applications that read PDB files, but may break PDB file loading in other
> applications which don't support it. PyMOL always wrote duplicated connect
> records and the new setting allows you to switch that off.
>
> Cheers,
> Thomas
>
> On 18 Aug 2014, at 15:04, Hong
Hi,
I am using PyMOL 1.7 open source version in Ubuntu 14.04.
I wanted to try a new setting pdb_conect_nodup in pymol 1.7.
It is listed as new features available for both "Open Source and Incentive"
at:
http://pymol.org/features#v1.7
when I set it to on, I got:
"Setting-Warning: not supported i
I found a previous report on the same issue and it is fixed in the svn:
http://www.mail-archive.com/pymol-users@lists.sourceforge.net/msg11581.html
I guess I will try the updated version.
Hongbo
--
October Webinars: Code
Hi,
I have downloaded PyMOL v1.6.0.0 from sourceforge and installed it on my
Ubuntu 12.04. It works very well. Recently I noticed there is a problem
when selecting residues from the sequence panel (Display -> Sequence). If I
select multiple residues using mouse in the sequence panel, only the firs
rd to
the DSSP plugin. The plugin will invoke DSSP to assign secondary
structures for each object in your specified input.
hongbo zhu
On 19.10.2011 4:15, lina wrote:
> On Wed, Oct 19, 2011 at 6:43 PM, Hongbo Zhu
> wrote:
>> I just ran dssp plugin for an NMR structure (randomly chosen
I just ran dssp plugin for an NMR structure (randomly chosen, 2LE0). In
my case, secondary structures are calculated for all the 10 states of
2LE0. The plugin can also update color and secondary structures for all
the 10 states of the NMR structure. I did not have to choose one state
and run, a
I have a slightly different answer using (almost:) only PyMOL commands:
# take 1acb as example
fetch 1acb, async=0
import numpy
# center is [x0,y0,z0]
x0,y0,z0=[1,2,3]
alldist = []
iterate_state 1, 1acb,
alldist.append(numpy.sqrt(numpy.sum([(x-x0)**2,(y-y0)**2,(z-z0)**2])))
# assign dist to b-
:
fetch pdb1 pdb2 pdb3 pdb4 pdbN
On 06/29/2011 03:56 PM, Hongbo Zhu wrote:
> would python module multiprocessing meet your need?
> is that simultaneity the kind of simultaneity you want?
>
> On 06/29/2011 03:36 PM, leila karami wrote:
>> Dear Hongbo
>>
>> very thanks
ailing 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
--
Hongbo ZHU
Postdoctoral Researcher
Structural Bioinformatics
Technische Universität Dresden
Biotechnology Center
Ta
users
> Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
--
Hongbo ZHU
Postdoctoral Researcher
Structural Bioinformatics
Technische Universität Dresden
Biotechnology Center
Tatzberg 47/49
01307 Dresden, Germany
Tel: +49 (0) 351 463-40083
Fax: +49 (0) 351 463-40087
E-M
et/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
--
Hongbo ZHU
Postdoctoral Researcher
Structural Bioinformatics
Technische Universität Dresden
Biotechnology Center
Tatzberg 47/49
01307 Dresden, Germany
Tel: +49 (0) 351 463-40083
Fax:
other people recently asked about the ligand surface, and Jason gave the
following answer on 02 Apr. Hope it is also helpful to your glycan case.
-
Hi Peter,
In order to do this you either need to extract the ligand to its own
object or unset the ignore flag on "rep
rall TCO of any competing solution.
> http://p.sf.net/sfu/whatsupgold-sd
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> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
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Hi, Harry,
I am curious. How do you merge objects resulting from >>distance<< ? Do
you mean to "group" them? If so, you can use ungroup command to, well,
ungroup them. But if the merged object is generated using a CGO, I doubt
you can unmerge the CGO object. But I don't know dash CGOs, either.
you can write your own loop in python to implement the function.
fh = open(pdbfilename)
coords =
numpy.array([[float(line[30:38]),float(line[38:46]),float(line[46:54])]
for line in fh.readlines() if line.startswith('ATOM ') or
line.startswith('HETATM')])
fh.close()
extent = (numpy.min(coords,a
estions are always welcome!
cheers,hongbo
On 04/12/2011 04:22 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:
>
>
011 05:16 PM, Thomas Holder wrote:
> 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
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
Hi, Martin,
how about this:
http://www.pymolwiki.org/index.php/Symmetry_Axis
also check out the script drawing X, Y, and Z reference axes by Robert:
http://pldserver1.biochem.queensu.ca/~rlc/work/pymol/axes_cyl.py
hope it helps,
hongbo
On 04/08/2011 04:29 PM, Martin Hediger wrote:
> Dear all
>
s.
>
> the CRYST1 record is sufficient for generating symmetry mates, so
> pymol most likely does not read REMARK 290.
