Re: [PyMOL] Logging the sculpt wizard
Hi Martin, I have a script that does almost exactly what you want (I guess). See attachment. Cheers, Thomas On Wed, Mar 23, 2011 at 11:19 PM, Martin Hediger wrote: > Dear List > I'm trying to automate the following sequence of steps in a PyMOL python > script: > 1. Start the mutagenesis wizard > 2. Mutate a reside according to an input from the script (some integer > to specify the id) > 3. "Apply" and close the mutagenesis wizard > 4. Start the Sculpt Wizard > 5. Fix all coordinates but the residue just mutated > 6. Start the sculpt algorithm to get a rough optimization of the side chain > 7. End the sculpt algorithm and close the sculpt wizard. > 8. Save the structure to a new file. > > I have the steps up to 3. ready in a script for generation of variants. > However, when running a log file while performing steps 4. onwards, > there are no commands written into the log file for the sculpting > functions. Pressing the "Sculpt" button in the PyMOLX11Hybrid does not > lead to a command I can see in the log file. > What would be the Python code to start the sculpt process? > > Any hints are welcome. > > Thanks a lot. -- Thomas Holder MPI for Developmental Biology Spemannstr. 35 D-72076 Tübingen mutate.py Description: Binary data -- Enable your software for Intel(R) Active Management Technology to meet the growing manageability and security demands of your customers. Businesses are taking advantage of Intel(R) vPro (TM) technology - will your software be a part of the solution? Download the Intel(R) Manageability Checker today! http://p.sf.net/sfu/intel-dev2devmar___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] Logging the sculpt wizard
there was a bug in the script, sorry. Corrected script attached. Cheers, Thomas On Thu, Mar 24, 2011 at 8:40 AM, Thomas Holder wrote: > Hi Martin, > > I have a script that does almost exactly what you want (I guess). See > attachment. > > Cheers, > Thomas -- Thomas Holder MPI for Developmental Biology Spemannstr. 35 D-72076 Tübingen mutate.py Description: Binary data -- Enable your software for Intel(R) Active Management Technology to meet the growing manageability and security demands of your customers. Businesses are taking advantage of Intel(R) vPro (TM) technology - will your software be a part of the solution? Download the Intel(R) Manageability Checker today! http://p.sf.net/sfu/intel-dev2devmar___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] Calling pymol from python - access to global variables
Hi Tsjerk,
use either the global pymol.stored variable or the alter_state 'space' argument.
--
#!/usr/bin/env python
if __name__ == "__main__":
import __main__
__main__.pymol_argv = [ 'pymol', '-cq' ]
import pymol
pymol.finish_launching()
else:
import pymol
def identity(x,y,z):
print "YEAH!"
return x,y,z
pymol.editor.build_peptide("G")
pymol.cmd.alter_state(1,"all","(x,y,z)=identity(x,y,z)",
space={'identity':identity})
# or:
# pymol.stored.identity = identity
# pymol.cmd.alter_state(1,"all","(x,y,z)=stored.identity(x,y,z)")
--
Cheers,
Thomas
On Tue, Mar 29, 2011 at 6:18 PM, Tsjerk Wassenaar wrote:
> Hi,
>
> I'm having some trouble accessing a function defined at top level with
> alter_state in a python script launching pymol. Maybe I shouldn't be
> wanting to do this, but what I'm trying, and failing to do is
> exemplified by this script:
>
> ###
>
> #!/usr/bin/env python
>
> import pymol
>
> if __name__ == "__main__":
> pymol.finish_launching()
>
> def identity(x,y,z):
> print "YEAH!"
> return x,y,z
>
> # Fix:
> # setattr(pymol,"identity",identity)
>
> pymol.editor.build_peptide("G")
> pymol.cmd.alter_state(1,"all","(x,y,z)=identity(x,y,z)")
>
> ###
>
> The problem is that the function 'identity' (which may be given a more
> sensical form by actually doing something with the coordinates), is
> sought in the pymol namespace. I can't really figure out where I
> should be looking to directly call the function. Of course, I can
> register the function in the pymol module (uncomment the setattr
> line), but I don't think it's proper meddling with established modules
> like that. Does anyone know a better/cleaner solution?
>
> In addition, does anyone know how to suppress the GUI stuff when
> launching pymol like this?
>
> Groetjes,
>
> Tsjerk
>
> --
> Tsjerk A. Wassenaar, Ph.D.
>
> post-doctoral researcher
> Molecular Dynamics Group
> * Groningen Institute for Biomolecular Research and Biotechnology
> * Zernike Institute for Advanced Materials
> University of Groningen
> The Netherlands
--
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MPI for Developmental Biology
Spemannstr. 35
D-72076 Tübingen
--
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Re: [PyMOL] RES: radius of gyration
Hi Tsjerk,
very nice script! I have added it to the PyMOLWiki at
http://pymolwiki.org/index.php/Radius_of_gyration
Cheers,
Thomas
Tsjerk Wassenaar wrote, On 03/31/11 16:07:
> Hi :)
>
> The radius of gyration is not that tough. Here's a python script to do
> it in pymol. Do note that the hydrodynamic radius is something
> related, but different.
>
> from pymol import cmd
> import math
>
> def rgyrate(selection):
> # Get the atoms for the selection
> model=cmd.get_model(selection).atom
> # Extract the coordinates
> x=[i.coord for i in model]
> # Get the masses
> mass=[i.get_mass() for i in model]
> # Mass-weighted coordinates
> xm=[(m*i,m*j,m*k) for (i,j,k),m in zip(x,mass)]
> # Sum of masses
> tmass=sum(mass)
> # First part of the sum under the sqrt
> rr=sum(mi*i+mj*j+mk*k for (i,j,k),(mi,mj,mk) in zip(x,xm))
> # Second part of the sum under the sqrt
> mm=sum((sum(i)/tmass)**2 for i in zip(*xm))
> # Radius of gyration
> rg=math.sqrt(rr/tmass-mm)
> # Print it...
> print "Radius of gyration:", rg
> return rg
>
> cmd.extend("rgyrate",rgyrate)
>
> Hope it helps,
>
> Tsjerk
--
Thomas Holder
MPI for Developmental Biology
Spemannstr. 35
D-72076 Tübingen
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Re: [PyMOL] Spectrumany bug?
Hi Tassos, as Folmer already suggested your PyMOL version, or rather your python version could be the problem. The line that throws the error uses generator syntax, which was introduced in python 2.4. This can easily be backported so you don't need another python version. I updated the script in the wiki so it should work with older python now. Can you download again and try? Cheers, Thomas On Tue, Apr 5, 2011 at 8:49 PM, Anastassis Perrakis wrote: > Hi - > > I am trying to use the script by Thomas Holder, Spectrumany > > http://www.pymolwiki.org/index.php/Spectrumany > > When I import the script (run) I get: > > PyMOL>run sp.pml > Traceback (most recent call last): > File "/Applications/MacPyMOL.app/pymol/modules/pymol/parser.py", > line 332, in parse > > parsing > .run_file(exp_path(layer.args[0]),self.pymol_names,self.pymol_names) > File "/Applications/MacPyMOL.app/pymol/modules/pymol/parsing.py", > line 455, in run_file > execfile(file,global_ns,local_ns) > File "sp.pml", line 81 > col_name = '0x%02x%02x%02x' % tuple(i * 255 for i in col_list) > ^ > SyntaxError: invalid syntax > > == > > any help? > > Tassos -- Thomas Holder MPI for Developmental Biology Spemannstr. 35 D-72076 Tübingen -- Xperia(TM) PLAY It's a major breakthrough. An authentic gaming smartphone on the nation's most reliable network. And it wants your games. http://p.sf.net/sfu/verizon-sfdev ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] Convert pml script to Pymol Python script
Jason Vertrees wrote, On 04/08/11 20:09: > Hi Matthias, > > There is no script that I'm aware of, but writing one should be rather > straightforward because of how the API is organized: > > commandName arg1, arg2, arg3 > > becomes > > cmd.commandName(arg1, arg2, arg3) I would use the cmd.keyword dictionary for the translation, I thinks not all commands have the exact same name in PyMOl API. Also pml scripts can contain python code which must not be translated. > The hardest part would be determining when to quote strings versus not > quoting numbers and variables. It should be save to just quote everything. Cheers, Thomas -- Xperia(TM) PLAY It's a major breakthrough. An authentic gaming smartphone on the nation's most reliable network. And it wants your games. http://p.sf.net/sfu/verizon-sfdev ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] Convert pml script to Pymol Python script
Michael Lerner wrote, On 04/08/11 20:16:
It's not elegant at all, but it's worth knowing that you can use
cmd.do("...") as a quick fix for lines that aren't immediately easy to
convert.
Even a mostly-working pml2py tool would be a useful addition to the wiki.
mostly-working script attached, have fun!
Cheers,
Thomas
--
Thomas Holder
MPI for Developmental Biology
Spemannstr. 35
D-72076 Tübingen
'''
http://sourceforge.net/mailarchive/message.php?msg_id=27331786
Subject: [PyMOL] Convert pml script to Pymol Python script
Date: Fri, 8 Apr 2011 18:01:32 +0100
'''
import sys
from pymol import cmd
def pml2py(filename, out=sys.stdout):
'''
DESCRIPTION
Convert a pml script to python syntax.
USAGE
pml2py infile [, outfile]
TODO
comments, aliases
'''
if isinstance(out, basestring):
out = open(out, 'w')
print >> out, '''
# automatically converted from '%s'
import pymol
from pymol import *
''' % (filename)
handle = open(filename)
for line in handle:
a = line.split(None, 1)
try:
name = a[0]
name = cmd.kwhash.shortcut.get(name, name)
assert name in cmd.keyword
func = cmd.keyword[name][0]
assert func.func_name != 'python_help'
except:
out.write(line)
continue
if len(a) > 1:
args = [i.strip() for i in a[1].split(',')]
else:
args = []
if name == 'python':
for line in handle:
if line.split() == ['python', 'end']:
break
out.write(line)
continue
print >> out, '%s.%s(%s)' % (func.__module__, func.func_name, ', '.join(map(repr, args)))
cmd.extend('pml2py', pml2py)
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Re: [PyMOL] Convert pml script to Pymol Python script
it's on the wiki now:
http://pymolwiki.org/index.php/Pml2py
Cheers,
Thomas
Thomas Holder wrote, On 04/09/11 11:17:
> Michael Lerner wrote, On 04/08/11 20:16:
>> It's not elegant at all, but it's worth knowing that you can use
>> cmd.do("...") as a quick fix for lines that aren't immediately easy to
>> convert.
>>
>> Even a mostly-working pml2py tool would be a useful addition to the wiki.
>
> mostly-working script attached, have fun!
>
> Cheers,
> Thomas
--
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MPI for Developmental Biology
Spemannstr. 35
D-72076 Tübingen
--
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Re: [PyMOL] How to color in a different way different helix types?
Hi Hongbo, very nice! Your plugin only accepts named selections, predefined selections like (all), (polymer) or object names do not work. Could you change this? Cheers, Thomas On Tue, Apr 12, 2011 at 4:22 PM, Hongbo Zhu wrote: > Hi, if anybody is still interested in the topic, I have made a DSSP > plugin for running DSSP and coloring proteins according to the DSSP > secondary structure assignment. Please have a look at: > > http://www.pymolwiki.org/index.php/DSSP > > This plugin invokes DSSP (presuming you already have DSSP binary on your > hard drive) and reads the output using BioPython. It then makes several > selections, each for a kind of secondary structure elements (SSE) if > there is at least one residue in the input selection is assigned with > the SSE. > > regards, > hongbo -- Thomas Holder MPI for Developmental Biology Spemannstr. 35 D-72076 Tübingen -- Forrester Wave Report - Recovery time is now measured in hours and minutes not days. Key insights are discussed in the 2010 Forrester Wave Report as part of an in-depth evaluation of disaster recovery service providers. Forrester found the best-in-class provider in terms of services and vision. Read this report now! http://p.sf.net/sfu/ibm-webcastpromo ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] labeling dna residues
Hi Leila, "b" is an atom property, so you cannot use it as a selection name. http://pymolwiki.org/index.php/Property_Selectors#Numeric_Selector_Table Cheers, Thomas On Thu, Apr 14, 2011 at 4:04 PM, leila karami wrote: > Dear pymol users > > My system contains protein (chain a) and dna (chain b). > > I did following: > > select a, chain a > select b, chain b > > then in b I labeled residues but: > > PyMOL>select b, chain b > Selector: selection "b" defined with 825 atoms. > Selector-Error: Misplaced ). > Selector-Error: Malformed selection. > ( ( name ca+C1*+C1' and ( byres ( b )<-- > > how to fix it? > > I want to know how label dna residues by command line? > > please guide me. > > best wishes > > -- > > Leila Karami > Ph.D. student of Physical Chemistry > K.N. Toosi University of Technology > Theoretical Physical Chemistry Group -- Thomas Holder MPI for Developmental Biology Spemannstr. 35 D-72076 Tübingen -- Benefiting from Server Virtualization: Beyond Initial Workload Consolidation -- Increasing the use of server virtualization is a top priority.Virtualization can reduce costs, simplify management, and improve application availability and disaster protection. Learn more about boosting the value of server virtualization. http://p.sf.net/sfu/vmware-sfdev2dev ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] change of color of dashed line in distance command
Hi Leila, > I want to know how to change color of dashed line. (color of dashed line > is yellow by default). it's the dash_color setting, so to make them blue for example type: set dash_color, blue http://www.pymolwiki.org/index.php/Dash_color Cheers, Thomas -- Thomas Holder MPI for Developmental Biology Spemannstr. 35 D-72076 Tübingen -- Benefiting from Server Virtualization: Beyond Initial Workload Consolidation -- Increasing the use of server virtualization is a top priority.Virtualization can reduce costs, simplify management, and improve application availability and disaster protection. Learn more about boosting the value of server virtualization. http://p.sf.net/sfu/vmware-sfdev2dev ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] Get Protein Dimension
On 04/26/2011 01:40 PM, Martin Hediger wrote:
> Dear all
>
> I found that PyMOL offer the cmd.get_extent('protein') function, which
> returns the dimensions of the selection.
> Is it complicated to make this function available from within an
> ordinary Pythonscript?
what do you mean with "ordinary Pythonscript"? Either your script is
called by PyMOL directly (with "pymol -cqr yourscript.py"), or you have
set up PYTHONPATH, PYMOL_PATH and PYMOL_DATA, run python and launch the
PyMOL process within the script.
Maybe these pages will help:
http://pymolwiki.org/index.php/Launching_From_a_Script
http://pymolwiki.org/index.php/Python_Integration
Cheers,
Thomas
--
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MPI for Developmental Biology
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Re: [PyMOL] Downloading the biological assembly from the PDB
Hi Martin, you may also consider these scripts from PyMOLWiki that generate the biological assembly from the asymmetric unit. http://pymolwiki.org/index.php/BiologicalUnit/Quat or http://pymolwiki.org/index.php/BiologicalUnit Cheers, Thomas Martin Hediger wrote, On 05/03/11 22:00: > Dear all > I would like to ask how it is possible to download the coordinate file > for the biological assembly of a protein structure from the PDB. > Naturally, this is not a question directly related to PyMOL, but I > thought I'll be reaching at least a couple of > Biochemists/Chrystallographers who know how to do this. > As an example, when downloading the PDB file of "1AVD", I get a file > with two chains. The biological assembly would be a tetramer, so I > wonder what URL I would require to write into a script that does the > downloading. > > Thanks for help on this. > Martin -- Thomas Holder MPI for Developmental Biology Spemannstr. 35 D-72076 Tübingen -- WhatsUp Gold - Download Free Network Management Software The most intuitive, comprehensive, and cost-effective network management toolset available today. Delivers lowest initial acquisition cost and overall TCO of any competing solution. http://p.sf.net/sfu/whatsupgold-sd ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] Simultaneous fading in and out of different representations
Hi Sena,
the second argument to mdo was not correct, there you had two strings
and a semicolon what must be one string and the semicolon within. Works
for me like this:
python
cmd.mset("1x100")
cmd.mdo(1,
"set cartoon_transparency, 1.0; set ribbon_transparency, 0.0")
for i in range(40,60):
cmd.mdo(i,
"set cartoon_transparency, %f; set ribbon_transparency, %f" %
(1-(i-40)/20.0, (i-40)/20.0))
cmd.frame(1)
python end
Cheers,
Thomas
Rajagopalan, Senapathy wrote, On 05/04/11 19:50:
> Hi Everyone,
>
> I am making a movie and want to show the transition between a cartoon
> and a ribbon representation smoothly (fading out cartoon and fading in
> ribbon) .
