Re: [ccp4bb] Off Topic: How to delete loops from a protein
I've found that predator is one of the best services of this sort: Ref: PROTEINS: Structure, Function, and Genetics 27:329–335 (1997) Server: http://mobyle.pasteur.fr/cgi-bin/portal.py?#forms::predator The server is slow but the service is good. James On Jul 18, 2011, at 10:47 PM, Francois Berenger wrote: Hi Obayed, If I understood your question well, you are looking for something called secondary structure prediction. I googled these keywords and found this server: http://bioinf.cs.ucl.ac.uk/psipred/ You may find other interesting servers on the web and some literature comparing them. I think such methods need only the sequence of your protein to predict its secondary structures. Hope this helps, Francois. On 07/19/2011 02:14 PM, Eric Larson wrote: Hi Obayed, you could give in situ protolysis a try. This is where you add a bit of protease along with you target protein to the crystallization drop. It has been quite successful for the folks at the SGC. Here are the relevant references: Dong A, et al. In situ proteolysis for protein crystallization and structure determination. Nat Methods. 2007 Dec;4(12):1019-21.PMID: 17982461. (http://www.ncbi.nlm.nih.gov/pubmed/17982461) Wernimont A, Edwards A. In situ proteolysis to generate crystals for structure determination: an update. PLoS One. 2009;4(4):e5094. PMID: 19352432. (http://www.ncbi.nlm.nih.gov/pubmed/19352432) good luck, Eric Eric T. Larson, PhD Biomolecular Structure Center Department of Biochemistry Box 357742 University of Washington Seattle, WA 98195 email: larso...@u.washington.edu On Mon, 18 Jul 2011, Obayed Ullah wrote: Hi all I wrote last time but got only one feedback. I know some of you guys must have this experience that how to delete loops from the protein. Please help me with suggestions. I am working with a human protein which have around 20% sequence identity with the other proteins of the same family. Structure of some of the proteins from this family have been solved. All the solved structures have around 20% identity with my protein. I am trying to crystallize the protein but it looks like very hard to get crystal. I have tried different N and C terminally truncated constructs for crystallization but no crystal. My feeling is that probably there is some flexible loops with in the protein which limiting the crystallization. So I want to delete the loops with in the protein (not to truncate in the terminal, I already have done this). I am not asking suggestion about how to delete the loop rather how to decide where the loop is. I am not sure how much it will be helpful to get a homology model of such a protein having low sequence identity. Is there any strategy to decide where the loop could be? Does anybody know any established/ rational method to do that. Waiting for your suggestions Obayed Ullah
[ccp4bb] Permissions and ownerships in ccp4 6.2.0
Hello, version 6.2.0 of ccp4 has strange permissions set to several setup/configuration scripts which are read while sourcing ccp4.setup. For a long time, ccp4 packages have been distributed with some arbitrary file and directory ownerships which users are obviously supposed to edit to meet their needs. On unix/linux workstations, we usually install under /usr/local and change all ownerships to root.root (default practice for third-party software). Up to now, this has not caused any problems. In version 6.2.0, however, ccp4.setup has permissions rwx r-- --- which makes it unreadable (and un-sourcable) for ordinary users! Strangely, ccp4-others.setup has the usual permissions rwx r-x r-x (although rw- r-- r-- should be sufficient for sourcing). After rectifying the permissions of ccp4.setup, additional errors appear, concerning permissions of several scripts in the xia2 and phaser trees: ccp4-6.2.0/share/xia2/setup.csh ccp4-6.2.0/share/xia2/xia2core/setup.csh ccp4-6.2.0/share/xia2/xia2/setup.csh ccp4-6.2.0/src/phaser/bin/machine_type ccp4-6.2.0/src/phaser/conf/version.csh All these files have the same problematic permissions as ccp4.setup. After fixing them, ccp4.setup can be sourced without errors. The bad thing is that there may be many more issues of this kind, which will only surface when trying to run a specific ccp4 program... Maybe the developers or packagers could comment on this issue. It looks like this ccp4 version is supposed to be installed in a user's home directory, so that he/she can take ownership of all the files. While in general there is nothing wrong with this type of installation, it should _NOT_ be considered the default on unix-type (i.e. multi-user) operating systems. Best regards, Oliver PD Dr. Oliver H. Weiergräber Institute of Complex Systems ICS-6: Structural Biochemistry Tel.: +49 2461 61-2028 Fax: +49 2461 61-1448 Forschungszentrum Juelich GmbH 52425 Juelich Sitz der Gesellschaft: Juelich Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498 Vorsitzender des Aufsichtsrats: MinDirig Dr. Karl Eugen Huthmacher Geschaeftsfuehrung: Prof. Dr. Achim Bachem (Vorsitzender), Dr. Ulrich Krafft (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt, Prof. Dr. Sebastian M. Schmidt
