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Re: [PyMOL] load dcd files problem
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From: Marius R. <mar...@gm...> - 2009-09-15 14:06:17
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I've just update my source code. So what you need to do is uncomment lines 126, 127, 146 and change the zero on line 293 with a 1. Let me now if this works. I don't have a dcd trajectory in order to test this. Marius On Tue, Sep 15, 2009 at 3:45 PM, Hugo G. de Teran <hug...@us...> wrote: > I did that now, run again > pymol setup.py build install > pymol setup2.py install > but still the same error ... > > Hugo > > Marius Retegan wrote: > > Did you uncomment in setup.py the lines related to VMD support? > > > > On Tue, Sep 15, 2009 at 3:07 PM, Hugo G. de Teran <hug...@us...> > wrote: > > > > > >> Hi, > >> > >> I am trying to use the load_traj command to load dcd files. Holever, I > >> get the following error: > >> PyMOL>load_traj ../../1bwb/dc1.dcd, initial, > >> ObjectMolecule-Error: sorry, VMD Molfile Plugins not compiled into this > >> build. > >> > >> I have installed pymol from source with the default method (i.e., python > >> install scripts) on my opensuse11.1 x86_64 > >> > >> Thanks for help, > >> > >> Hugo > >> > >> > >> > >> -- > >> Hugo G. de Teran, PhD. > >> "Parga Pondal" Research fellow > >> Fundación Pública Galega de Medicina Xenómica - SERGAS > >> Santiago de Compostela (SPAIN) > >> > >> Phone +34 981563100 ext 13873 > >> e-mail:hug...@us... <e-mail%3Ah...@us...> < > e-mail%3Ah...@us... <e-mail%253...@us...>> > >> http://web.usc.es/~hugogdt <http://web.usc.es/%7Ehugogdt> < > http://web.usc.es/%7Ehugogdt> > >> > >> > >> > >> > >> > ------------------------------------------------------------------------------ > >> Come build with us! The BlackBerry® Developer Conference in SF, CA > >> is the only developer event you need to attend this year. Jumpstart your > >> developing skills, take BlackBerry mobile applications to market and > stay > >> ahead of the curve. Join us from November 9-12, 2009. Register > now! > >> http://p.sf.net/sfu/devconf > >> _______________________________________________ > >> PyMOL-users mailing list (PyM...@li...) > >> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > >> Archives: http://www.mail-archive.com/pym...@li... > >> > >> > > > > --0016e6db2dbbff30f304739dc03a > > Content-Type: text/html; charset=O-8859-1 > > Content-Transfer-Encoding: quoted-printable > > > > Did you uncomment in setup.py the lines related to VMD > support?<br><br><div class="gmail_quote">On Tue, Sep 15, 2009 at 3:07 PM, > Hugo G. de Teran <span dir="ltr"><<a href="mailto:hug...@us...">hDelivered-To: > hu...@gm... > > Received: by 10.103.221.10 with SMTP id y10cs111217muq; > > Tue, 15 Sep 2009 06:29:04 -0700 (PDT) > > Received: by 10.211.171.14 with SMTP id y14mr8459245ebo.58.1253021301179; > > Tue, 15 Sep 2009 06:28:21 -0700 (PDT) > > Return-Path: <mar...@gm...> > > Received: from rojo2.usc.es (rojo2.usc.es [193.144.75.10]) > > by mx.google.com with ESMTP id > 25si5396218ewy.39.2009.09.15.06.28.19; > > Tue, 15 Sep 2009 06:28:20 -0700 (PDT) > > Received-SPF: neutral (google.com: 193.144.75.10 is neither permitted > nor denied by domain of mar...@gm...) client-ip 3.144.75.10; > > Authentication-Results: mx.google.com; spf=utral (google.com: > 193.144.75.10 is neither permitted nor denied by domain of > mar...@gm...) smtp.mail=mar...@gm...; > dkim=pass (test mode) header.i=@gmail.com > > Received: from localhost (rojo2 [127.0.0.1]) > > by rojo2.usc.es (Postfix) with ESMTP id 2291E464A5F > > for <hu...@gm...>; Tue, 15 Sep 2009 15:28:16 +0200 (CEST) > > X-Virus-Scanned: amavisd-new at usc.es > > Received: from rojo2.usc.es ([127.0.0.1]) > > by localhost (rojo2.usc.es [127.0.0.1]) (amavisd-new, port 10024) > > with ESMTP id 6KotJbBytw00 for <hu...