> So I tried writing a simple python script like:
> ---
> for i in range(40,60):
> cmd.mdo (i, "set cartoon_transparency,%f" %( 1-(60-i)/60.0 ); "set
> ribbon_transparency,%f" %( (60-i)/60.0 ) )
> ---
>
> And
> ---
> for i in range(40,60):
> cmd.mdo (i, "set cartoon_transparency,%f" %( 1-(60-i)/60.0 ) )
> for j in range (40,60):
> cmd.mdo (j, "set ribbon_transparency,%f" %( (60-j)/60.0 ) )
> --
>
>
> And various other combinations, but none seem to produce the result that
> I desire. Can anyone help me with the scripting as my python knowledge
> is very basic.
>
> Thanks
> Sena
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Re: [PyMOL] Fetching scripts
Hi Michael, it's a good idea! A working proof-of-concept userland script should be quick to implement I guess. I think the design should go together with the planned new plugin architecture (http://pymolwiki.org/index.php/PluginArchitecture ). Cheers, Thomas Michael Lerner wrote, On 05/04/11 17:59: > Hi all, > > I'm considering building in a mechanism for automatically fetching > scripts from the PyMOL Wiki. The goal is to allow users to say > > fetch findSurfaceResidues, type=script > findSurfaceResidues doShow=True, cutoff=0.5 > > The convenience benefits are obvious, especially for new users, and I > think that lowering the barrier to script usage will greatly increase > both the number of people who use various scripts and the incentive to > place scripts on the wiki (especially if the fetch mechanism makes it > easy for script authors to provide a citation/DOI/etc.). > > I've put up a tentative page about this on the wiki > (http://pymolwiki.org/index.php/Fetching_scripts), and I'd love comments > either via the list, private email or on the wiki, especially about > > - whether you think it's a good idea > - security and validation > - options you'd like > - implementation issues > > The plan is to write this as a userland script first. If issues relating > to security and validation can be resolved, we'll see if the official > builds want to include it. > > Cheers, > > -Michael > > -- > Michael Lerner, Ph.D. > IRTA Postdoctoral Fellow > Laboratory of Computational Biology NIH/NHLBI > 5635 Fishers Lane, Room T909, MSC 9314 > Rockville, MD 20852 (UPS/FedEx/Reality) > Bethesda MD 20892-9314 (USPS) -- Thomas Holder MPI for Developmental Biology Spemannstr. 35 D-72076 Tübingen -- WhatsUp Gold - Download Free Network Management Software The most intuitive, comprehensive, and cost-effective network management toolset available today. Delivers lowest initial acquisition cost and overall TCO of any competing solution. http://p.sf.net/sfu/whatsupgold-sd ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] nucleic acid (one or two letter) residue names
that's true, residue names should be right-justified. http://www.wwpdb.org/documentation/format32/sect1.html "Residue nameOne of the standard amino acid or nucleic acids, as listed below, or the non-standard group designation as defined in the HET dictionary. Field is right-justified." Cheers, Thomas On 05/17/2011 07:44 PM, Pascal Auffinger wrote: > Hi Jason, > > A more difficult one (at least for me) > Pymol seems to write (through save command) nucleic acid residue names > not as suggested by PDB convention. > > Here is an extract of a PDB file (any PDB file containing nucleic acid > residues shows the same – try 100D for example) > > ATOM 1 O5' C A 1 -4.549 5.095 4.262 1.00 28.71O > ATOM 2 C5' C A 1 -4.176 6.323 3.646 1.00 27.35C > ATOM 3 C4' C A 1 -3.853 7.410 4.672 1.00 24.41C > > When I save this file (save command in pymol) i get this > > Output from pymol > > X (this is added by me) > ATOM 1 O5' C A 1 -4.549 5.095 4.262 1.00 28.71O > ATOM 2 C5' C A 1 -4.176 6.323 3.646 1.00 27.35C > ATOM 3 C4' C A 1 -3.853 7.410 4.672 1.00 24.41C > > In one instance, the "C" residue name is left justified and right > justified in the other. > Of course, this cannot happen for the three letter residue names. > Any clue ? > > I tried the following : > > *pdb_truncate_residue_name* (boolean, default: off) controls whether or > not PDB residue names are truncated to three letters only. > > with no effect > > Thanks for help > > Pascal -- Thomas Holder MPI for Developmental Biology -- What Every C/C++ and Fortran developer Should Know! Read this article and learn how Intel has extended the reach of its next-generation tools to help Windows* and Linux* C/C++ and Fortran developers boost performance applications - including clusters. http://p.sf.net/sfu/intel-dev2devmay ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] nucleic acid (one or two letter) residue names
On 05/18/2011 02:23 PM, Pascal Auffinger wrote: > Thanks for confirmation. > > Any clues on how to fix this ??? it has to be fixed in the C-code. I guess it's CoordSetAtomToPDBStrVLA in layer2/CoordSet.c Cheers, Thomas -- Thomas Holder MPI for Developmental Biology -- What Every C/C++ and Fortran developer Should Know! Read this article and learn how Intel has extended the reach of its next-generation tools to help Windows* and Linux* C/C++ and Fortran developers boost performance applications - including clusters. http://p.sf.net/sfu/intel-dev2devmay ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] nucleic acid (one or two letter) residue names
Hi Pascal,
On 05/18/2011 04:46 PM, Pascal Auffinger wrote:
Thanks, could you do that and provide a binary ?
I can't provide a binary, sorry.
Or alternatively, could
you post precisely which line to change to what ? Or change it in the
source code so that we could download an updated version.
see attached patch (untested, since my build seems to be broken at the
moment).
This an
important bug (at least for me). I and many others on the list don't
master C languages (oups ... Am i the only one ?)
for sure you're not the only one ;-)
Cheers,
Thomas
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Thomas Holder
MPI for Developmental Biology
Index: layer2/CoordSet.c
===
--- layer2/CoordSet.c (revision 3948)
+++ layer2/CoordSet.c (working copy)
@@ -678,6 +678,13 @@
strcpy(resn, ai->resn);
if(SettingGetGlobal_b(G, cSetting_pdb_truncate_residue_name)) {
resn[3] = 0;/* enforce 3-letter residue name in PDB files */
+/* right-justify */
+int i = strlen(resn);
+if (i < 3) {
+ int j = 3;
+ while(i > 0) resn[--j] = resn[--i];
+ while(j > 0) resn[--j] = ' ';
+}
}
if(SettingGetGlobal_b(G, cSetting_pdb_formal_charges)) {
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Re: [PyMOL] nucleic acid (one or two letter) residue names
On 05/18/2011 05:01 PM, Jason Vertrees wrote: > This is a bug. Please file it on our open-source bug tracker > http://sourceforge.net/tracker/?group_id=4546&atid=104546. I will fix > it when I get the chance. Bugs item #3304003 https://sourceforge.net/tracker/?func=detail&aid=3304003&group_id=4546&atid=104546 Cheers, Thomas -- Thomas Holder MPI for Developmental Biology -- What Every C/C++ and Fortran developer Should Know! Read this article and learn how Intel has extended the reach of its next-generation tools to help Windows* and Linux* C/C++ and Fortran developers boost performance applications - including clusters. http://p.sf.net/sfu/intel-dev2devmay ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] PyMOL-users Digest, Vol 60, Issue 7
On 05/18/2011 06:50 PM, Sean Law wrote: > Hi PyMOL Community, > > I have a trajectory file loaded into PyMOL but I would like to play the > movie in reverse order. Is there a way to achieve this within PyMOL? If you have 100 states, type: mset 100-1 See also: http://www.pymolwiki.org/index.php/Mset Cheers, Thomas -- Thomas Holder MPI for Developmental Biology -- What Every C/C++ and Fortran developer Should Know! Read this article and learn how Intel has extended the reach of its next-generation tools to help Windows* and Linux* C/C++ and Fortran developers boost performance applications - including clusters. http://p.sf.net/sfu/intel-dev2devmay ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] How to display clashes
Hi Claudia,
those clash visualizations are drawn by the sculpting routine, so you
have to invoke sculpting in some way to get them.
This python function creates a copy of your selection, does one
sculpting cycle and shows bumps for it:
from pymol import cmd
def show_bumps(selection='(all)', name='bump_check', quiet=1):
cmd.delete(name)
cmd.create(name, selection, zoom=0)
cmd.sculpt_activate(name)
cmd.show_as('cgo', name)
cmd.set('sculpt_vdw_vis_mode', 1, name)
cmd.set('sculpt_field_mask', 0x020) # cSculptVDW
strain = cmd.sculpt_iterate(name, cycles=1)
if not int(quiet):
print 'VDW Strain:', strain
return strain
cmd.extend('show_bumps', show_bumps)
Cheers,
Thomas
On 06/06/2011 01:05 PM, Claudia Scotti wrote:
Please, I have modelled several mutants of a protein with FoldX and I
would like to display the clashes present in each case in PyMol.
I have seen that activating the "mutate" wizard I can display clashes
with red disks, but only for standard rotamers, which are not those
tipically used by FoldX.
Any suggestions, please?
Many thanks,
Claudia
Claudia Scotti
Dipartimento di Medicina Sperimentale
Sezione di Patologia Generale
Universita' di Pavia
Via Ferrata, 1
27100 Pavia
Italia
Tel. 0039 0382 986335/8/1
Facs 0039 0382 303673
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MPI for Developmental Biology
show_bumps.py
Description: application/chimera
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Re: [PyMOL] Generating Image of Periodic System
Hi Martin, have a look at: http://pymolwiki.org/index.php/Supercell Run something like this: supercell 2,2,2, withmates=1 Your structure file needs a CRYST1 record that holds the box dimensions. Cheers, Thomas On 06/14/2011 11:55 AM, Martin Hediger wrote: > Dear List > I am trying to prepare a figure. I have a protein structure, enclosed by > a rectangular box. Is it possible to copy/translate the enboxed > structure for a given amount of times? This would end up as something as > an illustration of a system with periodic boundaries. > I attached a figure on my blog <http://qmviews.blogspot.com/>. If I cant > come up with a PyMOL solution, then I guess I'll just try to find a > Python solution. > > Thanks for any hints on this. -- Thomas Holder MPI for Developmental Biology -- EditLive Enterprise is the world's most technically advanced content authoring tool. Experience the power of Track Changes, Inline Image Editing and ensure content is compliant with Accessibility Checking. http://p.sf.net/sfu/ephox-dev2dev ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] How to avoid the message "ObjectMoleculeGuessValences" in pymol1.4.1?
On 06/16/2011 04:24 PM, zjxu wrote: > (3) In pymol/trunk/pymol: > python setup.py install --prefix=/BioSoft/pymol1.4.1_2011-6-16/ > python setup2.py install > ./pymol > However, when I load a pdb, the warning comes again. "pymol -rkqc > script.py" complains again. have you set PYTHONPATH before running setup2.py and ./pymol? modules=/BioSoft/pymol1.4.1_2011-6-16/lib/python*/site-packages export PYTHONPATH=$modules:$PYTHONPATH python setup2.py install ./pymol If you have another (global) PyMOL installation which can be found by python, the launcher will use that one! (this could be improved I guess). Cheers, Thomas -- Thomas Holder MPI for Developmental Biology -- EditLive Enterprise is the world's most technically advanced content authoring tool. Experience the power of Track Changes, Inline Image Editing and ensure content is compliant with Accessibility Checking. http://p.sf.net/sfu/ephox-dev2dev ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] How to merge molecules in Pymol?
Hi Carsten, >> Is there an (un)documented way of merging multiple molecular objects in >> Pymol into one molecule... if you really want them in *one* molecule covalently linked, then also have a look at: * fuse * http://pymolwiki.org/index.php/Fuse "A copy of the object containing the first atom is moved [and rotated] so as to form an approximately resonable bond with the second, and is then merged with the first object." Cheers, Thomas -- Thomas Holder MPI for Developmental Biology -- EditLive Enterprise is the world's most technically advanced content authoring tool. Experience the power of Track Changes, Inline Image Editing and ensure content is compliant with Accessibility Checking. http://p.sf.net/sfu/ephox-dev2dev ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] Polar Contacts printed to text file.
Hi Amanda,
I am using the command:
cmd.dist("interest_polar_conts","exp_interest","exp_interest",quiet=1,mode=2,label=1,reset=1);cmd.enable("interest_polar_conts")
to find the polar contacts.
This command creates an object in the panel but I cannot figure out
how to print the information I am seeing, like the distance and the
atoms involved, in the viewer to a file.
as far as I know the "raw data" of distance objects cannot be accessed.
Have a look at the attached script, it does a very similar job to the
distance command but returns atom pairs with (model,index) keys.
pairlist = polarpairs("exp_interest", "exp_interest", cutoff=3.6, \
name="interest_polar_conts")
You can drop the 'name' argument if you don't need the object for visual
inspection but only the pair list.
Cheers,
Thomas
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Description: application/chimera
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Re: [PyMOL] next resi
Hi jpd, if your selection is named "sele", then try this: # previous resi iterate name C and neighbor byres sele, print (resi,resn) # next resi iterate name N and neighbor byres sele, print (resi,resn) More on selection operators: http://pymolwiki.org/index.php/Selection_Algebra Cheers, Thomas jp d wrote, On 06/24/11 22:57: > hi, > is there a way in pymol/python scripts to > determine what the next or previous resi would be? > > it needs to handle insertions and deletions > > thanks > jpd -- Thomas Holder MPI for Developmental Biology Spemannstr. 35 D-72076 Tübingen -- All of the data generated in your IT infrastructure is seriously valuable. Why? It contains a definitive record of application performance, security threats, fraudulent activity, and more. Splunk takes this data and makes sense of it. IT sense. And common sense. http://p.sf.net/sfu/splunk-d2d-c2 ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] Secondary structure bug?