>
> Cheers,
>Thomas
>
--
Hongbo ZHU
--
Enable your software for Intel(R)
ages/CASTpyMOL_v2.pyc
>
> I have pymol 1.3 (windows7 64bit)
>
> and I got:
>
> ImportError: Bad magic number in C:\Program Files
> (x86)\PyMOL\PyMOL/modules\pmg_tk\startup\CASTpyMOL_v2.pyc
> Error: unable to initialize plugin 'CASTpyMOL_v2'.
>
> Does a
.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
--
Hongbo ZHU
Postdoctoral Researcher
Structural Bioinformatics
Technische Universität Dresden
Biotechnology Center
Tatzberg 47/49
01307 Dresden, Germany
Tel: +49 (0) 351 46
Dear PyMOLers,
As many of you might be aware of, MSMS is an excellent program developed
by Michel Sanner for computing protein surface, especially solvent
excluded surface (SES). (see http://mgltools.scripps.edu/packages/MSMS/
). Due to its outstanding usability, Robert Campbell had already
pr
/lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
--
Hongbo ZHU
Postdoctoral Researcher
Structural Bioinformatics
Technische Universität Dresden
Biotechnology Center
Tatzberg 47/49
01307 Dresden,
>> I suppose.
>>>
>>> Jellyrolls (http://www.cathdb.info/cathnode/2.60.120) are an example
>>> of this, I seem to remember, as they have long strands that cross from
>>> one sheet to another. As the sheets are in a sandwich, the strand will
>>&g
o the source.
>
> I think this definition is useful when color e.g. beta-barrel, but
> definitely includes ambiguity.
> Then, how about defining front side as the C-beta direction of
> starting residue of sheet?
>
>
> Cheers,
>
> Keitaro
>
> 2011年3月8日火曜日 Hongbo Zhu
the same strand can have half of it facing the light source and
the other half turned opposite to the source.
>
> But I think any definition is ok if front and back could be alternated
> easily by user operation.
sounds like an interesting operation, though.
>
>
> Cheers,
>
&g
-
>> What You Don't Know About Data Connectivity CAN Hurt You
>> This paper provides an overview of data connectivity, details
>> its effect on application quality, and explores various alternative
>> solutions.
m the the simplified selection expression.
>
> Cheers,
>
> Tsjerk
>
> On Wed, Mar 2, 2011 at 11:06 AM, Hongbo Zhu
> wrote:
>> I believe the confusion is caused by the simplified selection expression
>> in PyMOL (and some other visualization tools as well). I r
: Index, Search& Analyze Logs and other IT data in
>> Real-Time with Splunk. Collect, index and harness all the fast moving IT
>> data
>> generated by your applications, servers and devices whether physical,
>> virtual
>> or in the cloud. Deliver compliance at lower cost and
in new business
> insights. http://p.sf.net/sfu/splunk-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.co
+++
>
> Finish: time:16 sec
>
> +++++++
+++
>
> Finish: time:16 sec
>
> +++++++
Hi Cun Zhuang,
I think what you need to do is adding one line in the end of mathexpr.py:
cmd.extend("SelectByExpr",Select)
then you can type in command line
SelectByExpr x>5
see the following page for more explanation:
http://www.pymolwiki.org/index.php/Simple_Scripting
hongbo
On 12/13/2010
_
> 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
--
Dr. Hongbo ZHU
Postdoctoral Researcher
Structural Bioinformatics
T
If you mean the GUI of PyMOL, I guess you can change your screen
resolution and then make a screenshot.
hongbo
On 11/23/2010 02:52 PM, David Hall wrote:
> Dear all,
>
> I want to take high resolution screenshots of the PyMol interface for
> figures in a methods paper where PyMol is used for some
ill change as atoms are added
or deleted. Whenever possible, use integral atom identifiers
instead of indices. "
I suppose you should use >>RANK<<, if you like to "find a way to get the
'linenumber-dependent' index of an atom".
cheers,
Hongbo Zhu
On 11
You can solve it by adding the following line in the msms_pymol.py you
downloaded from Robert's page to line 133, right before msms_cmd is defined.
if msms_path.startswith('C:/'): msms_path = '\"%s\"' % (msms_path,)
Basically, your problem was caused by the whitespace in the path to the
MS
can not change its color on the fly.
best,
Hongbo Zhu
On 05/11/2010 04:49 PM, pymol-users-requ...@lists.sourceforge.net wrote:
> Message: 3
> Date: Tue, 11 May 2010 09:04:51 -0400
> From: Jason Vertrees
> Subject: Re: [PyMOL] drawing a cloud of points?
> To: Jose Borreguero
>
rface. You can install it from PyMOL menu
Plugin-->Manage Plugins-->Install. You can use the plugin to invoke MSMS
for either a pdb file or a selection in PyMOL. It has been tested on
PyMOL 0.98 and 1.20.
best regards,
Hongbo Zhu
Hi Sujuan, Given that this is my script, I'll answe
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