http://www.briony.com/works/dream-II_1.html)
I studied biochemistry at Oxford in the mid-90s and did a specialisation in
DNA dynamics so I am not altogether wet behind the ears, but as I spend
most of my time now with plaster and clay, my in depth DNA knowledge is a
bit weak and I'm new to Pymol. I have been working from the ideal B-DNA PDB
file for all my measurements.
I am at the stage that I have made all 20 bases, and 20 sections of sugar
phosphate backbone in bronze, and I am about to start constructing my
double helix around a stainless steel central access.
1. I haven't worked out how to get the central axis of B-DNA to appear on
Pymol. Is there a way to do this?
If not, I would need a scale drawings of both base pairs with the central
axis point (of B-DNA) marked. This would allow me to make various
measurements to ensure I put the bases and sugar phospate sections together
accurately.
(In particular I need to know the distance between the central axis and the
N of each base pair that attaches to the backbone, and the angle between
these two lines within each base pair 'rung')
2. I was looking for advice on whether I can safely ignore the base pair
axis inclination (as this is only 1.2° I think so) and the propelor twist
of the base pairs (I was less sure about this). I think I can straightening
up the base pairs but ensure that where they attach to the backbone stays
in the same place. I'm hoping the only effect might be on the length and
orientation of the hydrogen bonds.
3. Final question for now - is there a standard colour convention for
representation of bases like there is for atoms? FYI, I had contemplated
doing the patina (colouring) of the sculpture according to the atomic
colour code, but with about 1000 atoms, this would be a very fiddly long
job. I am now considering colouring each base a different colour and was
wondering if there was a standard, such as Adenine is always represented
blue, etc..
Many thanks in advance for any help you can give.
Regards
Briony
*Briony Marshall - Sculptor
www.briony.com
<http://www.briony.com/>join my mailing list: www.briony.com/subscribe.html
or like me on facebook: www.facebook.com/brionymarshallsculptor
UK mobile: +44 (0)7956 107 893
Pangolin London Sculptor in Residence
 blog:
www.a-n.co.uk/link/creative-year
*

Hi PyMOL users
I wonder, what is a most meaningful way of programmatically determining 
that a line of text in an arbitrary file contains atomic coordinates? 
The context of this question is that I plan to write a program that 
reads two files containing coordinates and has to perform operations on 
pairs of coordinates r1 and r2, where ri is the coordinate value from 
file i.
Example format 1 (MOPAC):
C( <LABEL TEXT> ) 1.0 +0 1.0 +0 1.0 +0
Example format 2 (PDB):
ATOM 1 N ALA A 1 32.517 42.012 20.144 1.00 0.00 
PROT N
(some whitespace omitted).
In example 1, the coordinates are "1.0", "1.0" and "1.0", the "+0" are 
program specific labels to identify the coordinate as fixed or relaxed.
Can this really only be done by hardcoding the positions of the coordinates?
Can this be unittested? I mean, if it indeed is only possible to read 
the coordinate by collecting, say
[python]
s="ATOM 1 N ALA A 1 32.517 42.012 20.144 1.00 
0.00 PROT N"
def get_x(s):
 x=s[32:38]
 return x
[/python]
what would a unittest for get_x look like? Would it even make sense to 
write such a test?
Looking forward to discussions.
Martin

well, my point was just that they seem to be orientation sensitive although I didn't look at
entire script in any detail and that if you wanted to re-orient the fragment you would have to
recalculate these. Nothing difficult but just easier if there was a script that said something like
"put this thing here with this orientation wrt some prior fragment " ( no absolute directions 
at this point. )
----------------------------------------
> Date: Fri, 4 Jan 2013 15:52:13 +0100
> From: sp...@us...
> To: mar...@ho...
> CC: pym...@li...
> Subject: Re: [PyMOL] Building of the Carbon lattice
>
> Hi Mike,
>
> I simply measured x_shift and y_shift from a cyclohexane fragment. Use
> the graphical Builder or the "fragment" command to load stuff from the
> fragment library.
>
> PyMOL> fragment cyclohexane
>
> Cheers,
> Thomas
>
> Mike Marchywka wrote, On 01/04/13 15:44:
> > Where do you get the x_shift and y_shift values? I ended up writing a program to
> > take bond lengths and directions relative to select coord systems to generate periodic or
> > almost periodic things. Right now polyenes but extensible. Is there some program that
> > does this easily? This allows me to write a simple TcL script and reorient the whole
> > molecule by changing one parameter . I don't currently have a way to include library
> > items, like say a methyl group, and I was debating about doing this in python
> > but I wanted to have easy access to lapack etc for later extensions.
> > Thanks.
>
> --
> Thomas Holder
> PyMOL Developer
> Schrödinger Contractor
 		 	 		 