Matthias Schmidt wrote, On 06/28/11 13:37: > I am making a movie in pymol that I prepared with g_morph > > g_morph -f1 start.pdb -f2 end.pdb -o movie.pdb -nofit (gromacs 4.5.4) > > Pymol does not assign the secondary structure. > > load movie.pdb > dss, movie PyMOL calculates the consensus secondary structure over all states. You may produce distorted intermediates with g_morph, so that consensus might not be appropriate. To only consider first and last state, do this: dss movie, state=-4 Cheers, Thomas -- Thomas Holder MPI for Developmental Biology Spemannstr. 35 D-72076 Tübingen -- All of the data generated in your IT infrastructure is seriously valuable. Why? It contains a definitive record of application performance, security threats, fraudulent activity, and more. Splunk takes this data and makes sense of it. IT sense. And common sense. http://p.sf.net/sfu/splunk-d2d-c2 ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
[PyMOL] personal plugin directory
Hi pymolers, I wrote a script to use a personal plugin directory. http://pymolwiki.org/index.php/PluginDirectory Cheers, Thomas -- Thomas Holder MPI for Developmental Biology -- All of the data generated in your IT infrastructure is seriously valuable. Why? It contains a definitive record of application performance, security threats, fraudulent activity, and more. Splunk takes this data and makes sense of it. IT sense. And common sense. http://p.sf.net/sfu/splunk-d2d-c2 ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] Delete frames in movie
Hi Matthias, there is 'mdelete', 'madd' and 'minsert'. PyMOL>madd ? Usage: madd [ specification [, frame [, freeze ]]] PyMOL>mdelete ? Usage: mdelete [ count [, frame [, freeze [, object PyMOL>minsert ? Usage: minsert count [, frame [, freeze [, object]]] Cheers, Thomas Matthias Schmidt wrote, On 07/09/11 22:32: > Hi, > > I made a nice movie and it's fine and I would just like to delete a > part of it or to insert some frames. How is that possible? Mset resets > the whole movie and mview does not seem to do what I would like it to > do... > > Best, > > Matthias -- Thomas Holder MPI for Developmental Biology Spemannstr. 35 D-72076 Tübingen -- All of the data generated in your IT infrastructure is seriously valuable. Why? It contains a definitive record of application performance, security threats, fraudulent activity, and more. Splunk takes this data and makes sense of it. IT sense. And common sense. http://p.sf.net/sfu/splunk-d2d-c2 ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] Superimposing 2 or more Selections PyMOL GUI
Hi Spyros, > Creating selections the default way places pixel-size pink dots on > the structure, so I was wondering if there is some way to control > this for more complex visualization tasks? set active_selections, off set auto_show_selections, off both seem to hide the pixels, but I'm not sure which one is the better to use. To find such settings, I can recommend 'grepset' from the PyMOLWiki: http://pymolwiki.org/index.php/Grepset > Is there a way to color-code my selections, and visualize them > simultaneously on the structure to see if there is any overlap? See Tsjerk's reply. Cheers, Thomas -- Thomas Holder MPI for Developmental Biology -- All of the data generated in your IT infrastructure is seriously valuable. Why? It contains a definitive record of application performance, security threats, fraudulent activity, and more. Splunk takes this data and makes sense of it. IT sense. And common sense. http://p.sf.net/sfu/splunk-d2d-c2 ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] save new coordinate
> Thanks, but I still failed to get this new pdb.
>
> File -- Save molecular -->
>
> I wish the present coordinate will be saved as a new pdb after rotation.
I guess with present coordinate you mean what you see on screen. To get
this you need to transform the atom coordinates by current camera
orientation before saving to file.
This python code will do that:
def transform_by_camera_rotation():
view = list(cmd.get_view())
M = view[0:3] + [-view[12]] + \
view[3:6] + [-view[13]] + \
view[6:9] + [-view[14]] + \
view[12:15] + [1.]
cmd.transform_selection('(all)', M, transpose=1)
cmd.set_view([1,0,0,0,1,0,0,0,1] + view[9:])
cmd.extend('transform_by_camera_rotation', transform_by_camera_rotation)
Example:
fetch 2xwu
orient
transform_by_camera_rotation
save /tmp/withneworientation.pdb
Cheers,
Thomas
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Re: [PyMOL] save new coordinate
Hi Lina, >> transform_by_camera_rotation > > PyMOL>transform_by_camera_rotation > Traceback (most recent call last): > File "/usr/local/lib/python2.6/dist-packages/pymol/parser.py", line > 464, in parse > exec(layer.com2+"\n",self.pymol_names,self.pymol_names) > File "", line 1, in > NameError: name 'transform_by_camera_rotation' is not defined > > I don't know how achieve this part. Thanks again with best regards, sorry for not making this clear. You will find in the menu "File > Run..." to run python scripts. Or type into the command line: run transform_by_camera_rotation.py After that, PyMOL knows the transform_by_camera_rotation command. For more details see: http://pymolwiki.org/index.php/Run http://pymolwiki.org/index.php/Running_Scripts Cheers, Thomas -- Thomas Holder MPI for Developmental Biology Spemannstr. 35 D-72076 Tübingen -- 10 Tips for Better Web Security Learn 10 ways to better secure your business today. Topics covered include: Web security, SSL, hacker attacks & Denial of Service (DoS), private keys, security Microsoft Exchange, secure Instant Messaging, and much more. http://www.accelacomm.com/jaw/sfnl/114/51426210/ ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] euler-rod axis
Hi jpd, > from the get_object_matrix output, > i can use the euler-rodrigues transformation > http://en.wikipedia.org/wiki/Euler%E2%80%93Rodrigues_formula > and get the axis and angle of rotation. > > is there a way to place the axis? if I understand you correct, you are looking for the translation T so that for object matrix M it yields: M = T * R * T^-1 With python (and numpy): from numpy import reshape, linalg, identity M = cmd.get_object_matrix(object_name) M = reshape(M, (4,4)) t = linalg.solve(identity(3) - M[0:3,0:3], M[0:3,3]) see if this is correct: from numpy import identity, matrix R = identity(4) T = identity(4) R[0:3,0:3] = M[0:3,0:3] T[0:3,3] = t # should print two times the same matrix print M print matrix(T) * matrix(R) * matrix(T).I Hope that helps. Cheers, Thomas -- Thomas Holder MPI for Developmental Biology Spemannstr. 35 D-72076 Tübingen -- Magic Quadrant for Content-Aware Data Loss Prevention Research study explores the data loss prevention market. Includes in-depth analysis on the changes within the DLP market, and the criteria used to evaluate the strengths and weaknesses of these DLP solutions. http://www.accelacomm.com/jaw/sfnl/114/51385063/ ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] save new coordinate
Hi lina, lina wrote, On 07/22/11 12:55: > Thanks very much for your advice, but I don't know which part is wrong, > the new saved one is not the ideal one I wanted, which was supposed to > be the one I saw from screen. > > do I need to modify the transfrom_by_camera_rotation scrips a bit. > actually I don't get it very well. looks like I confused you, I'm sorry for that. No, you don't need to modify the script. The script defines a new command, so you first need to run the script, and then call the command, otherwise nothing will happen actually. run transform_by_camera_rotation.py# run the script transform_by_camera_rotation # call the new command save /tmp/withneworientation.pdb # save the file Is that clear? Cheers, Thomas -- Thomas Holder MPI for Developmental Biology Spemannstr. 35 D-72076 Tübingen -- Magic Quadrant for Content-Aware Data Loss Prevention Research study explores the data loss prevention market. Includes in-depth analysis on the changes within the DLP market, and the criteria used to evaluate the strengths and weaknesses of these DLP solutions. http://www.accelacomm.com/jaw/sfnl/114/51385063/ ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] Help for surface coloring
Hi Robert, you can set the distance between each atom and the center as b-factor, and then use spectrum (or spectrumany [1]) for coloring. I wrote a small python script that will do that, see attachment. Example (in PyMOL command line): run distancecoloring.py centerdistance2b (all) spectrum b, blue_white_red, (all) Cheers, Thomas [1] http://pymolwiki.org/index.php/Spectrumany On 07/28/2011 04:29 PM, Muench, Robert wrote: Dear community, I was searching the internet for several days now to find out how to perform a distance dependent coloring in pymol. The idea is to color the surface of a viral (spherical) structure. I would like to define the xyz-coordinates of the center of the viral structure an color all residues with a gradient depending on the distance from these xyz coordinates. Can anyone please help me out? All the best Robert *Robert Münch*** - Dipl. Biologist / PhD-Student *Paul-Ehrlich-Institut* Federal Institute for Vaccines and Biomedicines Division of Medical Biotechnology Section 6/5 - Viral Gene Transfer Medicinal Products 63225 Langen, Germany Phone: +49-6103-77-4222 Fax: +49-6103-77-1255 -- Thomas Holder MPI for Developmental Biology distancecoloring.py Description: application/chimera -- Got Input? Slashdot Needs You. Take our quick survey online. Come on, we don't ask for help often. Plus, you'll get a chance to win $100 to spend on ThinkGeek. http://p.sf.net/sfu/slashdot-survey___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] Extending PyMOL or Plugins
Hi Jeff, > I have several questions about extending PyMOL via modules or plugins. > > It appears that the primary difference between the two is windows for > modules are created at during start up and plugin windows can be brought up > on demand (from the plugins menu). Are there other differences? I would say a pymol plugin is just a module that provides a __init_plugin__ (or __init__) function which gets as argument the PMGApp instance, which is PyMOLs external GUI. This is of course required if the module wants to add items to the plugins menu or open dialogs. But extending the plugins menu or opening any windows is not mandatory for plugins or other modules. > What is the current status of wxPython versus Tkinter for the future of > PyMOL? I could look at wxPython, but I seem to be at a loss to find the > python binary for the prebuilt Mac OS PyMOL Application. > > This has probably been brought up before, what are the issues with using an > egg for extensions that have more than one file? If you stay with pure python and just import your module, there should be no issues. However the plugin architecture (modules within the pmg_tk/startup directory) so far only recognizes single python files (this will most likely change in the future). Cheers, Thomas -- Thomas Holder MPI for Developmental Biology Spemannstr. 35 D-72076 Tübingen -- Got Input? Slashdot Needs You. Take our quick survey online. Come on, we don't ask for help often. Plus, you'll get a chance to win $100 to spend on ThinkGeek. http://p.sf.net/sfu/slashdot-survey ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] Help
Hi Babban, regarding your questions on peptide building: > My last doubt is about creating polymers out a given PDB ? > I am studying the fibrils of some proteins and although the structure of > fibril is not know but through some analysis I have come to understand > the region in peptide which is leading to fibrillation. PyMOL has a builder where you can create a peptide with given secondary structure. In the external GUI click on "Builder" on the right and then "Protein" on the left side. You may also check this PyMOLWiki page: http://www.pymolwiki.org/index.php/Peptide_Sequence > I want to be able to create a PDB which has like 4/8/16 monomeric > peptide combined through some BETA PLEATED region(i.e the peptides will > join/aggregate around that region (beta region) of the peptide ) and all > I have is the PDB of the monomeric peptide. As far as I know there's no build-in PyMOL function that sticks together two beta-strands. In editing mode you can freely drag around objects: Right-click, "drag object coords", SHIFT+Middle-Mouse-Drag. More precide movements can be achived with translate and rotate commands: http://www.pymolwiki.org/index.php/Modeling_and_Editing_Structures#Translate_or_rotate_individual_objects If this is not precise enough for you and you want real beta-sheet modeling, you should use something like modeller. Cheers, Thomas -- Thomas Holder MPI for Developmental Biology Spemannstr. 35 D-72076 Tübingen -- Got Input? Slashdot Needs You. Take our quick survey online. Come on, we don't ask for help often. Plus, you'll get a chance to win $100 to spend on ThinkGeek. http://p.sf.net/sfu/slashdot-survey ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] radio buttons does not work (Plugin)
Hi Osvaldo,
set the master explicitly, otherwise it will use the PyMOL gui as master
I guess.
v = StringVar(master=master)
Cheers,
Thomas
On 08/03/2011 05:27 AM, Osvaldo Martin wrote:
> Hi,
>
> I am trying to write a PyMOL plugin with radio buttons. But I am having
> problems.
>
> 1) the last two radio button looks gray and checked. (I think the
> correct behavior should be; only one checked and none gray) setting a
> different default value (using ref_value.set()) does not change anything.
>
> 2) I always get the default value ("1" in this example) when hit the
> submit button.
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Re: [PyMOL] Saving each residue to file
Hi Martin,
there are for sure several ways to achieve this, one might be using the
"pop" command (there is no PyMOLWiki page, but "help pop" gives a quick
example how to use it).
fetch 2xwu, async=0
select _justca, byca 2xwu
python
while cmd.pop("_tmp", "_justca"):
cmd.iterate("_tmp", "stored.x='res-'+chain+'-'+resn+resi")
cmd.save(stored.x + ".pdb", "byres _tmp")
python end
delete _justca _tmp
Hope that helps.
Cheers,
Thomas
On 08/15/2011 09:14 AM, Martin Hediger wrote:
> Dear List
> I was wondering if there could be a way of having every residue of a
> protein structure being saved to a separate file. How could this be done?
> I believe the 'iterate' method might be useful in combination with the
> 'byres' identifier, but I havent figured out how to combine them in the
> right way.
> It would be great if the residues could be saved by increasing residue
> number, something like
> res-a001
> res-f002
> where 'a' and 'f' where the residue type and the number is the residue
> number in the chain.
>
> Any hints are very welcome.
> Martin
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Re: [PyMOL] Dynoplot : Interactive plot
On 08/16/2011 03:16 PM, Joseph André wrote: > Hi everybody, > > I want to build an interactive plot I tried to use and tweak dynoplot > but DynoPlot doesn't work properly : I can display the Tk window but > points aren't plotted. However the dihedrals angles are computed > correctly. There isn't any traceback or error reported on the console. > > Do you have experienced similar problems ? I can confirm that DynoPlot does not work. This needs to be fixed. Cheers, Thomas -- Thomas Holder MPI for Developmental Biology -- uberSVN's rich system and user administration capabilities and model configuration take the hassle out of deploying and managing Subversion and the tools developers use with it. Learn more about uberSVN and get a free download at: http://p.sf.net/sfu/wandisco-dev2dev ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] Dynoplot : Interactive plot
Hi Joseph, > thanks for your quick reply. I'm a newbie at Tk programming but from > what I understand, gui code for Dynoplot had been written from scratch. > Do you know if they are libraries that would facilitate the plotting and > the interaction with pymol? There are many libraries for plotting, for example matplotlib which is also shipped with recent PyMOL versions. Dynoplot however also could update the structure by dragging dots on the plot, I'm not aware of a plotting library that provides this functionality (which does not mean that none such exists :) ). Cheers, Thomas -- Thomas Holder MPI for Developmental Biology -- uberSVN's rich system and user administration capabilities and model configuration take the hassle out of deploying and managing Subversion and the tools developers use with it. Learn more about uberSVN and get a free download at: http://p.sf.net/sfu/wandisco-dev2dev ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] How to draw a cartoon representation on secondary structures containing beta-amino acids?
