[PyMOL] PyMOL at West Coast Meetings
Hi all, Just a quick note to let you know that PyMOL will be represented at the Schrodinger booths at the WCPCW in Monterey, CA (this week) and ACS in Anaheim (next week). So, if you're at either meeting, please feel free to stop by and come talk PyMOL, ask questions, or just chat. Cheers, -- Jason -- Jason Vertrees, PhD PyMOL Product Manager Schrodinger, LLC (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- 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] PyMOL at West Coast Meetings
I'll be at ACS! See you and the developers there. Paul -- Paul Rigor http://www.ics.uci.edu/~prigor On Tue, Mar 22, 2011 at 12:09 AM, Jason Vertrees wrote: > Hi all, > > Just a quick note to let you know that PyMOL will be represented at > the Schrodinger booths at the WCPCW in Monterey, CA (this week) and > ACS in Anaheim (next week). So, if you're at either meeting, please > feel free to stop by and come talk PyMOL, ask questions, or just chat. > > Cheers, > > -- Jason > > -- > Jason Vertrees, PhD > PyMOL Product Manager > Schrodinger, LLC > > (e) jason.vertr...@schrodinger.com > (o) +1 (603) 374-7120 > > -- > 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 > -- 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] New plugin: MSMS plugin for PyMOL
On 21/03/11 22:57, Hongbo Zhu wrote: > 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 > provided several very helpful PyMOL scripts about MSMS (see > http://pldserver1.biochem.queensu.ca/~rlc/work/pymol/ ). > > I have also been using the MSMS program heavily in my work and developed > a MSMS plugin for PyMOL with a graphical user interface (GUI). If you > have interest, please take a look at the plugin at: > --- > http://www.pymolwiki.org/index.php/MSMS > --- > Features: > MSMS can be configured and invoked in the GUI. > The triangulated protein SES can be rendered as mesh or/and vertices > plus normal vectors. > The color of surface mesh or vertices can also be configured. > > Your feedback and suggestions are particularly welcome! > > Best regards, > Hongbo > > -- > 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 Hi Hongbo, it is officially included in Gentoo Linux now [1]. It would be nice, if you could drop me a mail, in case you changed something, so that I can create a bumped version. thanks justin [1] http://packages.gentoo.org/package/sci-chemistry/pymol-plugins-msms Might take some hours to appear there -- Justin Lecher Institute of Complex Systems ICS-6 Structural Biochemistry Research Centre Juelich 52425 Juelich, Germany phone: +49 2461 61 2117 smime.p7s Description: S/MIME Cryptographic Signature -- 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] symexp
Hi, Kanika, The source code can be found at function ExecutiveSymExp() in the file ./trunk/pymol/layer3/Executive.c Normally, a PDB is equivalent to an ASU (except for some cases like capsid). "Symexp is used to reconstruct neighboring ASUs." ( http://pymolwiki.org/index.php/Symexp ) It seems REMARK 290 that contains crystallographic symmetry transformations is used for computing the positions of neighboring ASUs. But be careful with some of the capsid cases (e.g. 3p0s). The symexp will not generate any neighboring molecules as they are not related by crystallographic symmetry, but non-crystallographic symmetry. BTW, it seems symexp has a bug when running on 3p0s. It does not return after displaying the message: "ExecutiveSymExp: Generating symmetry mates..." regards, hongbo On 03/22/2011 06:44 AM, kanika sharma wrote: > I used symexp command for 3QK9 using distance of 2.75 to generate > ASU(asymmetric unit). Does symexp generate these symmetry mates from the > remark290 of PDB file? I couldnot find the code for symexp in pymolwiki. > Can anyone help out? > > > > > Regards, > Kanika > > > > -- > 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 -- 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-dresden.de -- 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] New plugin: MSMS plugin for PyMOL
