[PyMOL] PyMOL at West Coast Meetings

2011-03-22 Thread Jason Vertrees
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, --

Re: [PyMOL] PyMOL at West Coast Meetings

2011-03-22 Thread Paul Rigor
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 jason.vertr...@schrodinger.com wrote: Hi all, Just a quick note to let you know that PyMOL will be represented at the Schrodinger booths at

Re: [PyMOL] New plugin: MSMS plugin for PyMOL

2011-03-22 Thread Justin Lecher
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

Re: [PyMOL] symexp

2011-03-22 Thread Hongbo Zhu
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

Re: [PyMOL] New plugin: MSMS plugin for PyMOL

2011-03-22 Thread Ramiro Téllez Sanz
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

[PyMOL] CASTp plugin

2011-03-22 Thread Tomáš Kučera
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

Re: [PyMOL] CASTp plugin

2011-03-22 Thread Hongbo Zhu
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

Re: [PyMOL] symexp

2011-03-22 Thread Thomas Holder
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

[PyMOL] Saving molecule to pdb changes Si to S

2011-03-22 Thread Virasak Dungsrikaew
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

Re: [PyMOL] symexp

2011-03-22 Thread kanika sharma
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

Re: [PyMOL] symexp

2011-03-22 Thread Hongbo Zhu
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

Re: [PyMOL] symexp

2011-03-22 Thread Tsjerk Wassenaar
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:

Re: [PyMOL] Saving molecule to pdb changes Si to S

2011-03-22 Thread Tsjerk Wassenaar
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 vira...@gmail.com

Re: [PyMOL] CASTp plugin

2011-03-22 Thread Jed Goldstone
I had the same problem. Email Joe Dundas jdunda1 at gmail 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

Re: [PyMOL] Saving molecule to pdb changes Si to S

2011-03-22 Thread Tsjerk Wassenaar
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 vira...@gmail.com wrote: Hi Tsjerk, You are right. In my work, I almost working with XYZ format and all programs that I

[PyMOL] Pymol no longer fetches from pdb

2011-03-22 Thread Roger Rowlett
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. --

Re: [PyMOL] Pymol no longer fetches from pdb

2011-03-22 Thread Jason Vertrees
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

Re: [PyMOL] Pymol no longer fetches from pdb

2011-03-22 Thread Andreas Prlic
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 jason.vertr...@schrodinger.com wrote: Hi Roger, Has anyone else noticed that Pymol

Re: [PyMOL] Pymol no longer fetches from pdb

2011-03-22 Thread Jason Vertrees
Hi Roger, On Tue, Mar 22, 2011 at 9:20 AM, Roger Rowlett rrowl...@colgate.edu 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

Re: [PyMOL] Pymol no longer fetches from pdb

2011-03-22 Thread Jason Vertrees
Great, thanks, David. Just ensuring the problems been isolated. Cheers, -- Jason On Tue, Mar 22, 2011 at 9:53 AM, David Hall li...@cowsandmilk.net 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,

Re: [PyMOL] Pymol no longer fetches from pdb

2011-03-22 Thread David Hall
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 rrowl...@colgate.edu wrote: Hmm. At the RCSB site, I can see that the ftp server is ftp.wwpdb.org and it is currently

Re: [PyMOL] Pymol no longer fetches from pdb

2011-03-22 Thread Andreas Prlic
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 jason.vertr...@schrodinger.com wrote: Great, thanks, David.  Just ensuring the problems been

Re: [PyMOL] Pymol no longer fetches from pdb

2011-03-22 Thread Roger Rowlett
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 jason.vertr...@schrodinger.com wrote: Great, thanks, David. Just ensuring the problems been isolated. Cheers, --