Hi Baptiste, > I have a small helical pseudopeptide with mixed alpha and beta > amino-acids. How can I make a cartoon representation of this helix with > Pymol? For the moment, I have selected the peptide backbone atoms and > tried the "alter" command to force pymol to recognize the helix but it > do not work. are you sure? What happens if you try this: alter all, ss='H' as cartoon rebuild Cheers, Thomas -- Thomas Holder MPI for Developmental Biology Spemannstr. 35 D-72076 Tübingen -- uberSVN's rich system and user administration capabilities and model configuration take the hassle out of deploying and managing Subversion and the tools developers use with it. Learn more about uberSVN and get a free download at: http://p.sf.net/sfu/wandisco-dev2dev ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] loading gro files
To keep the original residue numbers from the gro file, you could also temporarily store additional numbering in the segment identifier, and after loading get it back from there: _pdbline= "ATOM %5i %-3s %3s%2s%4i" +\ "%8.3f%8.3f%8.3f%6.2f%6.2f %4s%2s \n" def pdbOut(atom,i=1): segi = '%02d%02d' % (i/10,atom[2]/1) stuff = [i%1e5,atom[0][:3],atom[1],atom[3],atom[2]%1e4] +\ list(atom[4:])+[1,40,segi,atom[0][0]] return _pdbline % tuple(stuff) And after cmd.read_pdbstr: cmd.alter(objname, '(ID,resi,segi)=' +\ '(ID+10*int(segi[:2]), resv+1*int(segi[2:]), "")') Cheers, Thomas On 08/18/2011 10:40 AM, Tsjerk Wassenaar wrote: > Hi Joseph, > > Sorry about that. A bit naive with the numbering. To fix it, change the > function > > def pdbOut(atom,i=1): > return _pdbline%((i,) + (atom[0][:3],) + (atom[1],) + (atom[3],) + > (atom[2],) + atom[4:] + (1,40) + (atom[0][0],)) > > to > > def pdbOut(atom,i=1): > stuff = > [i%1e5,atom[0][:3],atom[1],atom[3],atom[2]%1e4]+list(atom[4:])+[1,40,atom[0][0]] > return _pdbline % tuple(stuff) > > It worked for me on a .gro file with 160k atoms :) > > Cheers, > > Tsjerk > > 2011/8/18 Joseph André: >> Hi Tsjerk, >> Thanks for the script. It works great on my protein. However when I try to >> load the solvated system> 100.000 atoms I have problems with water >> molecules. Is it possible to handle gro files with more than 100.000 atoms >> and residues? >> Best -- Thomas Holder MPI for Developmental Biology -- Get a FREE DOWNLOAD! and learn more about uberSVN rich system, user administration capabilities and model configuration. Take the hassle out of deploying and managing Subversion and the tools developers use with it. http://p.sf.net/sfu/wandisco-d2d-2 ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] Multiple Structure Superposition
Hi Suda and Tsjerk, there is "alignto" which used cealign. There is also in the menu "Action > align > all to this" which uses cmd.util.mass_align (and that uses cmd.align). On Robert Campbell's site there is the "align_all.py" script: http://pldserver1.biochem.queensu.ca/~rlc/work/pymol/ On my PyMOLWiki user page there is a "extra_fit" script. http://pymolwiki.org/index.php/User:Speleo3 All those align to a reference object (or state, in case of intra_fit) instead of an all-against-all best fit. Cheers, Thomas On 08/29/2011 08:52 AM, Tsjerk Wassenaar wrote: > Hi Suda, > > Do you mean different structures of the same molecule or different > molecules? For a multistate object, there is intra_fit. for selections > comprising multiple objects it's not currently possible. But it's > being worked on. > > Cheers, > > Tsjerk > > On Mon, Aug 29, 2011 at 8:43 AM, Suda Ravindran wrote: >> Hi, >> >> I would like to know how to do structure based superposition using PyMol for >> 3 or more structures. Please help me out. >> >> Thanks, >> >> -Suda -- Thomas Holder MPI for Developmental Biology -- EMC VNX: the world's simplest storage, starting under $10K The only unified storage solution that offers unified management Up to 160% more powerful than alternatives and 25% more efficient. Guaranteed. http://p.sf.net/sfu/emc-vnx-dev2dev ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] Configuration of Player
Hi Martin, > Is it possible to run the "PyMOL-Player" in a way such that it does not > skip to the first frame once it reaches the end, but rather that it goes > "back and forward"? > I.e. if running over the models/frames in a multi frame file, it goes > from 1-10 and then from 10-1. As far as I know there is no "movie_back_and_forward" setting. You need to map states to frames with mset: mset 1-10 10-1 mplay http://pymolwiki.org/index.php/Mset http://pymolwiki.org/index.php/MovieSchool_2#Terminology Cheers, Thomas -- Thomas Holder MPI for Developmental Biology Spemannstr. 35 D-72076 Tübingen -- Special Offer -- Download ArcSight Logger for FREE! Finally, a world-class log management solution at an even better price-free! And you'll get a free "Love Thy Logs" t-shirt when you download Logger. Secure your free ArcSight Logger TODAY! http://p.sf.net/sfu/arcsisghtdev2dev ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] Script for Torsion angles
Hi Martin, http://pymolwiki.org/index.php/Get_Dihedral Cheers, Thomas On 09/02/2011 11:48 AM, Martin Hediger wrote: > Dear List > Does anyone have a script to calculate torsion angles lying around? > Ideally, i would like to be able to enter x1, x2, x3, x4 and get the > (smaller) angle between the two normals of the planes defined by x1, x2, > x3 and x2, x3, x4, respectively. For some odd reason the measurment > wizard in my PyMOL install does not display torsion angles..!? > > Kind regards and thanks for any feedback. > Martin -- Thomas Holder MPI for Developmental Biology -- Special Offer -- Download ArcSight Logger for FREE! Finally, a world-class log management solution at an even better price-free! And you'll get a free "Love Thy Logs" t-shirt when you download Logger. Secure your free ArcSight Logger TODAY! http://p.sf.net/sfu/arcsisghtdev2dev ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] Mutagenesis script
Hi Troels,
> cmd.(something) ALWAYS has to be in string format.
> So there is the cmd.frame wrong.
I'm sorry but this is not true, of course you can pass an integer to
cmd.frame
> Then you dont quit the mutagenesis wizard
which is not a problem as well.
> And you have a space in the cmd.save
I agree to avoid spaces between function name and parenthesis, but still
this is valid python syntax and works fine.
The full script posted by Rozaimi works fine for me by the way.
> cmd.set_wizard("done")
this doesn't quit the wizard, cmd.set_wizard() without arguments does.
Cheers,
Thomas
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Re: [PyMOL] (no subject)
Hi Noloofar and Lina, >> I would like to calculate partial charges of my pdb. Is it possible to do it > > In pymol: > > Action-> compute -> partial charge sum this doesn't calculate partial charges, sorry. This does: Action -> generate -> vacuum electrostatics But better would be to use pdb2pqr: http://www.poissonboltzmann.org/pdb2pqr >> I have another question too, when aligning two structure in Pymol, there is >> a RMSD for the total structure, is there any command to calculate the RMSD >> for a specific region of the alignment. If the two structures have the same sequence (same atom identifiers) and you don't need an "alignment", you can use rms_cur. http://pymolwiki.org/index.php/Rms_Cur Cheers, Thomas -- Thomas Holder MPI for Developmental Biology Spemannstr. 35 D-72076 Tübingen -- Special Offer -- Download ArcSight Logger for FREE! Finally, a world-class log management solution at an even better price-free! And you'll get a free "Love Thy Logs" t-shirt when you download Logger. Secure your free ArcSight Logger TODAY! http://p.sf.net/sfu/arcsisghtdev2dev ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] add polar/aromatic hydrogen
Hi lina, to add polar hydrogens, try this: h_add acceptors or donors I don't know if it's possible to select aromatic atoms in PyMOL. Cheers, Thomas On 09/06/2011 09:12 AM, lina wrote: > Hi, > > How to add polar/aromaic hydrogen's quickly? > > in A-->hydrogen -- only add all hydrogen, > > thanks for any suggestions, -- Thomas Holder MPI for Developmental Biology -- Special Offer -- Download ArcSight Logger for FREE! Finally, a world-class log management solution at an even better price-free! And you'll get a free "Love Thy Logs" t-shirt when you download Logger. Secure your free ArcSight Logger TODAY! http://p.sf.net/sfu/arcsisghtdev2dev ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] Mutagenesis script
Hi Rozaimi,
the only problem seems to be your last line, you save two objects (test,
1shr) to the same PDB file.
Try this:
cmd.save("kill.pdb", test)
Cheers,
Thomas
On 09/06/2011 03:25 PM, Rozaimi Razali wrote:
> Dear All,
>
> Sorry for the late reply and thank you for helping me out.
>
> Originally the wild residue (for 1shr) at position 36:B is a Proline. I
> want to mutate it to Histidine.
>
> I have tried the suggestion in this thread but the output file
> (kill.pdb) still gives PRO at position 36:B
>
> #Initialize
> fetch 1shr, async=0
> create test, 1shr
> cmd.wizard("mutagenesis")
> cmd.do("refresh_wizard")
>
> # Mutate
> cmd.get_wizard().set_mode("HIS")
> cmd.get_wizard().do_select("/test//B/36")
>
> cmd.frame("1")
> cmd.get_wizard().apply()
> cmd.set_wizard("done")
>
> # Save
> cmd.save("kill.pdb")
>
> I am not sure what is the problem here. I have also tried running the
> script on other machines and still the same problem is happening. FYI i
> am using Pymol version 1.3. Could this be the problem?
>
> I have tried using the log function + mutagenesis wizard in Pymol GUI
> but something strange is happening. The position 36:B did changed to His
> but
>
> e.g.
>
> input file - 1shr.pdb -> atom number for 36:B:CA is 1334
> output file - kill.pdb -> atom number 36:B:CA 1380
>
> log.pml -> ...byresi((1shr`1380))...
>
> Why does it tag the atom number from the output file? Shouldn't it tag
> the atom number from the input file (1shr)?
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Re: [PyMOL] Mutagenesis script
On 09/06/2011 03:43 PM, Thomas Holder wrote:
> Try this:
> cmd.save("kill.pdb", test)
sorry, forgot quotes, must be:
cmd.save("kill.pdb", "test")
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Re: [PyMOL] add polar/aromatic hydrogen
Hi Lina, > Hope you won't mind this email sent to you directly. not at all, that made it finally clear what you actually want! > Here I attached the pdb, > > which I want to add the aromatic H, > > The cur_1.pdb: only polar H was added. > > while cur_11.pdb I used h_add (selection of aromatic atom, namely C3, > C5, C6, C16, C17, C20) > > I only kept one H here, and removed another. PyMOL only knows bond valences for known amino acids, but your file contains a molecule which is not a protein. You can either explicitly define which bonds are aromatic or double bonds, or PyMOL can guess for you from geometry. # load molecule without hydrogens load cur_1.pdb remove hydro # show double-bonds in line or stick representation set valence # make rings aromatic and C=O double bonds valence guess, all, all # add hydrogens h_add all If it does not work to guess valences, you need explicit statements: # select rings select ring1, name C2+C3+C4+C5+C6+C7 select ring2, name C15+C16+C17+C18+C19+C20 # make rings aromatic valence aromatic, ring1, ring1 valence aromatic, ring2, ring2 # define double bonds valence 2, name C10, name O3 valence 2, name C12, name O4 Hope that helps, Cheers, Thomas -- Thomas Holder MPI for Developmental Biology -- Special Offer -- Download ArcSight Logger for FREE! Finally, a world-class log management solution at an even better price-free! And you'll get a free "Love Thy Logs" t-shirt when you download Logger. Secure your free ArcSight Logger TODAY! http://p.sf.net/sfu/arcsisghtdev2dev ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] print hydrogen bonds involved residues
Hi Lina, have a look at: http://pymolwiki.org/index.php/Polarpairs it takes two selections and has a state argument. Cheers, Thomas lina wrote, On 09/10/11 15:21: > Hi, > > After dist hb, proA, proB, mode=2 > > I can get the hydrogen bonds formation between protein A and protein B. > > But I don't know how to get the detailed involved residues very quickly, > suppose I have had 10 models in this structure. > > I googled before, > http://www.mail-archive.com/pymol-users@lists.sourceforge.net/msg06211.html > is helpful for the single one selections, > here I got two. > > Thanks for any suggestions, > > -- > Best Regards, > > lina -- Thomas Holder MPI for Developmental Biology Spemannstr. 35 D-72076 Tübingen -- Malware Security Report: Protecting Your Business, Customers, and the Bottom Line. Protect your business and customers by understanding the threat from malware and how it can impact your online business. http://www.accelacomm.com/jaw/sfnl/114/51427462/ ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] Writing a script yo pymol
Hi Yotam, > I'm sorry but this is too complected. Currently, I can't afford the time > to learn another scripting languish. Consider gnuplot script files, > which are simply a list of gnuplot commands. PyMOL understands two languages. The "PyMOL language" is indeed similar to gnuplot commands, that's what you usually type into the PyMOL command prompt or put into .pml script files. The other language is pure python (PyMOL API) and can be used to write more complicated routines (.py script files). http://pymolwiki.org/index.php/Running_Scripts > Sure you can do > some sophisticated stuff but you don't have to. All my files will be > simple atom list in xyz format (name \t x \t y \t z), and all I want to > do is select all the atoms of a certain name, color them and then rotate > the system. by "rotate the system" do you mean a movie-like 360° rotation? Then your simple list of PyMOL commands will be something like: # color everything gray and histidines blue color gray, all color blue, resn HIS # make 100 movie frames and do full rotation about Y-axis mset 1 x100 util.mroll mplay For documentation and more examples see: http://pymolwiki.org/index.php/Color http://pymolwiki.org/index.php/Util.mroll http://pymolwiki.org/index.php/Property_Selectors http://pymolwiki.org/index.php/Selection_Algebra Cheers, Thomas -- Thomas Holder MPI for Developmental Biology Spemannstr. 35 D-72076 Tübingen -- Doing More with Less: The Next Generation Virtual Desktop What are the key obstacles that have prevented many mid-market businesses from deploying virtual desktops? How do next-generation virtual desktops provide companies an easier-to-deploy, easier-to-manage and more affordable virtual desktop model.http://www.accelacomm.com/jaw/sfnl/114/51426474/ ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] print hydrogen bonds involved residues
> You have to make .pml file and put the python commands inside pymol > blocks. it's "python" blocks, see: http://pymolwiki.org/index.php/Python > ... do I need to put those code in another .py file? That's also possible, yes. Cheers, Thomas -- Thomas Holder MPI for Developmental Biology Spemannstr. 35 D-72076 Tübingen -- Doing More with Less: The Next Generation Virtual Desktop What are the key obstacles that have prevented many mid-market businesses from deploying virtual desktops? How do next-generation virtual desktops provide companies an easier-to-deploy, easier-to-manage and more affordable virtual desktop model.http://www.accelacomm.com/jaw/sfnl/114/51426474/ ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] compare crystal packing of two different Space Groups
Hi Shukun, why and how did the matrix_copy command fail? If you swap step (2) and (3) everything should be fine. Try this: fetch 2xwu 2x19, async=0 as ribbon symexp mates, 2x19, 2x19, 6.0, segi=1 align /2x19//B, /2xwu//B matrix_copy 2x19, mates* By the way, the segi=1 argument of the symexp command gives every symmetry mate a uniqe segment identifier, so if you would save them all to the same PDB file there is no need to rename chain IDs. Cheers, Thomas shukunluo wrote, On 09/11/11 10:51: > Dear Pymol users, > > I want to compare the crystal packing and contacts of two different > space groups of the same protein using pymol. Here's what I did: > (1)loaded two structures; (2) aligned two structures; (3) generated > symmetry-related objects of two structures. However, the > symmetry-related molecules didn't move with the source structure. I > tried in coot to superimposed two structures then save the moved > molecules, but the space group changed to the target structures. I also > tried the matrix_copy command with failure. > > Does anyone know how to do this? Thanks in advance. > > Best, > Shukun -- Thomas Holder MPI for Developmental Biology Spemannstr. 35 D-72076 Tübingen -- Doing More with Less: The Next Generation Virtual Desktop What are the key obstacles that have prevented many mid-market businesses from deploying virtual desktops? How do next-generation virtual desktops provide companies an easier-to-deploy, easier-to-manage and more affordable virtual desktop model.http://www.accelacomm.com/jaw/sfnl/114/51426474/ ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] compare crystal packing of two different Space Groups
Hi Shukun, > Thanks for your nice replies. I followed Tom's script, and the problem > solved. Also, I found there was no difference whether the > "segi=1"argument was appended or not. I've checked at the PymolWiki site > and haven't found any "matrix_copy" arguments like 'segi'. "matrix_copy" does not have a segi argument, but "symexp" has. I've updated the PyMOLWiki page: http://pymolwiki.org/index.php/Symexp > By the way, the old version of Pymol(0.99) may be the cause of failure > last time I used the "Matrix_copy" command? I upgraded pymol to the > version of 1.4.1, . yes, the matrix_copy command was introduced after 0.99! Cheers, Thomas -- Thomas Holder MPI for Developmental Biology -- BlackBerry® DevCon Americas, Oct. 18-20, San Francisco, CA Learn about the latest advances in developing for the BlackBerry® mobile platform with sessions, labs & more. See new tools and technologies. Register for BlackBerry® DevCon today! http://p.sf.net/sfu/rim-devcon-copy1 ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] pymol wildcards usage
this is an open issue:
http://sourceforge.net/tracker/?func=detail&aid=2182309&group_id=4546&atid=104546
> Have you tried
>
> delete all and not obj1
unfortunately this does not work, it will delete obj1.