El 22/03/11 09:34, Justin Lecher escribió: > On 21/03/11 22:57, Hongbo Zhu wrote: >> 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 >> provided several very helpful PyMOL scripts about MSMS (see >> http://pldserver1.biochem.queensu.ca/~rlc/work/pymol/ ). >> >> I have also been using the MSMS program heavily in my work and developed >> a MSMS plugin for PyMOL with a graphical user interface (GUI). If you >> have interest, please take a look at the plugin at: >> --- >> http://www.pymolwiki.org/index.php/MSMS >> --- >> Features: >> MSMS can be configured and invoked in the GUI. >> The triangulated protein SES can be rendered as mesh or/and vertices >> plus normal vectors. >> The color of surface mesh or vertices can also be configured. >> >> Your feedback and suggestions are particularly welcome! >> >> Best regards, >> Hongbo >> >> -- >> 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 > Hi Hongbo, > > it is officially included in Gentoo Linux now [1]. It would be nice, if > you could drop me a mail, in case you changed something, so that I can > create a bumped version. > > thanks justin > > [1] http://packages.gentoo.org/package/sci-chemistry/pymol-plugins-msms > Might take some hours to appear there > > > > -- > 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 Thanks, Justin. Gentoo is, in my humble opinion, the best Linux option to run biochemical software, and we owe it all to you. Whenever I read about the running/compilation problems others are having with pymol, I thank God for using Gentoo and having you on board. Best regards, Ramiro. -- 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
[PyMOL] CASTp plugin
Hello pymol users, I try to install this castp plugin: http://sts.bioengr.uic.edu/castp/pymol.php -> http://sts.bioengr.uic.edu/castp/infoPages/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 anyone have any idea how to fix this issue? Thanks, Tomas -- S pozdravy T. Kučera -- 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] CASTp plugin
Hi, Tomas, Usually, the "Bad magic number" is caused by wrong python version when running .pyc file (the .pyc must have been compiled using a different version of python than the one in PyMOL 1.3, which is python 2.5.4). Maybe you have also noticed on the first line of the CASTpyMOL webpage : "To use CASTpyMOL version 2, you must be using PyMOL version 0.99 " pymol 0.99 and pymol 1.3 uses different versions of python. Maybe you should contact the CASTpyMOL people to get a .py file so you can try them with your pymol 1.3, or ask them to compile a .pyc using python 2.5.4 for you. Or install pymol 0.99 in parallel to you pymol 1.3. good luck! hongbo On 03/22/2011 11:03 AM, Tomáš Kučera wrote: > Hello pymol users, > > I try to install this castp plugin: > http://sts.bioengr.uic.edu/castp/pymol.php > -> http://sts.bioengr.uic.edu/castp/infoPages/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 anyone have any idea how to fix this issue? > > Thanks, Tomas > -- 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-dresden.de -- 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] symexp
> It seems REMARK 290 that contains crystallographic symmetry > transformations is used for computing the positions of neighboring ASUs. the CRYST1 record is sufficient for generating symmetry mates, so pymol most likely does not read REMARK 290. Cheers, Thomas -- Thomas Holder MPI for Developmental Biology Spemannstr. 35 D-72076 Tübingen -- 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
[PyMOL] Saving molecule to pdb changes Si to S
Dear all, I am using PyMOL 1.2r2 on Ubuntu 10.10. When I click 'Save Molecule...' from 'File' menu and select a molecule that contained 'Si' atom, the output pdb will show 'S' instead of 'Si' on the right most column. I also try this with mol format, the result is the same. Is this a known bug or only ubuntu version bug? If this is a bug, how to fixed it? Thanks in advance. Regards, Virasak Dugnsrikaew -- 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] symexp
Should not the positions of ASU's generated by REMARK290 be same as the symmetry mates generated? -- 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] symexp
