Re: [ccp4bb] Refmac Problem - Permission Denied
The problem is that every directory in lib/data/monomers has to be world writeable in order to use nfsv4 for refmac to run. Something that clearly I don't want to do... And why just the monomers directory is refmac trying to write something, or is it a broken nfslock I can easily fix this with an NFS v3 mount. Which is what I have done. Just wondered if anyone else has experienced this. On Sep 2, 2009, at 4:45 AM, Adam Ralph wrote: Hi David, Do all the client machines have NFSv4? You can force a mount to use NFSv3 by using nfsvers=3 as a mount option. I guess that the server might have something similar. That would allow you to make more secure directory settings. I am not sure how to fix the problem, it could be a bug. Certainly permissions on the lower directories are important, 'x' allows you to `cd` into that directory. Adam On Tue, 1 Sep 2009, David Jones wrote: Hi Adam I can write to the server, I can edit the files. overrode default permission, mounted as rw etc... Turns out every directory under monomers has to be owned by the user or have rwx permission for everyone set. I have made sure extended access control lists are turned off, mounted with insecure locking etc etc. nfs3 works without any problem with default permissions... not sure what I am missing here.. David David N. M. Jones, Ph.D. Associate Professor Dept. of Pharmacology Univ. of Colorado Denver 12801 East 17th Ave MS 8303, PO Box 6511 Aurora, CO 80045 e-mail david.jo...@ucdenver.edu Tel. (303) 724-3600 Cell(303) 916-7246 On Sep 1, 2009, at 6:47 AM, Adam Ralph wrote: Hi David, You have probably sorted this by now but can you save any files remotely to the server? The nfs disk will have mount options that could make it readonly, these will supercede any local permissions. Check /etc/fstab. Adam On Sat, 29 Aug 2009, David Jones wrote: I would appreciate if any one has any ideas on this I have a strange NFS related problem, if anyone has any ideas... I am running refmac with the ccp4 directories mounted on an nfs share (v4) mounted under /usr/local I get the following error... #CCP4I TERMINATION STATUS 0 Last system error message: Permission denied Refmac_5.5.0072: Open failed: File: /usr/local/ccp4-6.1.1/ lib/data/monomers/mon_lib_ind.cif However, to test this I have changed the permissions to 777 and uid and gid to the user's account. The user can see the file, and can even edit the file on the remote server. and yet it still fails. If I run refmac from the users account on the nfs server directly, then it runs with no problem. This is running under CentOS 5.3, fully patched etc, with SE linux turned off David N. M. Jones, Ph.D. Associate Professor Dept. of Pharmacology Univ. of Colorado Denver 12801 East 17th Ave MS 8303, PO Box 6511 Aurora, CO 80045 e-mail david.jo...@ucdenver.edu Tel. (303) 724-3600 Cell(303) 916-7246
Re: [ccp4bb] Refmac Problem - Permission Denied
On Aug 29, 2009, at 2:02 PM, Roger Rowlett wrote: Does it work with NFS v.3? Yes, it works with nfs v3. This is hard to think of as a bug in nfs4, as I can edit this file when mounted via nfs4. Every thing else works fine with nfs4, it just reading the CIF file. Can anyone explain what refmac is actually doing when opening the CIF file. Is it trying to write something somewhere else? Thanks David Jones Cheers. --Original Message-- From: David Jones Sender: CCP4 bulletin board To: CCP4BB@JISCMAIL.AC.UK ReplyTo: David Jones Subject: [ccp4bb] Refmac Problem - Permission Denied Sent: Aug 29, 2009 3:32 PM I would appreciate if any one has any ideas on this I have a strange NFS related problem, if anyone has any ideas... I am running refmac with the ccp4 directories mounted on an nfs share (v4) mounted under /usr/local I get the following error... #CCP4I TERMINATION STATUS 0 Last system error message: Permission denied Refmac_5.5.0072: Open failed: File: /usr/local/ccp4-6.1.1/ lib/data/monomers/mon_lib_ind.cif However, to test this I have changed the permissions to 777 and uid and gid to the user's account. The user can see the file, and can even edit the file on the remote server. and yet it still fails. If I run refmac from the users account on the nfs server directly, then it runs with no problem. This is running under CentOS 5.3, fully patched etc, with SE linux turned off David N. M. Jones, Ph.D. Associate Professor Dept. of Pharmacology Univ. of Colorado Denver 12801 East 17th Ave MS 8303, PO Box 6511 Aurora, CO 80045 e-mail david.jo...@ucdenver.edu Tel. (303) 724-3600 Cell(303) 916-7246 Roger Rowlett Professor Dept. of Chemistry Colgate University
[ccp4bb] Refmac Problem - Permission Denied
I would appreciate if any one has any ideas on this I have a strange NFS related problem, if anyone has any ideas... I am running refmac with the ccp4 directories mounted on an nfs share (v4) mounted under /usr/local I get the following error... #CCP4I TERMINATION STATUS 0 Last system error message: Permission denied Refmac_5.5.0072: Open failed: File: /usr/local/ccp4-6.1.1/ lib/data/monomers/mon_lib_ind.cif However, to test this I have changed the permissions to 777 and uid and gid to the user's account. The user can see the file, and can even edit the file on the remote server. and yet it still fails. If I run refmac from the users account on the nfs server directly, then it runs with no problem. This is running under CentOS 5.3, fully patched etc, with SE linux turned off David N. M. Jones, Ph.D. Associate Professor Dept. of Pharmacology Univ. of Colorado Denver 12801 East 17th Ave MS 8303, PO Box 6511 Aurora, CO 80045 e-mail david.jo...@ucdenver.edu Tel. (303) 724-3600 Cell(303) 916-7246
[ccp4bb] Postdoctoral Position in Structural Biology, Denver Colorado
Post Doctoral Position in X-ray crystallography at University of Colorado Denver An NIH funded post-doctoral position in X-ray crystallography is available in the Department of Pharmacology at the University of Colorado Denver School of Medicine, working with Dr. David N. Jones (http://pharmacology.ucdenver.edu/faculty/jones/jones.shtm). The work will focus on structural and biophysical analysis of olfactory proteins from the malaria mosquito Anopheles gambiae. Future studies will focus on identifying compounds that can disrupt normal olfactory process in the mosquito as possible way to control transmission of malaria from mosquitoes to humans. Applicants should have demonstrated expertise in X-ray crystallography including crystallization, data collection, processing, model building and refinement. In addition, experience in molecular biology techniques for cloning, expression and purification of target proteins is highly desirable. Experience with biophysical methods such as fluorescence, calorimetry and CD spectroscopy is a The University of Colorado Denver School of Medicine has recently relocated to the Anschutz Medical Campus in Aurora Colorado. This is a new campus and has world class facilities available for structural biology, including part ownership of the Molecular Biology Consortium Beamline 4.2.2. at the Advanced Light Source in Berkley, CA, and a 900 MHz NMR spectrometer for solution studies located in the School of Medicine. To apply for this position, please send a complete resume and a list of references to: Dr. David N. Jones email david.jo...@ucdenver.edu Please include Apply for Postdoc in your subject. or apply on line at https://www.jobsatcu.com job number 807347