Hi Mike,
I simply measured x_shift and y_shift from a cyclohexane fragment. Use
the graphical Builder or the "fragment" command to load stuff from the
fragment library.
PyMOL> fragment cyclohexane
Cheers,
 Thomas
Mike Marchywka wrote, On 01/04/13 15:44:
> Where do you get the x_shift and y_shift values? I ended up writing a program to
> take bond lengths and directions relative to select coord systems to generate periodic or
> almost periodic things. Right now polyenes but extensible. Is there some program that
> does this easily? This allows me to write a simple TcL script and reorient the whole
> molecule by changing one parameter . I don't currently have a way to include library
> items, like say a methyl group, and I was debating about doing this in python
> but I wanted to have easy access to lapack etc for later extensions.
> Thanks.
-- 
Thomas Holder
PyMOL Developer
Schrödinger Contractor

Where do you get the x_shift and y_shift values? I ended up writing a program to
take bond lengths and directions relative to select coord systems to generate periodic or
almost periodic things. Right now polyenes but extensible. Is there some program that
does this easily? This allows me to write a simple TcL script and reorient the whole
molecule by changing one parameter . I don't currently have a way to include library
items, like say a methyl group, and I was debating about doing this in python
but I wanted to have easy access to lapack etc for later extensions.
Thanks.
----------------------------------------
Date: Fri, 4 Jan 2013 11:13:39 +0100
From: sp...@us...
To: jms...@gm...
CC: pym...@li...
Subject: Re: [PyMOL] Building of the Carbon lattice
Hi James,
just calculate the coordinates and write them out in PDB format, quite
simple task. Try the attached script.
Cheers,
Thomas
James Starlight wrote, On 01/04/13 09:14:
> Hi Mike,
>
> Chimera can build such lattices by means of it's build structure
> module. On other hand I want to build such 2D lattices
> http://imageshack.us/photo/my-images/543/lattice.png/
> made from SP3 carbons as the nodes via some automatic script to
> obtain lattices with desired dimensions.
>
> James
--
Thomas Holder
PyMOL Developer
Schrödinger Contractor
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Hi Soumya,
can you send me (off-list) the map file and pdb file?
Cheers,
 Thomas
Soumya Lipsa Rath wrote, On 12/29/12 13:41:
> Dear Users,
> 
> I am trying to calculate the electrostatic potential of my protein using
> Delphi software. However, when I load it to pymol, I see the red colour
> at the centre and blue in the rest of the part even if I vary the scale.
> It appears to me as if it is coloring based on the distance from the
> centre. 
> 
> These are the steps after loading it to pymol:
> 
> 1) load myfile.pdb
> 2) load myfile.phi, map
> 3) ramp_new e_lvl, map,
> 4) set surface_color, e_lvl, myfile
> 
> I have attached the Delphi log file for reference also. I would really appreciate any help in this regard.
> 
> Thanks,
> Soumya
--
Thomas Holder
PyMOL Developer
Schrödinger Contractor

Hi James,
just calculate the coordinates and write them out in PDB format, quite
simple task. Try the attached script.
Cheers,
 Thomas
James Starlight wrote, On 01/04/13 09:14:
> Hi Mike,
> 
> Chimera can build such lattices by means of it's build structure
> module. On other hand I want to build such 2D lattices
> http://imageshack.us/photo/my-images/543/lattice.png/
> made from SP3 carbons as the nodes via some automatic script to
> obtain lattices with desired dimensions.
> 
> James
-- 
Thomas Holder
PyMOL Developer
Schrödinger Contractor