You are right, Thomas! The information is redundant in REMARK 290. I just performed a small test which confirms your conclusion: remove CRYST1 will make symexp to complain "ExecutiveSymExp-Error: No symmetry loaded!" even if REMARK 290 is present, while removing REMARK 290 does not have any effect on symexp. don't know whether it make sense to monitor both cryst1 and remark 290... On 03/22/2011 10:19 AM, Thomas Holder wrote: >> It seems REMARK 290 that contains crystallographic symmetry >> transformations is used for computing the positions of neighboring ASUs. > > 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) 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] symexp
Hi Kanika, They should. The CRYST1 record holds all the information required to build the crystal. Do note that the symexp command generates neighbouring symmetry mates, given a cut off distance. It does not build the filled unit cell. Thomas put a script on the wiki last year to build you that: http://www.pymolwiki.org/index.php/Supercell Cheers, Tsjerk On Tue, Mar 22, 2011 at 11:43 AM, kanika sharma wrote: > Should not the positions of ASU's generated by REMARK290 be same as the > symmetry mates generated? > > > > -- > 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 > -- 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 -- 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] Saving molecule to pdb changes Si to S
Hi Virasak, It goes a bit far to call it a bug. It's a problem with the xyz format. It only has names for atoms, not element types, and Pymol can't go guessing, otherwise any CA would end up as calcium :S Cheers, Tsjerk On Tue, Mar 22, 2011 at 2:30 PM, Virasak Dungsrikaew wrote: > Hi Tsjerk, > > Thank you for your quick reply. I just follow your suggestion to show > all label, apparently that it's problem in loading XYZ file format > (got S instead of Si). If I use the same structure in PDB format, it > works fine. For now, I will use only PDB in my work. > > Anyway, the XYZ file should work, because it's come from conversion of > 'babel' program with the same input as the PDB file and it seem > correct in my eyes. Is it a bug in loading XYZ file format? > > Cheers, > Virasak Dungsrikaew > > > On Tue, Mar 22, 2011 at 6:36 PM, Tsjerk Wassenaar wrote: >> Hey Virasak, >> >> If you load the structure and do: >> >> label all, elem >> >> does the silicium show op as 'Si'? >> >> If it doesn't, you should check the input file. >> >> I did a quick test, reading in a PDB file with an atom modified to >> silicium and then saving it, which gave no problems with pymol 1.3. If >> you don't manage to solve the problem, can you isolate the silicium >> containing part, and post it together with the set of commands you >> used? >> >> Cheers, >> >> Tsjerk >> >> On Tue, Mar 22, 2011 at 11:26 AM, Virasak Dungsrikaew >> wrote: >>> Dear all, >>> >>> I am using PyMOL 1.2r2 on Ubuntu 10.10. >>> When I click 'Save Molecule...' from 'File' menu and select a molecule >>> that contained 'Si' atom, the output pdb will show 'S' instead of 'Si' >>> on the right most column. >>> I also try this with mol format, the result is the same. >>> Is this a known bug or only ubuntu version bug? >>> If this is a bug, how to fixed it? >>> >>> Thanks in advance. >>> >>> Regards, >>> Virasak Dugnsrikaew >>> >>> -- >>> 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 >>> >> >> >> >> -- >> 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 >> > -- 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 -- 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] CASTp plugin
I had the same problem. Email Joe Dundas for the .py source code .py file, and drop it into the modules/pmg_tk/startup folder. Jed Hongbo Zhu wrote: > Hi, Tomas, > Usually, the "Bad magic number" is caused by wrong python version when > running .pyc file (the .pyc must have been compiled using a different > version of python than the one in PyMOL 1.3, which is python 2.5.4). > Maybe you have also noticed on the first line of the CASTpyMOL webpage : > > "To use CASTpyMOL version 2, you must be using PyMOL version 0.99 " > > pymol 0.99 and pymol 1.3 uses different versions of python. > > Maybe you should contact the CASTpyMOL people to get a .py file so you > can try them with your pymol 1.3, or ask them to compile a .pyc using > python 2.5.4 for you. Or install pymol 0.99 in parallel to you pymol 1.3. > > good luck! > hongbo > > On 03/22/2011 11:03 AM, Tomáš Kučera wrote: > >> Hello pymol users, >> >> I try to install this castp plugin: >> http://sts.bioengr.uic.edu/castp/pymol.php >> -> http://sts.bioengr.uic.edu/castp/infoPages/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 anyone have any idea how to fix this issue? >> >> Thanks, Tomas >> >> > > -- Jed Goldstone, PhD Research Specialist Woods Hole Oceanographic Institution Redfield 3-52 MS#32 Woods Hole, MA 02543 http://www.whoi.edu/hpb/Site.do?id=481 Phone: 508-289-4823 -- 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] Saving molecule to pdb changes Si to S