@gm...>; > > Tue, 15 Sep 2009 15:28:16 +0200 (CEST) > > Received: from oro1.usc.es (oro1.usc.es [193.144.75.8]) > > by rojo2.usc.es (Postfix) with ESMTP id F357A464A3D > > for <hu...@gm...>; Tue, 15 Sep 2009 15:28:15 +0200 (CEST) > > Received: by oro1.usc.es (Postfix, from userid 100) > > id 712C23A02D; Tue, 15 Sep 2009 15:28:19 +0200 (CEST) > > Received: from oro1.usc.es ([unix socket]) > > by oro1 (Cyrus v2.1.18-IPv6-Debian-2.1.18-1+sarge2) with LMTP; Tue, > 15 Sep 2009 15:28:19 +0200 > > X-Sieve: CMU Sieve 2.2 > > Received: from rojo3.usc.es (rojo3.usc.es [193.144.75.13]) > > by oro1.usc.es (Postfix) with ESMTP id 4F4023A02B > > for <hug...@us...>; Tue, 15 Sep 2009 15:28:19 +0200 (CEST) > > Received: from localhost (localhost.localdomain [127.0.0.1]) > > by rojo3.usc.es (Postfix) with ESMTP id E285C3C184 > > for <hug...@us...>; Tue, 15 Sep 2009 15:28:18 +0200 (CEST) > > X-Virus-Scanned: amavisd-new at usc.es > > X-Spam-Score: 1.44 > > X-Spam-Level: * > > X-Spam-Status: No, score=44 tagged_above=-999 required=5 > > tests=[DNS_FROM_RFC_POST=1.44, HTML_MESSAGE=0.001, SPF_PASS=-0.001] > > Received: from rojo3.usc.es ([127.0.0.1]) > > by localhost (rojo3.usc.es [127.0.0.1]) (amavisd-new, port 10024) > > with ESMTP id 9yKch60LhdRg for <hug...@us...>; > > Tue, 15 Sep 2009 15:28:12 +0200 (CEST) > > Received: from mail-ew0-f216.google.com (mail-ew0-f216.google.com[209.85.219.216]) > > by rojo3.usc.es (Postfix) with ESMTP id AC3593C1B9 > > for <hug...@us...>; Tue, 15 Sep 2009 15:28:12 +0200 (CEST) > > Received: by ewy12 with SMTP id 12so4300853ewy.0 > > for <hug...@us...>; Tue, 15 Sep 2009 06:28:12 -0700 (PDT) > > DKIM-Signature: v= a=rsa-sha256; c=relaxed/relaxed; > > d=ail.com; s=gamma; > > h=mainkey-signature:mime-version:received:in-reply-to:references > > :date:message-id:subject:from:to:content-type; > > bh=OLbqHC0blM/1hvR9WlwEyAGmJc0RFi5NiQ9Vs6oHM=; > > > b=tDlCRIOw67VCrGxS1tDteIVhye1d75rnDoKsYR/f6TBCcnUAt+o3fgOee8amIGnxPq > > > dGXhRdZvsW53M9azY+R7ZiZtaYeVQryOWdNK00sRUZ2pNeZoqUQ7NVp6+p8gmlLHQ039 > > SucgLJXZfy5AH5ghpu24zOb4Puw+4eCVMqEW8DomainKey-Signature: > a=rsa-sha1; c=nofws; > > d=ail.com; s=gamma; > > > h=me-version:in-reply-to:references:date:message-id:subject:from:to > > :content-type; > > > b=wrAsR/GRRaZMt+sfbot3Ri4D26dbi1FU57bLRtLNCChSkaP0LE5XOLvP0xDM9V0d > > > Svrfo9UTldq4c5wfStz2vzvfhAIfIsbdWUyfrFNQYR+RgmtiokDIrQxjOVXMvEvQofyu > > q/SaB6w7rgBVUxCZHo9DXsHRIkNaQcbhcKoxQMIME-Version: 1.0 > > Received: by 10.216.89.138 with SMTP id c10mr1978084wef.47.1253021291851; > Tue, > > 15 Sep 2009 06:28:11 -0700 (PDT) > > In-Reply-To: <4AA...@us...> > > References: <4AA...@us...> > > Date: Tue, 15 Sep 2009 15:28:11 +0200 > > Message-ID: <522...@ma... > > > > Subject: Re: [PyMOL] load dcd files problem > > From: Marius Retegan <mar...@gm...> > > To: "Hugo G. de Teran" <hug...@us...> > > Content-Type: multipart/alternative; boundary > > --0016e6db2dbbff30f304739dc03a > > Content-Type: text/plain; charset=O-8859-1 > > Content-Transfer-Encoding: quoted-printable > > > > Did you uncomment in setup.py the lines related to VMD support? > > > > On Tue, Sep 15, 2009 at 3:07 PM, Hugo G. de Teran <hug...@us...> > wrote: > > > > > >> Hi, > >> > >> I am trying to use the load_traj command to load dcd files. Holever, I > >> get the following error: > >> PyMOL>load_traj ../../1bwb/dc1.dcd, initial, > >> ObjectMolecule-Error: sorry, VMD Molfile Plugins not compiled into this > >> build. > >> > >> I have installed pymol from source with the default method (i.e., python > >> install scripts) on my opensuse11.1 x86_64 > >> > >> Thanks for help, > >> > >> Hugo > >> > >> > >> > >> -- > >> Hugo G. de Teran, PhD. > >> "Parga Pondal" Research fellow > >> Fundación Pública Galega de Medicina Xenómica - SERGAS > >> Santiago de Compostela (SPAIN) > >> > >> Phone +34 981563100 ext 13873 > >> e-mail:hug...