Re: [PyMOL] Race condition when running scripts in stdin mode
Michael I've run in to something like this before (early ubuntu 12.04) using just using build_seq to write small peptide .pdbs in a loop, the work around I used (I think it was in the wiki at the time -- can't find it now) was to add a short wait at the end of the loop, 0.1 sec was enough on my machine at the time but that may be device/content specific. **not my skill set** IF I recall correctly the issue was explained as having a new run on the loop before the buffer on the old cleared (memory:cycles racing) Hope this helps Jacob Pessin Albert Einstein College of Medicine Diabetes Research Center SIMC Computational Chemistry Molecular Modeling jacob.pes...@einstein.yu.edu 1 718 839 7228 -- Message: 4 Date: Wed, 24 Jun 2015 00:13:26 +0200 From: Michael Banck mba...@debian.org Subject: [PyMOL] Race condition when running scripts in stdin mode To: pymol-users pymol-users@lists.sourceforge.net Message-ID: 20150623221325.gy8...@raptor.chemicalconnection.dyndns.org Content-Type: text/plain; charset=us-ascii Hi, on Debian, we got a bug report which looks like the bug reported here as well: http://sourceforge.net/p/pymol/bugs/130/ Unfortunately, there has been no discussion of this bug so far. There seems to be some race condition for scripts, does anybody a work-around, and/or fix for this? Or is this a platform-dependent (or even Debian/Ubuntu dependent) issue? Thanks, Michael Message: 6 Date: Tue, 23 Jun 2015 19:45:26 -0300 From: Osvaldo Martin aloctavo...@gmail.com Subject: Re: [PyMOL] Race condition when running scripts in stdin mode To: Michael Banck mba...@debian.org Cc: pymol-users pymol-users@lists.sourceforge.net Message-ID: cagmh68wyazrmopqxc5kwz+7t7knbfzb3zecbzu_jpectzz4...@mail.gmail.com Content-Type: text/plain; charset=utf-8 Hi MIchael, I can reproduce the error on a machine with Ubuntu 15.04 (64 bits) and PyMOL 1.7.2 On Tue, Jun 23, 2015 at 7:13 PM, Michael Banck mba...@debian.org wrote: Hi, on Debian, we got a bug report which looks like the bug reported here as well: http://sourceforge.net/p/pymol/bugs/130/ Unfortunately, there has been no discussion of this bug so far. There seems to be some race condition for scripts, does anybody a work-around, and/or fix for this? Or is this a platform-dependent (or even Debian/Ubuntu dependent) issue? Thanks, Michael -- Monitor 25 network devices or servers for free with OpManager! OpManager is web-based network management software that monitors network devices and physical virtual servers, alerts via email sms for fault. Monitor 25 devices for free with no restriction. Download now http://ad.doubleclick.net/ddm/clk/292181274;119417398;o ___ 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] Trouble with saving mol2 format
Hi, I've come across an issue saving .mol2 ( @TRIPOS ) files. MGL tools' PMV/ADT won't read them, babel/open babel issues a set of complaint and read errors. If I am reading the format correctly then ... In the atom content the columnation appears to be off after the X Y Z coordinates, the question marks under atom_type seem to throw a lot of scripts (not surprising). I'm not quite sure what the issue is, but it occurs when saving peptides and molecules built by a mouse or script as well as RCSB downloaded structures. seems the same on all builds and machines I've tried (listed at bottom) thanks for your time jacob # created with PyMOL @TRIPOSMOLECULE untitled 5757000 PROTEIN USER_CHARGES @TRIPOSATOM 1 N0.394-2.167-1.142??1.000 2 CA0.891-0.794-1.142??1.000 3 C2.400-0.765-1.142??1.000 4 O3.074-1.654-0.600??1.000 5 CB0.2860.0380.061??1.000 6 CG1-1.272-0.0100.168??1.000 ... saved from pymol 1.6 https://www.dropbox.com/s/jlpwa2lsub5ez8g/IPR.mol2 babel pipes https://www.dropbox.com/s/ruh23hcxfmbv0z8/babelmol2_mol2.txt babel out https://www.dropbox.com/s/3p41lkvybdlwhwc/IPR_mol2mol2_babeled.mol2https://www.dropbox.com/s/3p41lkvybdlwhwc/IPR_mol2mol2_babeled.mol2 tripos mol2 format pdf http://www.tripos.com/data/support/mol2.pdf hardware dell T3600 e5-1650 w/ quadro 600 xUbuntu 13.04 pymol 1.6.0 from source w/build_seq.py and seq_convert.py 1.5.2 from package (and lots of plugins) lenovo t420 nvs 400 windows 7 1.4.? (not sitting at it while typing) pre-built many plugins also xUbuntu 12.04 1.4 from package and 1.6 from source (w/nvidia-bumblebee, and just intel graphics) -- LIMITED TIME SALE - Full Year of Microsoft Training For Just $49.99! 1,500+ hours of tutorials including VisualStudio 2012, Windows 8, SharePoint 2013, SQL 2012, MVC 4, more. BEST VALUE: New Multi-Library Power Pack includes Mobile, Cloud, Java, and UX Design. Lowest price ever! Ends 9/20/13. http://pubads.g.doubleclick.net/gampad/clk?id=58041151iu=/4140/ostg.clktrk___ 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] how to get cealign outputs for mulitple structures
Hi all, can anyone suggest a straightforward way of collecting the cealign output in bulk, (RMS, #atoms compared), using alignto doesn't even print this to screen (I tried adjusting quiet=, to no avail). thanks in advance jacob https://owa.einstein.yu.edu/owa/?ae=Itema=Opent=IPM.Noteid=RgDDT2ZJXulBTI8H5G%2fACk3UBwBPSkr8RdqeRa4tSfsjXcRlSCziAABPSkr8RdqeRa4tSfsjXcRlAAAPdWIns=Draftpspid=_1369930182703_402002554# https://owa.einstein.yu.edu/owa/?ae=Itema=Opent=IPM.Noteid=RgDDT2ZJXulBTI8H5G%2fACk3UBwBPSkr8RdqeRa4tSfsjXcRlSCziAABPSkr8RdqeRa4tSfsjXcRlAAAPdWIns=Draftpspid=_1369930182703_402002554# -- Introducing AppDynamics Lite, a free troubleshooting tool for Java/.NET Get 100% visibility into your production application - at no cost. Code-level diagnostics for performance bottlenecks with 2% overhead Download for free and get started troubleshooting in minutes. http://p.sf.net/sfu/appdyn_d2d_ap1___ 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