Hi Virasak, In Pymol you can change the element type to match your needs: alter n. si, elem="si" Hope it helps, Tsjerk On Tue, Mar 22, 2011 at 2:44 PM, Virasak Dungsrikaew wrote: > Hi Tsjerk, > > You are right. In my work, I almost working with XYZ format and all > programs that I used is work without a problem. Some programs can also > load a variant format with atomic number instead of atom name. I guest > that for atom name, these programs match the longest name and also > respect character case, like Ca/CA. > > Thank you for you help. > Virasak Dungsrikaew > > On Tue, Mar 22, 2011 at 8:35 PM, Tsjerk Wassenaar wrote: >> Hi Virasak, >> >> It goes a bit far to call it a bug. It's a problem with the xyz >> format. It only has names for atoms, not element types, and Pymol >> can't go guessing, otherwise any CA would end up as calcium :S >> >> Cheers, >> >> Tsjerk >> >> On Tue, Mar 22, 2011 at 2:30 PM, Virasak Dungsrikaew >> wrote: >>> Hi Tsjerk, >>> >>> Thank you for your quick reply. I just follow your suggestion to show >>> all label, apparently that it's problem in loading XYZ file format >>> (got S instead of Si). If I use the same structure in PDB format, it >>> works fine. For now, I will use only PDB in my work. >>> >>> Anyway, the XYZ file should work, because it's come from conversion of >>> 'babel' program with the same input as the PDB file and it seem >>> correct in my eyes. Is it a bug in loading XYZ file format? >>> >>> Cheers, >>> Virasak Dungsrikaew >>> >>> >>> On Tue, Mar 22, 2011 at 6:36 PM, Tsjerk Wassenaar wrote: Hey Virasak, If you load the structure and do: label all, elem does the silicium show op as 'Si'? If it doesn't, you should check the input file. I did a quick test, reading in a PDB file with an atom modified to silicium and then saving it, which gave no problems with pymol 1.3. If you don't manage to solve the problem, can you isolate the silicium containing part, and post it together with the set of commands you used? Cheers, Tsjerk On Tue, Mar 22, 2011 at 11:26 AM, Virasak Dungsrikaew wrote: > Dear all, > > I am using PyMOL 1.2r2 on Ubuntu 10.10. > When I click 'Save Molecule...' from 'File' menu and select a molecule > that contained 'Si' atom, the output pdb will show 'S' instead of 'Si' > on the right most column. > I also try this with mol format, the result is the same. > Is this a known bug or only ubuntu version bug? > If this is a bug, how to fixed it? > > Thanks in advance. > > Regards, > Virasak Dugnsrikaew > > -- > 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 > -- 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 >>> >> >> >> >> -- >> 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 >> > -- 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 -- 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
[PyMOL] Pymol no longer fetches from pdb
Has anyone else noticed that Pymol (v 1.3 or 1.4) will no longer fetch data from the pdb server? If I issue 'set fetch_host, pdbe' I can fetch data OK, but if you 'set fetch_host, pdb' I'm getting a fetch error for any accession number. -- Roger S. Rowlett Professor Department of Chemistry Colgate University 13 Oak Drive Hamilton, NY 13346 tel: (315)-228-7245 ofc: (315)-228-7395 fax: (315)-228-7935 email: rrowl...@colgate.edu -- 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] Pymol no longer fetches from pdb
