Hello, Hi I am Purushotham I am using X-plore for structural refinement using RDC, I have passing problem regarding how to start? and how to use it? please kindly help me in this regard.
On Tue, Apr 2, 2013 at 3:26 AM, <xplor-nih-request at nmr.cit.nih.gov> wrote: > Send Xplor-nih mailing list submissions to > xplor-nih at nmr.cit.nih.gov > > To subscribe or unsubscribe via the World Wide Web, visit > http://dcb.cit.nih.gov/mailman/listinfo/xplor-nih > or, via email, send a message with subject or body 'help' to > xplor-nih-request at nmr.cit.nih.gov > > You can reach the person managing the list at > xplor-nih-owner at nmr.cit.nih.gov > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Xplor-nih digest..." > > > Today's Topics: > > 1. Re: adding cis Proline in water refinment (Richard Harris) > 2. XPLOR problem (Allison Didychuk) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Mon, 1 Apr 2013 16:07:35 +0000 > From: Richard Harris <richard.harris at einstein.yu.edu> > Subject: Re: [Xplor-nih] adding cis Proline in water refinment > To: Charles Schwieters <charles at schwieters.org> > Cc: "xplor-nih at nmr.cit.nih.gov" <xplor-nih at nmr.cit.nih.gov> > Message-ID: > < > 7BB704B92F102A4C86305311C23C6F50243B7FBA at YUWEXCPM11.yuad.uds.yu.edu> > Content-Type: text/plain; charset="us-ascii" > > Hi Charles > > Thanks for the quick fix - that's done the job. > > cheers > Richard > > ________________________________________ > From: Charles Schwieters [charles at schwieters.org] > Sent: Monday, April 01, 2013 11:37 AM > To: Richard Harris > Cc: xplor-nih at nmr.cit.nih.gov > Subject: Re: [Xplor-nih] adding cis Proline in water refinment > > Hello Richard-- > > > > > I'm trying to include a cisProline in water refinement calculations - > > I'm > > using a modified version of the script found in > > eginput/gb1_rdc/wrefine.py. > > In earlier posts on this matter its suggested that there are two ways > > of > > doing this: > > > > 1) load a pre-generated PSF using protocol.initStruct, and then load > > the structure with protocol.initCoords instead of > > protocol.loadPDB. > > This will not work unless, in generating your psf, you use the water > refinement topology files as specified in wrefine.py. A psf generated > using standard Xplor-NIH topology settings will not work with water > refinement. > > > > > > 2) load the structure with protocol.loadPDB, and then correct the PSF > > information using psfGen.cisPeptide. > > > > In the script I have: > > import psfGen > > protocol.loadPDB(inputStructures[0],deleteUnknownAtoms=True) > > psfGen.cisPeptide(110) > > Unfortunately, the definition of the ``patch'' differs between > standard Xplor-NIH topologies and those used for water refinement. The > only way to do this on the fly here is to call the old XPLOR command > > xplor.command(''' > patch CIPP reference=nil=(resid XX) > ''') > > replacing XX with the appropriate residue number. psfGen.cisPeptide > should be fixed to give a more appropriate error message. > > best regards-- > Charles > > > > > ------------------------------ > > Message: 2 > Date: Mon, 01 Apr 2013 16:56:11 -0500 > From: Allison Didychuk <didychuk at wisc.edu> > Subject: [Xplor-nih] XPLOR problem > To: xplor-nih at nmr.cit.nih.gov > Message-ID: <76b0d26f1dbaa1.5159bc2b at wiscmail.wisc.edu> > Content-Type: text/plain; charset="iso-8859-1" > > ?Hello, > > ?I'm having trouble using an XPLOR script that you originally gave to > Jordan Burke to refine the structure of an RNA using data from SAXS, RDCs, > and minimal additional NMR data. Have you ever encountered this error > before? > > > ?This is the end of the log file: > > ?X-PLOR> > ?X-PLOR>end > ?