@us... <e-mail%3Ah...@us...> < > e-mail%3Ah...@us... <e-mail%253...@us...>> > >> http://web.usc.es/~hugogdt <http://web.usc.es/%7Ehugogdt> < > http://web.usc.es/%7Ehugogdt> > >> > >> > >> > >> > >> > ------------------------------------------------------------------------------ > >> Come build with us! The BlackBerry® Developer Conference in SF, CA > >> is the only developer event you need to attend this year. Jumpstart your > >> developing skills, take BlackBerry mobile applications to market and > stay > >> ahead of the curve. Join us from November 9-12, 2009. Register > now! > >> http://p.sf.net/sfu/devconf > >> _______________________________________________ > >> PyMOL-users mailing list (PyM...@li...) > >> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > >> Archives: http://www.mail-archive.com/pym...@li... > >> > >> > > > > --0016e6db2dbbff30f304739dc03a > > Content-Type: text/html; charset=O-8859-1 > > Content-Transfer-Encoding: quoted-printable > > > > Did you uncomment in setup.py the lines related to VMD > support?<br><br><div class="gmail_quote">On Tue, Sep 15, 2009 at 3:07 PM, > Hugo G. de Teran <span dir="ltr"><<a href="mailto:hug...@us..."> > hug...@us...</a>></span> wrote:<br> > > <blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, > 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">Hi,<br> > > <br> > > I am trying to use the load_traj command to load dcd files. Holever, > I<br> > > get the following error:<br> > > PyMOL>load_traj ../../1bwb/dc1.dcd, initial,<br> > > ObjectMolecule-Error: sorry, VMD Molfile Plugins not compiled into > this<br> > > build.<br> > > <br> > > I have installed pymol from source with the default method (i.e., > python<br> > > install scripts) on my opensuse11.1 x86_64<br> > > <br> > > Thanks for help,<br> > > <br> > > Hugo<br> > > <br> > > <br> > > <br> > > --<br> > > Hugo G. de Teran, PhD.<br> > > "Parga Pondal" Research fellow<br> > > Fundación Pública Galega de Medicina Xenómica - SERGAS<br> > > Santiago de Compostela (SPAIN)<br> > > <br> > > Phone +34 981563100 ext 13873<br> > > <a href="mailto:e-mail%3Ah...@us...<e-mail%253...@us...> > ">e-mail:hug...@us... <e-mail%3Ah...@us...></a> <a > href="http://web.usc.es/%7Ehugogdt" target="_blank"> > http://web.usc.es/~hugogdt <http://web.usc.es/%7Ehugogdt></a><br> > > <br> > > <br> > > <br> > > > ------------------------------------------------------------------------------<br> > > Come build with us! The BlackBerry&reg; Developer Conference in SF, > CA<br> > > is the only developer event you need to attend this year. Jumpstart > your<br> > > developing skills, take BlackBerry mobile applications to market and > stay<br> > > ahead of the curve. Join us from November 9&#45;12, 2009. Register > now&#33;<br> > > <a href="http://p.sf.net/sfu/devconf" target="_blank"> > http://p.sf.net/sfu/devconf</a><br> > > _______________________________________________<br> > > PyMOL-users mailing list (<a href="mailto: > PyM...@li...">PyM...@li... > </a>)<br> > > Info Page: <a href=" > https://lists.sourceforge.net/lists/listinfo/pymol-users" target="_blank"> > https://lists.sourceforge.net/lists/listinfo/pymol-users</a><br> > > Archives: <a href=" > http://www.mail-archive.com/pym...@li..." > target="_blank"> > http://www.mail-archive.com/pym...@li...</a><br> > > </blockquote></div><br> > > > > --0016e6db2dbbff30f304739dc03a-- > > > > > -- > Hugo G. de Teran, PhD. > "Parga Pondal" Research fellow > Fundación Pública Galega de Medicina Xenómica - SERGAS > Santiago de Compostela (SPAIN) > > Phone +34 981563100 ext 13873 > e-mail:hug...@us... <e-mail%3Ah...@us...> > http://web.usc.es/~hugogdt <http://web.usc.es/%7Ehugogdt> > > > |