Re: [PyMOL] option pdb_conect_nodup unavailable in OpenSource version 1.7

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, Hongbo Zhu 朱宏博 hongbo.zhu...@gmail.com wrote: Hi, I am using PyMOL 1.7 open source version in Ubuntu

[PyMOL] Residue selection problem in PyMOL 1.6

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

Re: [PyMOL] Residue selection problem in PyMOL 1.6

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

Re: [PyMOL] regarding the dssp plugins

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,

Re: [PyMOL] Help for surface coloring

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

Re: [PyMOL] how to load two separate pdb files simultaneously

-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-Mail: hongbo.zhu at biotec Webpage: www.biotec.tu

Re: [PyMOL] how to load two separate pdb files simultaneously

://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 -- Hongbo ZHU

Re: [PyMOL] how to load two separate pdb files simultaneously

/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: +49 (0) 351 463-40087 E-Mail

Re: [PyMOL] how to load two separate pdb files simultaneously

: 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 for your attention. None of fetch 1A00

Re: [PyMOL] glycan surface

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

Re: [PyMOL] Get Protein Dimension

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 =

Re: [PyMOL] Hiding individual dash/distance objects within a merged-dash object

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.

Re: [PyMOL] How to color in a different way different helix types?

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: http://www.pymolwiki.org/index.php/DSSP This plugin invokes DSSP

Re: [PyMOL] How to color in a different way different helix types?

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 PM, Hongbo Zhu hongbo@biotec.tu-dresden.de wrote: Hi

Re: [PyMOL] How to color in a different way different helix types?

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

Re: [PyMOL] Display coordinate vectors

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

Re: [PyMOL] symexp

://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 -- Hongbo ZHU

Re: [PyMOL] CASTp plugin

(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 anyone have any idea how to fix this issue? Thanks, Tomas -- Hongbo ZHU Postdoctoral Researcher

Re: [PyMOL] symexp

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) Active Management Technology to meet the growing manageability

[PyMOL] New plugin: MSMS plugin for PyMOL

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

Re: [PyMOL] plugin dependencies

___ 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 -- Hongbo ZHU Postdoctoral Researcher

Re: [PyMOL] Different color on each side of strand

. 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 hongbo@biotec.tu-dresden.de: Hi, Keitaro, On 03/08/2011 03:11 AM, Keitaro Yamashita wrote: Dear Hongbo, For example, user can put something like

Re: [PyMOL] Different color on each side of strand

/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-Mail: hongbo.zhu at biotec Webpage: www.biotec.tu

Re: [PyMOL] Selecting ASP and GLU

@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 Tatzberg 47/49 01307 Dresden

Re: [PyMOL] Selecting ASP and GLU

:06 AM, Hongbo Zhu hongbo@biotec.tu-dresden.de wrote: I believe the confusion is caused by the simplified selection expression in PyMOL (and some other visualization tools as well). I remember that one of my colleagues once questioned strongly the reason of using OR instead

Re: [PyMOL] installing_running vasco

Thank you for your help. -Yarrow -- Hongbo ZHU Postdoctoral Researcher Structural Bioinformatics Technische Universität Dresden Biotechnology Center Tatzberg 47/49 01307 Dresden

Re: [PyMOL] installing_running vasco

Thank you for your help. -Yarrow -- Hongbo ZHU Postdoctoral Researcher Structural Bioinformatics Technische Universität Dresden Biotechnology Center Tatzberg 47/49 01307

Re: [PyMOL] rotation of protein

___ 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 -- Hongbo ZHU Postdoctoral Researcher Structural Bioinformatics Technische

Re: [PyMOL] msms_pymol.py

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

Re: [PyMOL] msms_pymol.py

. 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 answer. :) On Tue, 11 May