[stdin](428): protocol.initDynamics(dyn, > ?[stdin](429): initVelocities=1, > ?[stdin](430): bathTemp=init_t, > ?[stdin](431): potList=potList, > ?[stdin](432): numSteps=10000, > ?[stdin](433): finalTime=10) > ?[stdin](434): dyn.run() > ?HBONDS: allocating space for 2025 h-bond interactions. > ?HBONDS: 0 distance exclusions and 0 angle exclusions > ?HBONDS: 205918 fixed h-bonds, currently 0 h-bonds present > ?HBONDS: allocating space for 2025 h-bond interactions. > ?HBONDS: ran out of space. Starting over. > ?HBONDS: allocating space for 4050 h-bond interactions. > ?HBONDS: 200042 distance exclusions and 3334 angle exclusions > ?HBONDS: 0 fixed h-bonds, currently 2542 h-bonds present > ?MAKINB: mode 3 found 0 exclusions, 0 interactions(1-4) and 0 GB exclusions > ?MAKINB: mode 3 found 8922 exclusions, 0 interactions(1-4) and 8922 GB > exclusions > ?HEAP: maximum use=440784760 current use=436363876 > ?X-PLOR: total CPU time= 3398.3701 s > ?X-PLOR: entry time at 17:05:14 28-Mar-13 > ?X-PLOR: exit time at 18:06:20 28-Mar-13 > > I've attached my script. When I comment out the dynamics step before the > anneal, the last part of the log file is: > > AT_Build::buildNode: cycle link found between atoms 2808 GUA 88 C3' and > 2784 GUA 88 C4' > removing bond. > AT_Build::buildNode: cycle link found between atoms 2834 GUA 89 C5 and > 2824 GUA 89 C4 > removing bond. > AT_Build::buildNode: cycle link found between atoms 2836 GUA 89 C8 and > 2823 GUA 89 N9 > removing bond. > AT_Build::buildNode: cycle link found between atoms 2842 GUA 89 C3' and > 2818 GUA 89 C4' > removing bond. > AT_Build::buildNode: cycle link found between atoms 2858 CYT 90 C6 and > 2857 CYT 90 N1 > removing bond. > AT_Build::buildNode: cycle link found between atoms 2873 CYT 90 C3' and > 2852 CYT 90 C4' > removing bond. > HBONDS: allocating space for 2025 h-bond interactions. > HBONDS: 0 distance exclusions and 0 angle exclusions > HBONDS: 205918 fixed h-bonds, currently 0 h-bonds present > HBONDS: allocating space for 2025 h-bond interactions. > HBONDS: ran out of space. Starting over. > HBONDS: allocating space for 4050 h-bond interactions. > HBONDS: 200042 distance exclusions and 3334 angle exclusions > HBONDS: 0 fixed h-bonds, currently 2542 h-bonds present > MAKINB: mode 3 found 0 exclusions, 0 interactions(1-4) and 0 GB exclusions > MAKINB: mode 3 found 8922 exclusions, 0 interactions(1-4) and 8922 GB > exclusions > HEAP: maximum use=440784760 current use=436363876 > X-PLOR: total CPU time= 3326.4299 s > X-PLOR: entry time at 19:25:21 31-Mar-13 > X-PLOR: exit time at 20:25:07 31-Mar-13 > > > If you have any suggestions on how to fix this, that would be great! Thank > you! > > > Allison Didychuk > Butcher Lab > -------------- next part -------------- > A non-text attachment was scrubbed... > Name: U4U6-xplor-no-rigid_DC1.py > Type: application/octet-stream > Size: 13710 bytes > Desc: not available > Url : > http://dcb.cit.nih.gov/pipermail/xplor-nih/attachments/20130401/e33d5411/attachment.obj > > ------------------------------ > > _______________________________________________ > Xplor-nih mailing list > Xplor-nih at nmr.cit.nih.gov > http://dcb.cit.nih.gov/mailman/listinfo/xplor-nih > > > End of Xplor-nih Digest, Vol 120, Issue 2 > ***************************************** > -- *P.Purushotham Reedy * * NMR division,IICT. * * * -------------- next part -------------- An HTML attachment was scrubbed... URL: http://dcb.cit.nih.gov/pipermail/xplor-nih/attachments/20130402/fb8fa1c0/attachment.html