Hi Roger, > Has anyone else noticed that Pymol (v 1.3 or 1.4) will no longer fetch data > from the pdb server? If I issue 'set fetch_host, pdbe' I can fetch data OK, > but if you 'set fetch_host, pdb' I'm getting a fetch error for any accession > number. I just checked v1.4 and I'm not having any issues with it, which means the server is up and the paths are still the same. Is it possible you were having connectivity issues with the PDB server? That's my best guess because by telling PyMOL to pull the PDBs from the Europan server, you were able to download. PyMOL v1.3 will most likely not work, because the PDB changed their PDB paths last year. Cheers, -- Jason -- Jason Vertrees, PhD PyMOL Product Manager Schrodinger, LLC (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- 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] Pymol no longer fetches from pdb
Hi Jason, Can you clarify what URL is being used to download the files from RCSB PDB? I don't think that there was any change regarding those last year. Andreas On Tue, Mar 22, 2011 at 9:02 AM, Jason Vertrees wrote: > Hi Roger, > >> Has anyone else noticed that Pymol (v 1.3 or 1.4) will no longer fetch data >> from the pdb server? If I issue 'set fetch_host, pdbe' I can fetch data OK, >> but if you 'set fetch_host, pdb' I'm getting a fetch error for any accession >> number. > > I just checked v1.4 and I'm not having any issues with it, which means > the server is up and the paths are still the same. Is it possible you > were having connectivity issues with the PDB server? That's my best > guess because by telling PyMOL to pull the PDBs from the Europan > server, you were able to download. PyMOL v1.3 will most likely not > work, because the PDB changed their PDB paths last year. > > Cheers, > > -- Jason > > -- > Jason Vertrees, PhD > PyMOL Product Manager > Schrodinger, LLC > > (e) jason.vertr...@schrodinger.com > (o) +1 (603) 374-7120 > > -- > 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 > -- --- Dr. Andreas Prlic Senior Scientist, RCSB PDB Protein Data Bank University of California, San Diego (+1) 858.246.0526 --- -- 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] Pymol no longer fetches from pdb
Hi Roger, On Tue, Mar 22, 2011 at 9:20 AM, Roger Rowlett wrote: > Hmm. At the RCSB site, I can see that the ftp server is ftp.wwpdb.org and it > is currently generating a "cannot be found" error". I'll investigate > further. This may be the issue with pymol if it is using that server path. This is clearly the reason for the error. PyMOL looks for PDBs at the main PDB site at the following path: ftp://ftp.wwpdb.org/pub/pdb/data/structures/divided/pdb/ and then appends the appropriate extension, which resolves and lists PDBs just fine (from my machine). Is anyone else having this error or just Roger? Cheers, -- Jason -- Jason Vertrees, PhD PyMOL Product Manager Schrodinger, LLC (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- 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] Pymol no longer fetches from pdb
Great, thanks, David. Just ensuring the problems been isolated. Cheers, -- Jason On Tue, Mar 22, 2011 at 9:53 AM, David Hall wrote: > Resolves fine for me. > > -David > > On Mar 22, 2011, at 12:30 PM, Jason Vertrees > wrote: > >> Hi Roger, >> >> On Tue, Mar 22, 2011 at 9:20 AM, Roger Rowlett wrote: >>> Hmm. At the RCSB site, I can see that the ftp server is ftp.wwpdb.org and it >>> is currently generating a "cannot be found" error". I'll investigate >>> further. This may be the issue with pymol if it is using that server path. >> >> This is clearly the reason for the error. PyMOL looks for PDBs at the >> main PDB site at the following path: >> >> ftp://ftp.wwpdb.org/pub/pdb/data/structures/divided/pdb/ >> >> and then appends the appropriate extension, which resolves and lists >> PDBs just fine (from my machine). >> >> Is anyone else having this error or just Roger? >> >> Cheers, >> >> -- Jason >> >> -- >> Jason Vertrees, PhD >> PyMOL Product Manager >> Schrodinger, LLC >> >> (e) jason.vertr...@schrodinger.com >> (o) +1 (603) 374-7120 >> >> -- >> 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 > -- Jason Vertrees, PhD PyMOL Product Manager Schrodinger, LLC (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- 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] Pymol no longer fetches from pdb