The expected result could be achieved with this workaround:
python
def delete2(selection):
names = cmd.get_names(selection=selection)
cmd.delete(' '.join(names))
cmd.extend('delete', delete2)
python end
Cheers,
Thomas
> Hi all! I have a question about wildcards usage in pymol.
> For example if I want to delete all except obj1 I write:
> delete not obj1
> but this expression does not works as expected...
>
> Is there a way in pymol to delete all except [something]?
> In selections these experssions work. But in object names they don't.
>
>
> --
>
> Andrew Gontchar
--
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Re: [PyMOL] refresh molecule display in python script
Hi Matthias,
use "spawn" instead of "run".
http://pymolwiki.org/index.php/Fork
Cheers,
Thomas
On 09/14/2011 02:30 PM, Matthias Schmidt wrote:
> Hi,
>
> I am loading a pdb file in a python script for pymol.
>
> The script has the following structure:
>
> def script
> do something
> cmd.load("file.pdb")
> do lot more
> cmd.extend("script", script)
>
> When the python script is completed, the molecule file.pdb is shown
> in the openGL display, but not before. How can I show the molecule
> file.pdb in the display immediately after loading it and before "do
> lot more" is executed?
>
> Best,
>
> Matthias
> --
> Structural Bioinformatics and Computational Biochemistry Unit
> Dept. of Biochemistry
> University of Oxford
>
> http://sbcb.bioch.ox.ac.uk/schmidt.php
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Re: [PyMOL] regarding the dssp plugins
Hi Lina,
as far as I know the secondary structure atom property is not state
specific, so you cannot assign per state. But you can split states to
individual objects. The DSSP plugin (I guess you are talking about
http://www.pymolwiki.org/index.php/DSSP) however does not deal well with
multiple objects (Hongbo, can you fix that?). The build-in command "dss"
does, maybe you can use that?
Example:
fetch 1d7q, async=0
as cartoon
split_states 1d7q
delete 1d7q
dss all
rebuild
http://pymolwiki.org/index.php/Split_States
http://pymolwiki.org/index.php/Dss
I can also offer you my own dssp script which works with multiple
objects, see attachment. It provides the PyMOL commands "dssp" and
"stride". Check "help dssp".
Cheers,
Thomas
lina wrote, On 09/16/11 17:45:
Hi,
a quick question,
how can update the ss for all states, not check one by one,
and run dssp and update ...
Thanks for any advice,
--
Best Regards,
lina
--
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MPI for Developmental Biology
Spemannstr. 35
D-72076 Tübingen
'''
(c) 2010 Thomas Holder, Max Planck Institute for Developmental Biology
PyMOL wrapper for DSSP and STRIDE
'''
from pymol import cmd, stored
from subprocess import Popen, PIPE
import tempfile, os
def _common_ss_alter(selection, ss_dict, ss_map, raw=''):
'''
DESCRIPTION
Shared code of 'dssp' and 'stride' functions.
'''
if raw != 'ss':
cmd.alter(selection, 'ss = ss_map.get(ss_dict.get((model,chain,resi)), "")',
space={'ss_dict': ss_dict, 'ss_map': ss_map})
if raw != '':
cmd.alter(selection, raw + ' = ss_dict.get((model,chain,resi), "")',
space={'ss_dict': ss_dict})
cmd.rebuild(selection, 'cartoon')
def dssp(selection='(all)', exe='dsspcmbi', raw=''):
'''
DESCRIPTION
Secondary structure assignment with DSSP.
http://swift.cmbi.ru.nl/gv/dssp/
ARGUMENTS
selection = string: atom selection {default: all}
exe = string: name of dssp executable {default: dsspcmbi}
raw = string: atom property to load raw dssp class into {default: ''}
EXAMPLE
dssp all, /sw/bin/dsspcmbi, raw=text_type
color gray
color red, text_type H
color orange, text_type G
color yellow, text_type E
color wheat, text_type B
color forest, text_type T
color green, text_type S
set cartoon_discrete_colors, 1
SEE ALSO
dss, stride
'''
ss_map = {
'B': 'S', # residue in isolated beta-bridge
'E': 'S', # extended strand, participates in beta ladder
'T': 'L', # hydrogen bonded turn
'G': 'H', # 3-helix (3/10 helix)
'H': 'H', # alpha helix
'I': 'H', # 5 helix (pi helix)
'S': 'L', # bend
' ': 'L', # loop or irregular
}
tmpfilepdb = tempfile.mktemp('.pdb')
ss_dict = dict()
for model in cmd.get_object_list(selection):
cmd.save(tmpfilepdb, '%s and (%s)' % (model, selection))
process = Popen([exe, '-na', tmpfilepdb], stdout=PIPE)
for line in process.stdout:
if line.startswith(' # RESIDUE'):
break
for line in process.stdout:
resi = line[5:11].strip()
chain = line[11].strip()
ss = line[16]
ss_dict[model,chain,resi] = ss
os.remove(tmpfilepdb)
_common_ss_alter(selection, ss_dict, ss_map, raw)
cmd.extend('dssp', dssp)
def stride(selection='(all)', exe='stride', raw=''):
'''
DESCRIPTION
Secondary structure assignment with STRIDE.
http://webclu.bio.wzw.tum.de/stride/
SEE ALSO
dss, dssp
'''
ss_map = {
'C': 'L',
'B': 'S',
'b': 'S',
'E': 'S',
'T': 'L',
'G': 'H',
'H': 'H',
}
tmpfilepdb = tempfile.mktemp('.pdb')
ss_dict = dict()
for model in cmd.get_object_list(selection):
cmd.save(tmpfilepdb, '%s and (%s)' % (model, selection))
process = Popen([exe, tmpfilepdb], stdout=PIPE)
for line in process.stdout:
if not line.startswith('ASG'):
continue
chain = line[9].strip('-')
resi = line[11:16].strip()
ss = line[24]
ss_dict[model,chain,resi] = ss_map.get(ss)
os.remove(tmpfilepdb)
_common_ss_alter(selection, ss_dict, ss_map, raw)
cmd.extend('stride', stride)
# tab-completion
cmd.auto_arg[0].update({
'dssp' : [ cmd.selection_sc , 'selection' , ', ' ],
'stride' : [ cmd.selection_sc , 'selection' , ', ' ],
})
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Re: [PyMOL] regarding the dssp plugins
Hi Lina, >> I can also offer you my own dssp script which works with multiple objects, >> see >> attachment. It provides the PyMOL commands "dssp" and "stride". Check "help >> dssp". > > Thanks, I tried, > > PyMOL>dssp all, /home/lina/dssp, raw=text_type > Traceback (most recent call last): > File "/usr/local/lib/python2.6/dist-packages/pymol/parser.py", line 254, in > parse > self.result=apply(layer.kw[0],layer.args,layer.kw_args) > File "dssp.py", line 70, in dssp > process = Popen([exe, '-na', tmpfilepdb], stdout=PIPE) > File "/usr/lib/python2.6/subprocess.py", line 623, in __init__ > errread, errwrite) > File "/usr/lib/python2.6/subprocess.py", line 1141, in _execute_child > raise child_exception > OSError: [Errno 2] No such file or directory does /home/lina/dssp point to your dssp executable? Cheers, Thomas PS: I just realized that there is a new dssp-2 and it does not understand the -na option, thus will fail with my script without modifying it. -- Thomas Holder MPI for Developmental Biology Spemannstr. 35 D-72076 Tübingen -- BlackBerry® DevCon Americas, Oct. 18-20, San Francisco, CA http://p.sf.net/sfu/rim-devcon-copy2 ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] how to organize those .py
Hi Lina, you can put a .pymolrc file in your home directory, it's a script that PyMOL will read on each startup. You can have it either in PyMOL syntax or as a python script, depending on the file extension. /home/lina/.pymolrc (in PyMOL syntax) /home/lina/.pymolrc.py (in python syntax) http://www.pymolwiki.org/index.php/Pymolrc Then create a directory -- lets say /home/lina/.pymol -- and put the PyMOLWiki scripts there. And in your .pymolrc you put lines like these (PyMOL syntax): run /home/lina/.pymol/Grepsel.py run /home/lina/.pymol/Polarpairs.py run /home/lina/.pymol/Propka.py ... and so on Cheers, Thomas lina wrote, On 09/19/11 07:10: > Hi, > > Just a quick Q: > > How can I better organize those *.py I mainly obtained from pymol wiki, > not those can be installed by the plugins, > > pymol run in different directory each time. > > Thanks, > > -- > Best Regards, > > lina -- Thomas Holder MPI for Developmental Biology Spemannstr. 35 D-72076 Tübingen -- BlackBerry® DevCon Americas, Oct. 18-20, San Francisco, CA Learn about the latest advances in developing for the BlackBerry® mobile platform with sessions, labs & more. See new tools and technologies. Register for BlackBerry® DevCon today! http://p.sf.net/sfu/rim-devcon-copy1 ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] How to print sequence based on structure
Hi Lina, > Another question here, > > can I show the whole residue as a ball, and different residues connect > by (virtual) bonds. combine ribbon and CA spheres: hide everything show ribbon show spheres, name CA set sphere_scale, 0.5 set ribbon_width, 5 Cheers, Thomas -- Thomas Holder MPI for Developmental Biology Spemannstr. 35 D-72076 Tübingen -- BlackBerry® DevCon Americas, Oct. 18-20, San Francisco, CA Learn about the latest advances in developing for the BlackBerry® mobile platform with sessions, labs & more. See new tools and technologies. Register for BlackBerry® DevCon today! http://p.sf.net/sfu/rim-devcon-copy1 ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] Dynoplot : Interactive plot
Hi, I reworked the broken DynoPlot script. Changes and improvements include: * much faster calculation of Phi/Psi angles * can open multiple plot windows * center on residue with right-mouse-click * different plot symbols for GLY and PRO http://pymolwiki.org/index.php/DynoPlot Cheers, Thomas Thomas Holder wrote, On 08/16/11 15:51: > On 08/16/2011 03:16 PM, Joseph André wrote: >> Hi everybody, >> >> I want to build an interactive plot I tried to use and tweak dynoplot >> but DynoPlot doesn't work properly : I can display the Tk window but >> points aren't plotted. However the dihedrals angles are computed >> correctly. There isn't any traceback or error reported on the console. >> >> Do you have experienced similar problems ? > > I can confirm that DynoPlot does not work. This needs to be fixed. > > Cheers, > Thomas -- Thomas Holder MPI for Developmental Biology Spemannstr. 35 D-72076 Tübingen -- All the data continuously generated in your IT infrastructure contains a definitive record of customers, application performance, security threats, fraudulent activity and more. Splunk takes this data and makes sense of it. Business sense. IT sense. Common sense. http://p.sf.net/sfu/splunk-d2dcopy1 ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] A quick Q: zoom
Hi Lina, if you are looking for a way to "zoom in", use your right mouse button or type: move z, 10 The "zoom" command however will set the current view to cover the given atom selection (or all if no selection is given). http://pymolwiki.org/index.php/Move http://pymolwiki.org/index.php/Zoom Cheers, Thomas On 09/21/2011 04:47 PM, lina wrote: > Hi, > > I tried to zoom in, make it large, > > but seems not work, neither, > zoom > zoom complete 1 or 0 > zoom center > > Thanks for some suggestions, > > -- > Best Regards, > > lina -- Thomas Holder MPI for Developmental Biology -- All the data continuously generated in your IT infrastructure contains a definitive record of customers, application performance, security threats, fraudulent activity and more. Splunk takes this data and makes sense of it. Business sense. IT sense. Common sense. http://p.sf.net/sfu/splunk-d2dcopy1 ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] Write in a file the number of water at a distance from a protein surface
Hi Stephane,
you can select those waters using the "within" or "gap" selection
operators. "within" measures from the atom centre, whereas "gap" takes
the VDW radius into accout but selects everything beyond instead of
near. Have a look at those examples:
# use '... within ...'
select firstshell, solvent within 3.5 of polymer
# or use 'not (... gap ...)'
select firstshell, solvent and not (polymer gap 0.5)
# shows the selected water molecules as a sphere
show spheres, firstshell and elem O
# writes the results in a file
python
stored.out = open('/tmp/water-IDs.txt', 'w')
print >> stored.out, '## At 0.5 Ang of the protein surface there are',
print >> stored.out, cmd.count_atoms('firstshell and elem O'),
print >> stored.out, 'water molecules'
print >> stored.out, '## Water ID and resi are'
cmd.iterate('firstshell', 'print >> stored.out, ID, resi')
stored.out.close()
python end
http://www.pymolwiki.org/index.php/Selection_Algebra
http://www.pymolwiki.org/index.php/Iterate
Hope that helps,
Cheers,
Thomas
On 09/21/2011 11:03 PM, ABEL Stephane 175950 wrote:
> Hi All,
>
> I have simulated a protein in water cubic box and I would like to
> know how to show and obtain the number of water in the first shell of
> the protein (or at x Ang of the protein surface) using a pymol
> script. I can to do this using the pymol GUI but I would prefer that
> the script :
>
> - shows the selected water molecules as a sphere
> - and writes the results in a file with the water ID (i.e. residue
> number), for example like this:
>
> ## At x Ang of the protein surface there are XX water molecules
> ## Water ID are
>
> Thanks in advance for your help.