Hi Mike,
Chimera can build such lattices by means of it's build structure
module. On other hand I want to build such 2D lattices
http://imageshack.us/photo/my-images/543/lattice.png/
 made from SP3 carbons as the nodes via some automatic script to
obtain lattices with desired dimensions.
James
2013年1月3日, James Starlight <jms...@gm...>:
> Hi Mike,
>
>
> Chimera can build such lattices by means of it's build structure
> module. On other hand I want to build such 2D lattices
> http://imageshack.us/photo/my-images/543/lattice.png/
> made from SP3 carbons via some automatic script.
>
>
>
> James
>
> 2012年12月28日, Mike Marchywka <mar...@ho...>:
>>
>>
>>
>> What does Chimera do? I finally wrote my own c++ tool that let's a TcL
>> script
>> specify a molecule's layout in terms of relevance like bond length and
>> angle.
>> I decided it was worth the effort since I didn't want to look around much
>> for existing
>> stuff and would eventually add my own stuff for analysis. The real
>> decision
>> was
>> to learn python or just use TcL. I guess if I was looking for a tool to
>> generate
>> from a script I'd probably prefer python. Thanks.
>>
>>
>>
>>
>> ----------------------------------------
>>> Date: 2012年12月28日 05:42:27 -0800
>>> From: jms...@gm...
>>> To: pym...@li...
>>> Subject: Re: [PyMOL] Building of the Carbon lattice
>>>
>>> Hi Tsjerk!
>>>
>>> This is the example of such lattice which I've built using Chimera!
>>> http://imageshack.us/photo/my-images/543/lattice.png/
>>>
>>> this is simple model of the Carbon-contained lattice without hydrogens.
>>> So I'd like to build such lattices from different atoms as nodes
>>> defining only atom type as well as number of nodes.
>>>
>>> Also I'd like to simulate this model using PBC so it seems that big
>>> dimensions of such lattice doesn't matter, doesn’t it ? ( It will be
>>> simpler to build smaller symmetric model )
>>>
>>> James
>>>
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>>> much more. Get web development skills now with LearnDevNow -
>>> 350+ hours of step-by-step video tutorials by Microsoft MVPs and
>>> experts.
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>>> Archives: http://www.mail-archive.com/pym...@li...
>>
>

James,
alter my_sele, name=CA
PyMOL might act quirky after doing that, though.
Cheers,
-- Jason
On Thu, Jan 3, 2013 at 8:37 AM, James Starlight <jms...@gm...> wrote:
> Dear Pymol users!
>
>
> I want to rename all atoms within selection to the selected name. I've
> found that the renamecommand can do it but the syntax of that comand
> is not quite understood for me :( Could you provide me with some
> example ? e.g my mollecule consist of 120 carbon atoms named as the
> C1, C2... C120. I want to rename all atoms to CA ( the same index for
> all atoms).
>
>
> Thanks for help
>
>
> James
>
> ------------------------------------------------------------------------------
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-- 
Jason Vertrees, PhD
Director of Core Modeling Product Management
Schrödinger, Inc.
(e) Jas...@sc...
(o) +1 (603) 374-7120

Dear all,
on our RHEL computers (6.2, 64-bit) with PyMOL compiled from CVS, the 
APBS2 plugin isn't functioning anymore. The plugin window opens just 
fine and the executables are found.
When I select "Use PDB2PQR" in the Main tab, clicking on Set grid 
produces the following error:
Error: 1
<type 'exceptions.UnboundLocalError'> Exception in Tk callback
 Function: <function <lambda> at 0x7fc2b0705410> (type: <type 'function'>)
 Args: ()
Traceback (innermost last):
 File "/usr/lib/python2.6/site-packages/Pmw/Pmw_1_3_3/lib/PmwBase.py", 
line 1747, in __call__
 return apply(self.func, args)
 File 
"/usr/lib/python2.6/site-packages/Pmw/Pmw_1_3_3/lib/PmwDialog.py", line 
153, in <lambda>
 command=lambda self=self, name=name: self._doCommand(name))
 File 
"/usr/lib/python2.6/site-packages/Pmw/Pmw_1_3_3/lib/PmwDialog.py", line 
132, in _doCommand
 return command(name)
 File 
"/usr/lib64/python2.6/site-packages/pmg_tk/startup/apbs_tools.py", line 
1075, in execute
 self.runPsize()
 File 
"/usr/lib64/python2.6/site-packages/pmg_tk/startup/apbs_tools.py", line 
1096, in runPsize
 good = self.generatePqrFile()
 File 
"/usr/lib64/python2.6/site-packages/pmg_tk/startup/apbs_tools.py", line 
1007, in generatePqrFile
 good = self._generatePdb2pqrPqrFile()
 File 
"/usr/lib64/python2.6/site-packages/pmg_tk/startup/apbs_tools.py", line 
1615, in _generatePdb2pqrPqrFile
 if retval != 0:
<type 'exceptions.UnboundLocalError'>: local variable 'retval' 
referenced before assignment
When I chose "User PyMOL generated PQR and PyMOL generated Hydrogens and 
termini" or "User PyMOL generated PQR and existing hydrogens and 
termini", I can set the grid, run APBS and visualize the result just fine.
I'm happy with that, but maybe someone has an idea of why the first 
approach fails.
Thanks.
Andreas
-- 
 Andreas Förster, Research Associate
 Paul Freemont & Xiaodong Zhang Labs
Department of Biochemistry, Imperial College London
 http://www.msf.bio.ic.ac.uk