Resolves fine for me. -David On Mar 22, 2011, at 12:30 PM, Jason Vertrees wrote: > Hi Roger, > > On Tue, Mar 22, 2011 at 9:20 AM, Roger Rowlett wrote: >> Hmm. At the RCSB site, I can see that the ftp server is ftp.wwpdb.org and it >> is currently generating a "cannot be found" error". I'll investigate >> further. This may be the issue with pymol if it is using that server path. > > This is clearly the reason for the error. PyMOL looks for PDBs at the > main PDB site at the following path: > > ftp://ftp.wwpdb.org/pub/pdb/data/structures/divided/pdb/ > > and then appends the appropriate extension, which resolves and lists > PDBs just fine (from my machine). > > Is anyone else having this error or just Roger? > > Cheers, > > -- Jason > > -- > Jason Vertrees, PhD > PyMOL Product Manager > Schrodinger, LLC > > (e) jason.vertr...@schrodinger.com > (o) +1 (603) 374-7120 > > -- > 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 -- 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] Pymol no longer fetches from pdb
Hi Roger, Just to clarify, for the FTP protocol the correct prefix is ftp://ftp.wwpdb.org/ and NOT http://ftp ... Hope that makes sense, Andreas On Tue, Mar 22, 2011 at 9:54 AM, Jason Vertrees wrote: > Great, thanks, David. Just ensuring the problems been isolated. > > Cheers, > > -- Jason > > On Tue, Mar 22, 2011 at 9:53 AM, David Hall wrote: >> Resolves fine for me. >> >> -David >> >> On Mar 22, 2011, at 12:30 PM, Jason Vertrees >> wrote: >> >>> Hi Roger, >>> >>> On Tue, Mar 22, 2011 at 9:20 AM, Roger Rowlett wrote: Hmm. At the RCSB site, I can see that the ftp server is ftp.wwpdb.org and it is currently generating a "cannot be found" error". I'll investigate further. This may be the issue with pymol if it is using that server path. >>> >>> This is clearly the reason for the error. PyMOL looks for PDBs at the >>> main PDB site at the following path: >>> >>> ftp://ftp.wwpdb.org/pub/pdb/data/structures/divided/pdb/ >>> >>> and then appends the appropriate extension, which resolves and lists >>> PDBs just fine (from my machine). >>> >>> Is anyone else having this error or just Roger? >>> >>> Cheers, >>> >>> -- Jason >>> >>> -- >>> Jason Vertrees, PhD >>> PyMOL Product Manager >>> Schrodinger, LLC >>> >>> (e) jason.vertr...@schrodinger.com >>> (o) +1 (603) 374-7120 >>> >>> -- >>> 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 >> > > > > -- > Jason Vertrees, PhD > PyMOL Product Manager > Schrodinger, LLC > > (e) jason.vertr...@schrodinger.com > (o) +1 (603) 374-7120 > > -- > 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 > -- --- Dr. Andreas Prlic Senior Scientist, RCSB PDB Protein Data Bank University of California, San Diego (+1) 858.246.0526 --- -- 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] Pymol no longer fetches from pdb
Thanks, all. Looks like I'll have to investigate local issues with our institutional firewall. Sigh. Not the first time... Roger Rowlett On Mar 22, 2011 12:58 PM, "Jason Vertrees" wrote: > Great, thanks, David. Just ensuring the problems been isolated. > > Cheers, > > -- Jason > > On Tue, Mar 22, 2011 at 9:53 AM, David Hall wrote: >> Resolves fine for me. >> >> -David >> >> On Mar 22, 2011, at 12:30 PM, Jason Vertrees < jason.vertr...@schrodinger.com> wrote: >> >>> Hi Roger, >>> >>> On Tue, Mar 22, 2011 at 9:20 AM, Roger Rowlett wrote: Hmm. At the RCSB site, I can see that the ftp server is ftp.wwpdb.organd it is currently generating a "cannot be found" error". I'll investigate further. This may be the issue with pymol if it is using that server path. >>> >>> This is clearly the reason for the error. PyMOL looks for PDBs at the >>> main PDB site at the following path: >>> >>> ftp://ftp.wwpdb.org/pub/pdb/data/structures/divided/pdb/ >>> >>> and then appends the appropriate extension, which resolves and lists >>> PDBs just fine (from my machine). >>> >>> Is anyone else having this error or just Roger? >>> >>> Cheers, >>> >>> -- Jason >>> >>> -- >>> Jason Vertrees, PhD >>> PyMOL Product Manager >>> Schrodinger, LLC >>> >>> (e) jason.vertr...@schrodinger.com >>> (o) +1 (603) 374-7120 >>> >>> -- >>> 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 >> > > > > -- > Jason Vertrees, PhD > PyMOL Product Manager > Schrodinger, LLC > > (e) jason.vertr...@schrodinger.com > (o) +1 (603) 374-7120 -- 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