>
> Stephane
--
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Re: [PyMOL] help needed
Hi Anasuya, > I have around 19,200 unique PDB files. Each of them have one or more > ligands in it. For each ligand, I have to extract a zone which > contains complete residues within 4.5Angstroms of the ligand [ i.e. > ZONE1] and then extract another zone, which has complete residues > within 4.5Angstroms of ZONE1, [i.e.ZONE2] I need to store these two > zones in two separate .pdb files. > How can this be done? So far I have managed to extract ZONE1 for all > the PDB ID's and saved their corresponding .pdb files, but, I was > stuck at the next step. I guess you mean residues that have any atom within 4.5 Angstroms of the ligand? And for ZONE2 residues that have any atom within 9.0 Angstroms of the ligand, but are not already in ZONE1, right? # select first ligand select ligand, byres (first organic) # zone 1 select ZONE1, byres (ligand around 4.5) # zone 2 select ZONE2, byres (ligand around 9.0) and not ZONE1 # save to files save zone1.pdb, ZONE1 save zone2.pdb, ZONE2 Have a look at http://pymolwiki.org/index.php/Selection_Algebra Cheers, Thomas -- Thomas Holder MPI for Developmental Biology -- All of the data generated in your IT infrastructure is seriously valuable. Why? It contains a definitive record of application performance, security threats, fraudulent activity, and more. Splunk takes this data and makes sense of it. IT sense. And common sense. http://p.sf.net/sfu/splunk-d2dcopy2 ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
[PyMOL] comparison of distance operators
Hi all, since there were two "selection by distance" related questions this week, I put a table on the wiki that compares the different distance operators available in the PyMOL selection language. http://pymolwiki.org/index.php/Selection_Algebra#Comparison_of_distance_operators Cheers, Thomas -- Thomas Holder MPI for Developmental Biology Spemannstr. 35 D-72076 Tübingen -- All of the data generated in your IT infrastructure is seriously valuable. Why? It contains a definitive record of application performance, security threats, fraudulent activity, and more. Splunk takes this data and makes sense of it. IT sense. And common sense. http://p.sf.net/sfu/splunk-d2dcopy2 ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] how to change atom name
Hi Lina, atom properties can be changed with the "alter" command. It takes a selection (the atoms that should be modified) and an assignment expression in python syntax. Example: alter name H01, name="H22" It's important to quote strings in the assignment expression! More details and examples: http://pymolwiki.org/index.php/Alter Cheers, Thomas On 09/27/2011 09:35 AM, lina wrote: > Hi, > > how can I change the atom such as > > H01 to H22 in command > > Thanks ahead, > > -- > Best Regards, > > lina -- Thomas Holder MPI for Developmental Biology -- All the data continuously generated in your IT infrastructure contains a definitive record of customers, application performance, security threats, fraudulent activity and more. Splunk takes this data and makes sense of it. Business sense. IT sense. Common sense. http://p.sf.net/sfu/splunk-d2dcopy1 ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
[PyMOL] Fwd: Rendering 3D Surveys with Pymol
Dear PyMOL users, I don't know how many cavers are in this audience, but if you are curious what PyMOL can be used for apart from displaying molecules, have a look at the post below! Cheers, Thomas Original Message Subject: Rendering 3D Surveys with Pymol Date: Wed, 5 Oct 2011 18:04:13 +0100 From: Jarvist Moore Frost To: survex@... Dear Survex users, I thought you may be interested in a cludge I developed a few weeks ago to go from Survex .3d file to Pymol (a free, python based, 3D molecule viewer heavily used in the computational biology community). Pymol is a very nice tool to make pretty renders, an also has a number of 3D display modes (including anaglyphs, shutter glasses and cross-eye / wall-eye stereo). Code, and a link to a high-def youtube vid of the resulting ray trace movie is available here: http://migovec.posterous.com/cave-survey-survex-rendering-with-pymol As usual, the program started around midnight being as general as possible, then had ever more specific hacks hardcoded in. Never the less, it does colouring by depth on the HSV colour wheel, includes a set of cardinal axes, and estimates survey shot passage dimension based on the shot length. At some point, I'd quite like to add a chequerboard grid, and expose more details of the survey to pymol as attributes so that you can use the nice python tools to do fun things such as take over the colouring (for instance, a rainbow colour scheme based on survey trip?), expose the station labels, perform RMSD fits & distance calculations etc. I also have some python code that generates .svx files for DEM data from a text-based ASCII Tuple format (originally converted from some proprietary geo stats format). I've found that a mixture of grid based DEM data, as well as contour-like (or rather, traces) parallel lines over the mountain range. Drop me an email if you think this may be useful, and I'll package it up. May your surveys rotate in a manner truly sublime, Jarv -- Survex http://lists.survex.com/mailman/listinfo/survex -- All the data continuously generated in your IT infrastructure contains a definitive record of customers, application performance, security threats, fraudulent activity and more. Splunk takes this data and makes sense of it. Business sense. IT sense. Common sense. http://p.sf.net/sfu/splunk-d2dcopy1 ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] Rotation of a Protein
Hi Kanika, you can do this with the "rotate" command, without any additional script (like Michael already suggested). Note: for a dimer the the center of mass does not yet define an axis, my example uses an arbitrary axis on the mirror plane between the monomers. # get some homodimer fetch 3p8d, dimer, async=0 # create copies of one monomer create copy1, dimer and chain A create copy2, dimer and chain A create copy3, dimer and chain A create copy4, dimer and chain A # orient will put the (unweighted) center of mass in the middle of # the window and both monomers on the camera x-axis orient dimer # now rotate around the z-axis in camera space rotate z, 60, copy1 rotate z, 120, copy2 rotate z, 180, copy3 rotate z, 240, copy4 Have a look at: http://pymolwiki.org/index.php/Orient http://pymolwiki.org/index.php/Rotate If you need more fine control, go for Troels suggestion. There are also center-of-mass scripts on the PyMOLWiki. Cheers, Thomas kanika sharma wrote, On 10/09/11 07:47: > I need to rotate the second unit of the dimeric protein on the line > joining their center of masses. rotate it at a atep of 60 degrees till > 240 degree.. > > 2011/10/8 Troels Emtekær Linnet <mailto:tlin...@gmail.com>> > > If you need rotations around an line, instead of axis, check out > > http://www.pymolwiki.org/index.php/Rotkit > > Troels Emtekær Linnet > Karl-Liebknecht-Straße 53, 2 RE <http://maps.google.dk/> > 04107 Leipzig, Tyskland > Mobil: +49 1577-8944752 > > > > 2011/10/7 kanika sharma <mailto:ksharma...@gmail.com>> > > Hello everyone, > I Have a protein with 2 chains. > I have to rotate the second chain of the protein by > 60,120,180,240 degrees each. > Is there a script in PyMol that can do that? > > Best, > Kanika -- Thomas Holder MPI for Developmental Biology Spemannstr. 35 D-72076 Tübingen -- All the data continuously generated in your IT infrastructure contains a definitive record of customers, application performance, security threats, fraudulent activity and more. Splunk takes this data and makes sense of it. Business sense. IT sense. Common sense. http://p.sf.net/sfu/splunk-d2dcopy1 ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] How did they generate this figure
Hi Lina, this is volume representation of a density map. http://pymol.org/volume http://pymolwiki.org/index.php/Volume Cheers, Thomas lina wrote, On 10/09/11 16:13: > Hi, > > The picture in > > http://www.pymol.org/ > > is gorgeous, just wonder how did it produce such purple cloud effect? > > Thanks for any hint. -- Thomas Holder MPI for Developmental Biology Spemannstr. 35 D-72076 Tübingen -- All the data continuously generated in your IT infrastructure contains a definitive record of customers, application performance, security threats, fraudulent activity and more. Splunk takes this data and makes sense of it. Business sense. IT sense. Common sense. http://p.sf.net/sfu/splunk-d2dcopy1 ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] how can quickly make a fractional atoms into one
On 10/11/2011 10:16 AM, Tsjerk Wassenaar wrote:
> Not really a Pymol question, is it?
well, it's the segment identifier column, so you can do with PyMOL:
set pdb_retain_ids
load input.pdb
alter all, segi=''
save output.pdb
Cheers,
Thomas
> On linux you can use sed:
>
> sed '/^\(ATOM\|HETA\)/s/^\(.\{72\}\)/\1/' filein.pdb> fileout.pdb
>
> That means:
>
> /^\(ATOM\|HETA\)/ :: Match lines starting with ATOM or with HETA, and
> on those lines execute:
> s/^\(.\{72\}\)/\1/ :: Subsitute the first 72 characters and
> the following four by the first 72 and four spaces. '\1' refers to the
> 72 stored characters: \(.\{72\}\}
>
> Hope it helps,
>
> Tsjerk
>
>
> On Tue, Oct 11, 2011 at 9:59 AM, lina wrote:
>> Hi,
>>
>> I wish to change
>>
>> ATOM822 H01 PDB 1 32.103 36.531 -0.203 -0.11 0.02 .296
>> H
>> ATOM823 C12 PDB 1 34.140 35.147 -0.218 -0.18 -0.01 .122
>> C
>>
>> to:
>>
>> ATOM822 H01 PDB 1 32.103 36.531 -0.203 -0.11
>> 0.02 H
>> ATOM823 C12 PDB 1 34.140 35.147 -0.218 -0.18
>> -0.01 C
>>
>> only the last field.
>>
>> How can I quickly achieve it.
>>
>> Thanks,
--
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MPI for Developmental Biology
--
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Re: [PyMOL] Ray Trace Mode 1 and Labels
Hi Jack, you could render the labels to a separate image and assemble both images using Photoshop, Gimp, etc. set ray_trace_mode, 1 hide labels png image1.png, ray=1 set ray_trace_mode, 0 as labels set label_font_id, 7 set label_size, 20 set label_color, black set label_outline_color, white png image2.png, ray=1 Cheers, Thomas Tsjerk Wassenaar wrote, On 10/15/11 08:13: > Hi Jack, > > Unfortunately, that is not possible. The ray-trace mode affects the > behaviour/display of edges during raytracing, It's basically doing > edge detection, similar to what can be done in image processing > afterwards. So, it's similar to having an image and wanting to enhance > edges on some, but not on other objects, using photoshop or so. It's > impossible to do that automatically. > > In principle, it would be possible to modify the behaviour of the > raytracer, though. But I think it would require quite a bit of effort > coding that. But it could be interesting, also to use different line > colors for different selections :) > > Sorry, > > Tsjerk > > On Fri, Oct 14, 2011 at 3:38 PM, Jack Orford wrote: >> Is there a way to stop ray_trace_mode 1 putting an outline on labels? >> Although the outline looks quite good for the graphics, especially once they >> are printed, it makes the text look like blocky typewriter font. Any advice >> appreciated. >> >> Thanks -- Thomas Holder MPI for Developmental Biology Spemannstr. 35 D-72076 Tübingen -- All the data continuously generated in your IT infrastructure contains a definitive record of customers, application performance, security threats, fraudulent activity and more. Splunk takes this data and makes sense of it. Business sense. IT sense. Common sense. http://p.sf.net/sfu/splunk-d2d-oct ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] how to activate pymol from remote server
Hi Masataka,
do you have a X server running on Windows? It works for me with Cygwin
with installed X and GL libraries (but it's not very convenient because
quite slow).
ssh -Y linuxserver
pymol
If pymol is set up on that linux server correct and runs there by just
typing "pymol", it should as well from an X-forwarded ssh connection. No
need to export variables. Don't use the -R and -display arguments.
Cheers,
Thomas
grantaka36 wrote, On 10/14/11 07:35:
> Dear list members,
>
> Would you please tell me the way, how to activate pymol from remote
> server? i.e. how to start pymol in [S] by scripting from [C]
>
> --
> - From Windows client [C], SSH2 logging in to the remote server [S]
> (Linux x64, Ubuntu 10)
> - [S]
> -- installed PyMOL 1.2 r2, PATH includes '/usr/bin/pymol' so only
> 'pymol' entering enable to activate pymol GUI
> -- 'python' returns
> -- Python 2.6.6 (r266:84292, Sep 15 2010, 16:22:56)
> -- [GCC 4.4.5] on linux2
> - [C]
> -- first trying the following:
> PYMOL_PATH=/usr/bin/pymol
> HOST_ID=`uname -n`
> pymol -R -display:${HOST_ID}:0.0
> -- returns:
> Traceback (most recent call last):
> File "/usr/lib/python2.6/runpy.py", line 122, in _run_module_as_main
> "__main__", fname, loader, pkg_name)
> File "/usr/lib/python2.6/runpy.py", line 34, in _run_code
> exec code in run_globals
> File "/usr/lib/pymodules/python2.6/pymol/__init__.py", line 495, in
> invocation.parse_args(pymol_argv)
> File "/usr/lib/pymodules/python2.6/pymol/invocation.py", line 251,
> in parse_args
> options.stereo_mode = int(av.pop())
> IndexError: pop from empty list
> --
>
> By referring,
> http://www.pymolwiki.org/index.php/Launching_PyMOL#Launching_PyMOL_from_an_external_application
>> If PYMOL_PATH, LD_LIBRARY_PATH, and TCL_LIBRARY are correctly defined, then
>> you can launch PyMOL from an external Python program
> But I don't know which path to designate LD_LIBRARY_PATH and TCL_LIBRARY
>
>
> Regards,
> Masataka
--
Thomas Holder
MPI for Developmental Biology
Spemannstr. 35
D-72076 Tübingen
--
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definitive record of customers, application performance, security
threats, fraudulent activity and more. Splunk takes this data and makes
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Re: [PyMOL] how to activate pymol from remote server
Hi Masataka, > Sorry for lack of information, what all I'd like to do is: > - Scripting in [C] (on Cygwin or telnet over Command Prompt etc. > welcome), which includes login procedure to [S] by 'ssh -l (loginname) > (hostname)' > - pymol GUI open in [S]'s window (not in [C]) that was not clear before, I assumed the GUI should be opened on [C]. Then you do not need X-forwarding. Instead, on [S] there must be a running X from the same user and you need to know the DISPLAY variable there! ssh -l loginname hostname export DISPLAY=:0.0 # just as example! pymol -qip # this will listen for commands on the command line Also check: http://pymolwiki.org/index.php/Command_Line_Options http://pymolwiki.org/index.php/Launching_From_a_Script And yet to mention: Troels is right, it's not really a PyMOL issue. Try launching a simple program (like xclock) and if you are successful, then try the same with PyMOL. Cheers, Thomas -- Thomas Holder MPI for Developmental Biology -- All the data continuously generated in your IT infrastructure contains a definitive record of customers, application performance, security threats, fraudulent activity and more. Splunk takes this data and makes sense of it. Business sense. IT sense. Common sense. http://p.sf.net/sfu/splunk-d2d-oct ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] about Display CCP4 Maps
Hi Lina, do you already have any electron density or reflection file (*.map, *.mtz, ...) or do you want to create a "fake" density from your structure? It's not clear from your question. Cheers, Thomas On 10/25/2011 10:28 AM, lina wrote: > Hi, > > I went through the pymolwiki and cross this page: > > http://www.pymolwiki.org/index.php/Display_CCP4_Maps > > I have some questions: > > 1] do I need generate the map from ccp4 > > (I have already installed the ccp4i, but seems not easy to know how > to get the map) > > 2] For small molecular (ligand), the ccp4 is the best way to obtain > its electron density map? > > Seems those questions are not so-pymol-related, but I wish if someone > are familiar with this, can give me some advice?? > > Those questions might be easy, but to me at present it seems very confusing. > > Thanks with best regards, -- Thomas Holder MPI for Developmental Biology -- The demand for IT networking professionals continues to grow, and the demand for specialized networking skills is growing even more rapidly. Take a complimentary Learning@Cisco Self-Assessment and learn about Cisco certifications, training, and career opportunities. http://p.sf.net/sfu/cisco-dev2dev ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] about Display CCP4 Maps
On 10/25/2011 02:27 PM, lina wrote: > On Tue, Oct 25, 2011 at 7:56 PM, Thomas Holder > wrote: >> Hi Lina, >> >> do you already have any electron density or reflection file (*.map, *.mtz, >> ...) or do you want to create a "fake" density from your structure? It's not > > I don't have the reference electron density file. > > mainly wish to calculate a density map based on the structure? what you want is the "map_new" command in PyMOL. Have a look at this example: http://pymolwiki.org/index.php/Map_set#Detailed_Example And read the help for the map_new command (there is no wiki page yet): PyMOL>help map_new Cheers, Thomas -- Thomas Holder MPI for Developmental Biology -- The demand for IT networking professionals continues to grow, and the demand for specialized networking skills is growing even more rapidly. Take a complimentary Learning@Cisco Self-Assessment and learn about Cisco certifications, training, and career opportunities. http://p.sf.net/sfu/cisco-dev2dev ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] about Display CCP4 Maps
> And read the help for the map_new command (there is no wiki page yet): > PyMOL>help map_new now the wiki page is there: http://pymolwiki.org/index.php/Map_new Cheers, Thomas -- Thomas Holder MPI for Developmental Biology -- The demand for IT networking professionals continues to grow, and the demand for specialized networking skills is growing even more rapidly. Take a complimentary Learning@Cisco Self-Assessment and learn about Cisco certifications, training, and career opportunities. http://p.sf.net/sfu/cisco-dev2dev ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] Pymol: Cartoon representation for .pdb file with multible entries
Hi Alexander, by default PyMOL recognized secondary structure as the minimum consensus over all states. So if a residue is not recognized as helix or sheet in _all_ states, it will be assigned as loop. You might be happy with this: # type after loading the file dss state=1 For detailed explanation what values are valid for the "state" argument see the PyMOLWiki page: http://pymolwiki.org/index.php/Dss Cheers, Thomas On 10/26/2011 11:04 AM, Alexander Schulz wrote: > Hi everyone, > > I'm quite new to Pymol and I hope that I don't ask something that has > been answered several times before, but I didn't find anything about > this topic that could solve my problem. > > I've prepared a .pdb file containing one protein at different times in > the simulation. I'd like to prepare a video from this file, which is why > I'd like to keep everything in one .pdb file. > > When I select "cartoon" as a representation, the backbone is visualized > as a tibe (as always), but no secondary strucutres are recognized. When > I copy one of the snaphots out of the .pdb and open in seperately, the > secondary structure is shown correctly. > > How can I make Pymol show the structure of the multible states in one > file correctly? > > Thanks in advance for answers! > > Cheers, > Alexander -- Thomas Holder MPI for Developmental Biology -- The demand for IT networking professionals continues to grow, and the demand for specialized networking skills is growing even more rapidly. Take a complimentary Learning@Cisco Self-Assessment and learn about Cisco certifications, training, and career opportunities. http://p.sf.net/sfu/cisco-dev2dev ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] Putting a protein molecule into a grid and traversing through the grid
Hi Anasuya,
> how do i put a protein molecule inside a cube with x-axis spanning till the
> largest x-coordinate, y-axis spanning till the largest y-coordinate, and
> z-axis
> spanning till the largest z-coordinate?
>
> Once i do this, can i divide the larger cube(i.e. the one holding the entire
> protein) into smaller ones of lesser dimensions? Say, 5A x 5A x 5A?
I'm not aware of any straightforward solution for this. You could write
a python script that creates selections for each (sub)cube, but I guess
it will be a quite complex script. Have a look at
http://pymolwiki.org/index.php/SelInside which should cover all
necessary API functions.
> Once i generate these smaller cubes, is there a way via pymol, by which i can
> navigate through the protein molecule, (smaller)cube by (smaller)cube?
> As in, can pymol be used to tell me which residues are lying in which
> (smaller)
> cube and so on?
If you have selections for each cube, try this to lookup cubes that
contain atoms of residue number 10:
print cmd.get_names('public_selections', 0, 'resi 10')
> Can all this be done in a single pymol window/script?
> please let me know.
>
> Thanks
> -Anasuya
Cheers,
Thomas
--
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MPI for Developmental Biology
--
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demand for specialized networking skills is growing even more rapidly.
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Re: [PyMOL] Pymol movie
Hi Guridis, you need to store object matrices with the "mview store" command and use "rotate" instead of "turn" (object versus camera rotation). And you should avoid "B" as object name, because it's the b-factor keyword in the PyMOL selection language. mset 1x100 frame 1 mview store, object=molB frame 100 rotate x, 90, object=molB mview store, object=molB mplay Cheers, Thomas On 10/29/2011 09:23 PM, guri...@imbb.forth.gr wrote: > I want to make a movie with two objects.One object should remain > static(A) while the other(B) should rotate 90 degrees in x-axis. I > cannot keep object A immobile. > The commands i am using are: > >> show surface,A >> show surface,B >> super B,A >> mset 1x100 >> frame 1 >> scene 001,store >> mview store,scene=001 >> frame 100 >> hide surface,A >> turn x,90 > but i see object A turned >> show surface,A >> scene=002,store >> mview store,scene=002 > mplay > > and i see both objects to rotate 90 degrees with respect to their-axis. > How can i solve this problem? > > Guridis Georgios > Post-doc > IMBB,Crete,Greece -- Thomas Holder MPI for Developmental Biology -- Get your Android app more play: Bring it to the BlackBerry PlayBook in minutes. BlackBerry App World™ now supports Android™ Apps for the BlackBerry® PlayBook™. Discover just how easy and simple it is! http://p.sf.net/sfu/android-dev2dev ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] Put scripts in a svn folder
Hi Troels, your idea sounds good, indeed! We are working on a improved plugin system for PyMOL that supports fetching from repositories, versioning and metadata for plugins. It will handle "scripts" and "plugins" the same way. It will rather not include the subversion <> wiki interface as you suggested, but other functionality that will provide similar convenience. More news about that soon. Cheers, Thomas Troels Emtekær Linnet wrote, On 11/09/11 23:57: > Hi Pymolers. > > I sometimes find small errors in my scripts, which I then correct. > But then I get a little "sad", that now my "unfinished" script still > lives "out there". > > So I think, why is the pymolwiki scripts not under subversion control? > > Then authors could push corrections to their scripts to the subversion > directory, and users would get these corrections. > > I dont know if the pymol wiki could fetch and display the scripts from > the subversion folder. > > How does this idea sounds? > > Bes > Troels -- Thomas Holder MPI for Developmental Biology Spemannstr. 35 D-72076 Tübingen -- RSA(R) Conference 2012 Save $700 by Nov 18 Register now http://p.sf.net/sfu/rsa-sfdev2dev1 ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] Filled rings for cyclic molecules?
Hi Francis, > I'm looking for a way to get filled rings for cyclic molecules. An > example is the tetrapyrrole rings in heme. It's very similar in > representation to the nucleic acid ring mode (filled bases), but I'd > like it for an arbitrary ring . try this: set cartoon_ring_finder, 4 set cartoon_ring_mode, 3 as cartoon It's a bit hidden in the PyMOLWiki: http://pymolwiki.org/index.php/Examples_of_nucleic_acid_cartoons#Cartoon_ring_finder Cheers, Thomas -- Thomas Holder MPI for Developmental Biology Spemannstr. 35 D-72076 Tübingen -- RSA(R) Conference 2012 Save $700 by Nov 18 Register now http://p.sf.net/sfu/rsa-sfdev2dev1 ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] Editing of the pdb structure
Hi James, > Recently I've opened such topic but I didnt obtain answer on this > question so I try to paraphrase my task. Also I want to specify this > topic on questions lincked with the processing of pdbs. > > 1) I need to remove some elements fron my structure described as the > individual residue and place another element of the same size on the > place of the first element. > > In particular I have two different peptides both of wich have small cap > groups on C and N termi. ( attached) > > I need to remove all caps ( two caps FOR and ETA because there are two > identical chains in that structure) from the 1MAG structure and build > exactly on this place another cap groups wich I'd like to copy from the > second peptide ( KALP). the "Mutagenesis Wizard" comes in handy for editing caps. However it fails with non-standard amino acis as far as I know. Then you have to do it manually. These commands could be a good start for your task: http://pymolwiki.org/index.php/Remove http://pymolwiki.org/index.php/Fuse > So I'd like to change FOR- > ACE and ETA-> NH2 > twisely for the 1MAG dtructure hm, shouldn't it be the other way round? FOR is N-terminus and ETA is C-terminus? Cheers, Thomas -- Thomas Holder MPI for Developmental Biology Spemannstr. 35 D-72076 Tübingen -- RSA(R) Conference 2012 Save $700 by Nov 18 Register now http://p.sf.net/sfu/rsa-sfdev2dev1 ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] RMSD between two structures
Hi Martin,
is it the transform=0 argument what you are looking for?
http://pymolwiki.org/index.php/Align#PYMOL_API
x = cmd.align('foo', 'bar', transform=0)
print 'RMSD:', x[0]
About the "some kind of refinement": There are arguments "cutoff" and
"cycles" that control this behaviour.
Cheers,
Thomas
On 11/11/2011 02:46 PM, Martin Hediger wrote:
> Dear List.
> When aligning two structures using the PyMOL align command, one gets a
> final RMS value indicating some kind of "convergence" i would say. Can I
> somehow access the function for calculating this value directly from the
> pymol prompt without aligning?
>
> Thanks for hints
> Martin
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Re: [PyMOL] Torsion angles
Hi James, ramachandran plot for the *current* state can be created with the DynoPlot plugin: http://pymolwiki.org/index.php/DynoPlot It uses the API function "get_phipsi", which can calculate phi/psi angles for given states: cmd.get_phipsi(selection='(name ca)', state=-1) Torsion angles other than phi/psi can be calculated with the "get_dihedral" fuction: http://pymolwiki.org/index.php/Get_Dihedral You can also modify torsion angles with "torsion" and "set_dihedral": http://pymolwiki.org/index.php/Set_Dihedral http://pymolwiki.org/index.php/Torsion And you can modify torsion angles interactively using the mouse while in editing mode (pick one atom, then CTRL-Drag). Hope that helps. Cheers, Thomas On 11/16/2011 06:50 PM, James Starlight wrote: > Dear PyMol Users! > > I wounder to know about posible ways to plot for my structures different > torsion angles (phy, psi, chi ) on the ramachandran map via pymol. > > In particular I would like to obtain the next information > > 1- I d like to visualise and measure different torsions for my structure > and plot this values on the ramachandran plot > > 2- I'd like to make such measurements for the enssemble of the pdb > structures and plot on the ramachandran map values for each structure ( > by points or other markers) > > Finaly could you show me some tutorials wich could help me working with > torsions in pymol? > > Thanks for your help, > > James -- Thomas Holder MPI for Developmental Biology -- All the data continuously generated in your IT infrastructure contains a definitive record of customers, application performance, security threats, fraudulent activity, and more. Splunk takes this data and makes sense of it. IT sense. And common sense. http://p.sf.net/sfu/splunk-novd2d ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] Fwd: Torsion angles
Hi James, I've tested DynoPlot and have some questions 1- What are the meaning of the symbols in the ramachandran plot ? As I understood the tringle always for the Gly and the square for the Pro. What is the circle ? circle is for all other amino acids that are not Gly or Pro. Could I make some changges that the circle and squire were for any residues in the alpha- helix and betta sheet respectually ? sure, it requires little modifications in the script. 2- I'm intresting in working with the enssembles of the pdbs' So I 'd like to compare torsions of different residues for different structures in one plot. But when Ive done such comparison I noticed that residues from differen structures were marked on Ramachandran map with the one default colour. How I can specify that residued from different strctures were represented with different colour ? almost the same modification as for previous question. See attachment for modified script. It colors by atom color and has symbols for secondary structure (sheet=square, helix=triangle). 3- Finally I'd like to compare Chi-1 angle ( rotation on first bond beetween backbone and side chain groups) for my enssemble. How I could mark Chi-1 angle for all my structures and plot in on Rama map? I don't know of any easy solution to that, sorry. Maybe someone else? Cheers, Thomas -- Thomas Holder MPI for Developmental Biology DynoPlot.py Description: application/chimera -- All the data continuously generated in your IT infrastructure contains a definitive record of customers, application performance, security threats, fraudulent activity, and more. Splunk takes this data and makes sense of it. IT sense. And common sense. http://p.sf.net/sfu/splunk-novd2d___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] Fwd: Torsion angles
Hi James,
> Could you tell me in what strings the marker for the particular ss
> element is defined ( e.g I want to change from triangle to oval
> representation for alpha-helixes )?
look for this line:
mark = {'H': 'Tri', 'S': 'Rect'}.get(ss, self.mark)
I just updated the PyMOLWiki page with the modifications (but markers by
secondary structure are disabled by default to not change the previous
behaviour).
http://pymolwiki.org/index.php/DynoPlot
Cheers,
Thomas
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Re: [PyMOL] Expose PyMOL API
Hi Martin,
the recommended way is to use PyMOL as your python interpreter, so
instead of:
python file.py
do this:
pymol -cqr file.py
However, launching a PyMOL process from a python terminal as you
suggested is also possible. Have a look at Example 2 of
http://pymolwiki.org/index.php/Launching_From_a_Script , the important
lines are those:
import pymol
pymol.pymol_argv = ['pymol','-qc']
pymol.finish_launching()
Cheers,
Thomas
Martin Hediger wrote, On 11/22/11 09:26:
> Dear PyMOL List
> It comes up once in a while, is it possible to use PyMOL features from
> outside of PyMOL? An example, the below is a script (inspired by Thomas
> Holder) which saves down to disk all amino acids of a protein structure
> into separate PDB files.
>
> # *
> from pymol import cmd
> from pymol import stored
> from pymol.exporting import _resn_to_aa as one_letter
> # *
> def seq(state, selection="name ca or resn hoh or resn lig"):
> print "Generating seqs."
> cmd.select("prot", selection)
> while cmd.pop("_tmp", "prot"):
> cmd.iterate("_tmp", "stored.x=(resn,resv)")
> #print stored.x[0], stored.x[1]
>
> # Special case 1: Waters.
> if stored.x[0] == 'HOH':
> filename = 'seq-x%s-%s.pdb' % (stored.x[1], state)
> # Special case 2: Substrate.
> elif stored.x[0] == 'LIG':
> filename = 'seq-x%s-%s.pdb' % (stored.x[1], state)
> # Other: protein back-bone.
> else:
> filename = 'seq-%s%d-%s.pdb' % (one_letter[stored.x[0]].lower(),
> stored.x[1], state)
> cmd.save(filename, "byres _tmp")
> cmd.delete('_tmp prot')
>
> cmd.extend('seq', seq)
> # -
>
> Is it possible to somehow include this in a Python script, and running
> it from the command line? If not, why?
>
>
> Thanks for any feedback.
--
Thomas Holder
MPI for Developmental Biology
Spemannstr. 35
D-72076 Tübingen
--
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contains a definitive record of customers, application performance,
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Re: [PyMOL] Work with pdb's enssemble
Hi James, paste the following piece of code into the PyMOL command line. It does more or less the same as "A > align > all to this" but with "super" instead of "align". names = cmd.get_object_list() for name in names[1:]: cmd.super(name, names[0], object='aln') The first object in the list will be used as reference structure. The "aln" object which will be created represents the "all to reference" alignment. Cheers, Thomas James Starlight wrote, On 11/22/11 10:11: > By the way also I've tried use super_all script wich can do multiple > alignment via Super command > pldserver1.biochem.queensu.ca/~rlc/work/ > <http://pldserver1.biochem.queensu.ca/~rlc/work/>pymol/super_all.py > > but as the consequense the resulted sequence alignment in CGO in > pair-wise manner. How could I make something like this super all but for > just one reference ( similar to the align ) so I'd like to obtain > multiple sequence alignment on one reference based on the multiple > structure alignment. > > Thanks > > James > > 2011/11/21 James Starlight <mailto:jmsstarli...@gmail.com>> > > Jason, > > but as I've understood super did alignment only for two structures, > Is there any way to do the same operation for ensemble ? (for CE as > I understood this could be done by alignto command but it lack for > seq alignment iin this case) > > > > James > > 2011/11/21 Jason Vertrees <mailto:jason.vertr...@schrodinger.com>> > > Hi James, > > > set fetch_host, pdbe > > Your PyMOL looks to be outdated. This was added to the > open-source in > v1.3r1, I think. > > > By the way could you also help me with the alignment of my > structure ( I've > > posted this question today at this topic). I think that I > should use the > > combination of the structure alignment ( like CEalign) with > the common seq. > > alignment but I dont know exactly how :( > > You should use the 'cealign' or 'super' commands to do this. Cealign > uses only structure, whereas 'super' uses both structure and > sequence. > Please continue to post questions like this to the list for best > results: there are some very smart people on our PyMOL list. > > Cheers, > > -- Jason -- Thomas Holder MPI for Developmental Biology Spemannstr. 35 D-72076 Tübingen -- All the data continuously generated in your IT infrastructure contains a definitive record of customers, application performance, security threats, fraudulent activity, and more. Splunk takes this data and makes sense of it. IT sense. And common sense. http://p.sf.net/sfu/splunk-novd2d ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] Expose PyMOL API
Hi Martin,
I don't have a Mac so I can't test this, sorry.
I suspect that the _cmd module is built into the MacPyMOL executable.
This would imply that you cannot use MacPyMOL like in the
"Launching_From_a_Script" examples. Maybe someone of the MacPyMOL users
knows more?
Cheers,
Thomas
Martin Hediger wrote, On 11/22/11 13:14:
> Thanks Thomas for the reply. I tried it under Mac OS X 10.5.8.
>
> me @ ~/PROG_TEST $ python
> Python 2.6.5 (r265:79359, Mar 24 2010, 01:32:55)
> [GCC 4.0.1 (Apple Inc. build 5493)] on darwin
> Type "help", "copyright", "credits" or "license" for more information.
> imported numpy
> from PyQt4.QtGui imported *
> from PyQt4.QtCore imported *
>>>> import os, sys
>>>> import readline
>>>> import rlcompleter
>>>> readline.parse_and_bind('tab: complete')
>>>> moddir='/Applications/PyMOLX11Hybrid.app/pymol/modules'
>>>> sys.path.insert(0, moddir)
>>>> os.environ['PYMOL_PATH'] = os.path.join(moddir, 'pymol/pymol_path')
>>>> import pymol
> Traceback (most recent call last):
> File "", line 1, in
> File
> "/Applications/PyMOLX11Hybrid.app/pymol/modules/pymol/__init__.py", line
> 472, in
> import _cmd
> ImportError: No module named _cmd
>>>> import pymol
>
>
> What could be the problem? Could it be that the 'pymol/pymol_path' call
> is not exactly right? In the modules/pymol directory, there is a module
> 'pymol/launch_pymol', but I have a similar error ("No module named
> _cmd") when I try to import it.
> Martin
>
>
>
>
>
>
> Am 22.11.11 09:47, schrieb Thomas Holder:
>> Hi Martin,
>>
>> the recommended way is to use PyMOL as your python interpreter, so
>> instead of:
>>
>> python file.py
>>
>> do this:
>>
>> pymol -cqr file.py
>>
>>
>> However, launching a PyMOL process from a python terminal as you
>> suggested is also possible. Have a look at Example 2 of
>> http://pymolwiki.org/index.php/Launching_From_a_Script , the important
>> lines are those:
>>
>> import pymol
>> pymol.pymol_argv = ['pymol','-qc']
>> pymol.finish_launching()
>>
>> Cheers,
>> Thomas
>>
>>
>> Martin Hediger wrote, On 11/22/11 09:26:
>>> Dear PyMOL List
>>> It comes up once in a while, is it possible to use PyMOL features
>>> from outside of PyMOL? An example, the below is a script (inspired by
>>> Thomas Holder) which saves down to disk all amino acids of a protein
>>> structure into separate PDB files.
>>>
>>> # *
>>> from pymol import cmd
>>> from pymol import stored
>>> from pymol.exporting import _resn_to_aa as one_letter
>>> # *
>>> def seq(state, selection="name ca or resn hoh or resn lig"):
>>> print "Generating seqs."
>>> cmd.select("prot", selection)
>>> while cmd.pop("_tmp", "prot"):
>>> cmd.iterate("_tmp", "stored.x=(resn,resv)")
>>> #print stored.x[0], stored.x[1]
>>>
>>> # Special case 1: Waters.
>>> if stored.x[0] == 'HOH':
>>> filename = 'seq-x%s-%s.pdb' % (stored.x[1], state)
>>> # Special case 2: Substrate.
>>> elif stored.x[0] == 'LIG':
>>> filename = 'seq-x%s-%s.pdb' % (stored.x[1], state)
>>> # Other: protein back-bone.
>>> else:
>>> filename = 'seq-%s%d-%s.pdb' %
>>> (one_letter[stored.x[0]].lower(), stored.x[1], state)
>>> cmd.save(filename, "byres _tmp")
>>> cmd.delete('_tmp prot')
>>>
>>> cmd.extend('seq', seq)
>>> # -
>>>
>>> Is it possible to somehow include this in a Python script, and
>>> running it from the command line? If not, why?
>>>
>>>
>>> Thanks for any feedback.
--
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Spemannstr. 35
D-72076 Tübingen
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Re: [PyMOL] measuring helix angle
Hi Hena, you don't need to edit the script. If you paste the script to a file named script.py, then you can continue by typing into the PyMOL command line: run script.py angle_between_helices chain A and resi 6-20, chain A and resi 26-39 Cheers, Thomas Hena Dutta wrote, On 11/22/11 20:50: > Hi, > > Can anyone guide me how to use the pymol script to calculate the angle > between two helices? > Where and how to edit the script? I have 2 helices in a pdb file as follows: > > protein.pdb > hel1 is chain A: 6-20 > hel2 is chain A: 26-39 > > Thanking you in advance... > Hena -- Thomas Holder MPI for Developmental Biology Spemannstr. 35 D-72076 Tübingen -- All the data continuously generated in your IT infrastructure contains a definitive record of customers, application performance, security threats, fraudulent activity, and more. Splunk takes this data and makes sense of it. IT sense. And common sense. http://p.sf.net/sfu/splunk-novd2d ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] creating PDB structure
Hi James,
check this PyMOLWiki page: http://pymolwiki.org/index.php/Fab
However, the "fab" command does not take user defined phi/psi angles,
only 4 predefined conformations ("ss" argument). User defined phi/psi
can be handled by these scripts:
http://pymolwiki.org/index.php/CreateSecondaryStructure
http://pldserver1.biochem.queensu.ca/~rlc/work/pymol/#model
Cheers,
Thomas
James Starlight wrote, On 11/23/11 11:43:
> Dear PyMol Users!
>
> I wounder to know about possible ways of creation of the peptide
> structures via PyMol Builder module. In particular I need create a
> linear structure of my protein ( with fixed phi and psi angles) for
> futher folding molecular dynamics simulation of that peptide. But in
> builder module I found only helix and sheet conformations for each aa.
> residue. How I can specify desired values for both torsion angles ?
>
> Also I'd like to know is there any module for pymol wich could be used
> for obtaining linear unfolded structure for the defined sequence or
> folded protein ( in pdb) ?
>
> Thanks,
>
>
> James
--
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Re: [PyMOL] creating PDB structure
Hi James, > C could not find if all those scripts are able to make CAPS on the residues > > but if it's not possible Iwant to add some CAP group ( e.g ACE to the N > term) via builder module. So I've chose ACE residue from that module and > obtained message > > pick location to attach ace > > how now i could specify exactly location of that attachment if i want > that ACE just be the first residue in my pdb ( linked with the actual > first residue on the N term )? display your protein as lines or sticks and just pick the N atom with the mouse. Or, prior to clicking the "Ace" button type this: edit first (name N) Cheers, Thomas -- Thomas Holder MPI for Developmental Biology Spemannstr. 35 D-72076 Tübingen -- All the data continuously generated in your IT infrastructure contains a definitive record of customers, application performance, security threats, fraudulent activity, and more. Splunk takes this data and makes sense of it. IT sense. And common sense. http://p.sf.net/sfu/splunk-novd2d ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] H-bonds representation
Hi James, > As I've understood there are no posible ways to represent H-bonds in > proteins in explicit manner. So I'm looking for possible way to do it > via some plugin or another way. PyMOL can find polar contacts and represent them as dashed lines. You don't need any extra plugin. http://pymolwiki.org/index.php/Displaying_Biochemical_Properties#Hydrogen_bonds_and_Polar_Contacts It's the "distance" command with mode=2 that does the job. http://pymolwiki.org/index.php/Distance There are various dash_* settings that control the appearance of the dashed lines: http://pymolwiki.org/index.php/Dash_Length http://pymolwiki.org/index.php/Dash_color (and many others...) > In particular I need > 1) to visualize H-bonds in some structural motifs like coiled coil wich > are dimers of alpha helices ( so I'd like to see H-bonds beetwen > separate alpha helices ) Try this (lets say helix 1 is resi 1-100 and helix 2 is resi 101-200): # add hydrogens (if not already present) h_add donors # detect polar contacts distance hb_coiled_coil, resi 1-100, resi 101-200, mode=2 > 2) to visualize H-bonds in spicified SS structure ( e.g during formation > of the alpha helices)- so I'd like to see H-bonds beetwen amide and > Carboxy groups in specified amino acid sequence. just like example 1, but with other selections: distance hb_backbone, name O, name N, mode=2 > 3) Finally I'd like to check H-bond in protein-ligand complex ( beetwenn > specified ligand groups as well as some amino acid residues of the > ligand binding pocket) just like before, but with ligand as selection 1 and receptor as selection 2. Hope that helps. Cheers, Thomas -- Thomas Holder MPI for Developmental Biology Spemannstr. 35 D-72076 Tübingen -- All the data continuously generated in your IT infrastructure contains a definitive record of customers, application performance, security threats, fraudulent activity, and more. Splunk takes this data and makes sense of it. IT sense. And common sense. http://p.sf.net/sfu/splunk-novd2d ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] H-bonds representation
Hi James, most trivial manner: as cartoon show sticks, resn LEU+ILE+VAL set cartoon_side_chain_helper and eventually something like this: show spheres, resn LEU+ILE+VAL and not name N+O+C set sphere_transparency, 0.5 Cheers, Thomas On 11/28/2011 02:58 PM, James Starlight wrote: > Another question also linked with the non-covalent interaction. > > In particular I wounder to know how i Could represent all hydrophobic ( > Ley Ile Val etc) sidechains in my proteins in most trivial manner? I'd > like to represent the hydrophobic core of the proteins made from those > residues. > > Thanks, > > James -- Thomas Holder MPI for Developmental Biology Spemannstr. 35 D-72076 Tübingen -- All the data continuously generated in your IT infrastructure contains a definitive record of customers, application performance, security threats, fraudulent activity, and more. Splunk takes this data and makes sense of it. IT sense. And common sense. http://p.sf.net/sfu/splunk-novd2d ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] RMSD between two structures
One should emphasize that this alignment is a *sequence* alignment in case of the "align" command. Cheers, Thomas On 11/30/2011 11:19 AM, Tsjerk Wassenaar wrote: > Hi Martin, > > It does an alignment, finding matching pairs of atoms, removing > outliers and calculating the RMSD over the remaining matches. > > Cheers, > > Tsjerk > > On Wed, Nov 30, 2011 at 11:05 AM, Martin Hediger wrote: >> How does PyMOL calculate the RMSD between two structures where the >> number of atoms is different? >> Martin -- Thomas Holder MPI for Developmental Biology Spemannstr. 35 D-72076 Tübingen -- All the data continuously generated in your IT infrastructure contains a definitive record of customers, application performance, security threats, fraudulent activity, and more. Splunk takes this data and makes sense of it. IT sense. And common sense. http://p.sf.net/sfu/splunk-novd2d ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] Installation PyMOL failure in Linux (CentOS)
Hi Masataka, this is really a weird problem. I have none of CentOS, gcc45 or python2.4 so can't really simulate any of your setup. But from the message I would say it's related to the C preprocessor rather than the compiler or python itself. Also, a google search pointed me to this messages: http://www.mail-archive.com/pymol-users@lists.sourceforge.net/msg05501.html http://archives.neohapsis.com/archives/linux/immunix/2004-q1/0011.html The fact that it says macro "fprintf" suggests that fprintf has been replaced by a preprocessor macro, which may interfere with the macro that PyMOL defines in this case I guess. You do compile with -D_FORTIFY_SOURCE=2, could you remove that? If it does not help, check if you have FormatGuard installed. Cheers, Thomas grantaka36 wrote, On 12/05/11 02:50: > Hi, Marius, Troels and David, > > I appreciate very much for guiding, tried in three ways but no success > currently. > > - I also think some difference on distributions (CentOS 5 here,) trapped at >> function 'IsosurfGetRange' > Does anyone have information to workaround? > - Do you think if any dependency on Python version (2.4.3 here)? > > Attached '20111205_script_and_error.zip' is for information sharing: > - 'install_pymol.sh' : followed by below, some package name modified for > CentOS > http://www.pymolwiki.org/index.php/Linux_Install#Ubuntu.2FMint_Compile_and_install_with_MPEG_support > - 'install_pymol_sh_error.txt' >> layer0/Isosurf.c:2197:1: error: unterminated argument list invoking macro >> "fprintf" >> layer0/Isosurf.c: In function 'IsosurfGetRange': > > - 'install_pymol_gcc45.sh' - aiming to use default installed gcc4.5 > instead of 4.4 > - 'install_pymol_gcc45_sh_error.txt' >> layer0/Isosurf.c: In function 'IsosurfGetRange': >> layer0/Isosurf.c:2197:0: error: unterminated argument list invoking macro >> "fprintf" > > - 'compile_pymol.sh' : again by initial trying > http://www.pymolwiki.org/index.php/Linux_Install#Install_from_source > - 'compile_pymol_sh_error.txt' >> layer0/Isosurf.c: In function 'IsosurfGetRange': >> layer0/Isosurf.c:2197:0: error: unterminated argument list invoking macro >> "fprintf" > > > Regards, > Masataka > > > 2011/12/3 David Hall : >> the builds on >> https://build.opensuse.org/package/show?package=pymol&project=devel%3Alanguages%3Apython >> for opensuse 11.3 and 11.4 use gcc4.5 successfully. I blame ubuntu or >> linux mint. >> >> -David >> >> On Dec 2, 2011, at 10:21 AM, Marius Retegan >> wrote: >> >>> Could you please specified what exactly did the gcc 4.5 broke in Pymol? >>> Maybe this is not the case for every linux distribution. >>> >>> Cheers, >>> Marius >>> >>> 2011/12/2 Troels Emtekær Linnet : >>>> Try Following this script. >>>> >>>> http://www.pymolwiki.org/index.php/Linux_Install#Ubuntu.2FMint_Compile_and_install_with_MPEG_support >>>> >>>> Please report if you are successful. >>>> It would be interesting to see how it works on CentOS >>>> >>>> /T >>>> >>>> >>>> >>>> 2011/12/2 grantaka36 >>>>> Referring the following, I'm trying to install PyMOL 1.4.1 with >>>>> attached 'compile_pymol.sh', but no success. Would you please help to >>>>> finish installation, or give me some advices? If information >>>>> inadequate, please contact me. >>>>> >>>>> http://www.pymolwiki.org/index.php/Linux_Install >>>>> - Requirements >>>>> - Get latest Source from SVN >>>>> - Compile and install >>>>> - Problems - "gcc-4.5 is broken for pymol install, use gcc-4.4" >>>>> -- My distribution has gcc4.5, so installed /usr/bin/gcc44, >>>>> /usr/bin/g++44. >>>>> >>>>> Attached 'install_error.txt' gathers some information: >>>>> - Original module files are in $HOME/install_module/pymol-archive >>>>> - Intends to install in $HOME/pymol-svn >>>>> - Original log has some Japanese messages so I added /* means ... */ >>>>> >>>>> Regards, >>>>> Masataka -- Thomas Holder MPI for Developmental Biology Spemannstr. 35 D-72076 Tübingen -- All the data continuously generated in your IT infrastructure contains a definitive record of customers, application performance, security threats, fraudulent activity, and more. Splunk takes this data and makes sense of it. IT sense. And common sense. http://p.sf.net/sfu/splunk-novd2d ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
[PyMOL] frames around code in PyMOLWiki
can we have frames around code blocks like before? Or am I the only one who misses them? Cheers, Thomas -- Thomas Holder MPI for Developmental Biology Spemannstr. 35 D-72076 Tübingen -- All the data continuously generated in your IT infrastructure contains a definitive record of customers, application performance, security threats, fraudulent activity, and more. Splunk takes this data and makes sense of it. IT sense. And common sense. http://p.sf.net/sfu/splunk-novd2d ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