[ccp4bb] phenix.phaser params.eff labin problems
Dear all, I am now writing a script for phenix.phaser. In the input file params.eff there is a keyword labin which corresponds to the labels inside input mtz files. The important columns in my ccp4 mtz file are FP, SIGFP. I edit the line of labin as: labin F=FP SIGF=SIGFP when running the script, it returns me: Syntax error: expected =, found F (file params.eff, line 9) So, I changed it like: labin=FP SIGFP when running, it gave me the message: Sorry: Couldn't find array FP SIGP in file I also tried: labin=FP or labin = FP SIGFP or labin=labin F=FP and so on. With nothing it can find the right columns. My mtz file should be no problem. I checked with mtzdmp, the columns FP and SIGFP were there and with phenix GUI this file works well. Would someone know exactly how to edit this line in params.eff? Many thanks! GP
Re: [ccp4bb] Permissions and ownerships in ccp4 6.2.0
Dear Oliver and others, an alternative way of installing system-wide third party software is with a non-root account that is in the same group as all the users. Use that account to install software centrally and initialize in each user's .bashrc. (Root is used only for administrative tasks on the local machines and installation of RPMs.) Users can use all the software but have no permission to tinker with it and potentially screw it up. Still, with this setup, there's a problem with ccp4 6.2. ccp4-6.2.0/src/phaser/bin/machine_type needs to be made executable for the group. Andreas On 19/07/2011 11:25, Weiergräber, Oliver H. wrote: Hello, version 6.2.0 of ccp4 has strange permissions set to several setup/configuration scripts which are read while sourcing ccp4.setup. For a long time, ccp4 packages have been distributed with some arbitrary file and directory ownerships which users are obviously supposed to edit to meet their needs. On unix/linux workstations, we usually install under /usr/local and change all ownerships to root.root (default practice for third-party software). Up to now, this has not caused any problems. In version 6.2.0, however, ccp4.setup has permissions rwx r-- --- which makes it unreadable (and un-sourcable) for ordinary users! Strangely, ccp4-others.setup has the usual permissions rwx r-x r-x (although rw- r-- r-- should be sufficient for sourcing). After rectifying the permissions of ccp4.setup, additional errors appear, concerning permissions of several scripts in the xia2 and phaser trees: ccp4-6.2.0/share/xia2/setup.csh ccp4-6.2.0/share/xia2/xia2core/setup.csh ccp4-6.2.0/share/xia2/xia2/setup.csh ccp4-6.2.0/src/phaser/bin/machine_type ccp4-6.2.0/src/phaser/conf/version.csh All these files have the same problematic permissions as ccp4.setup. After fixing them, ccp4.setup can be sourced without errors. The bad thing is that there may be many more issues of this kind, which will only surface when trying to run a specific ccp4 program... Maybe the developers or packagers could comment on this issue. It looks like this ccp4 version is supposed to be installed in a user's home directory, so that he/she can take ownership of all the files. While in general there is nothing wrong with this type of installation, it should _NOT_ be considered the default on unix-type (i.e. multi-user) operating systems. Best regards, Oliver PD Dr. Oliver H. Weiergräber Institute of Complex Systems ICS-6: Structural Biochemistry Tel.: +49 2461 61-2028 Fax: +49 2461 61-1448 Forschungszentrum Juelich GmbH 52425 Juelich Sitz der Gesellschaft: Juelich Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498 Vorsitzender des Aufsichtsrats: MinDirig Dr. Karl Eugen Huthmacher Geschaeftsfuehrung: Prof. Dr. Achim Bachem (Vorsitzender), Dr. Ulrich Krafft (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt, Prof. Dr. Sebastian M. Schmidt -- Andreas Förster, Research Associate Paul Freemont Xiaodong Zhang Labs Department of Biochemistry, Imperial College London http://www.msf.bio.ic.ac.uk
Re: [ccp4bb] Permissions and ownerships in ccp4 6.2.0
We are working to relax the permissions on the files to rwx r-x r-x Charles Ballard CCP4 On 19 Jul 2011, at 11:25, Weiergräber, Oliver H. wrote: Hello, version 6.2.0 of ccp4 has strange permissions set to several setup/configuration scripts which are read while sourcing ccp4.setup. For a long time, ccp4 packages have been distributed with some arbitrary file and directory ownerships which users are obviously supposed to edit to meet their needs. On unix/linux workstations, we usually install under /usr/local and change all ownerships to root.root (default practice for third-party software). Up to now, this has not caused any problems. In version 6.2.0, however, ccp4.setup has permissions rwx r-- --- which makes it unreadable (and un-sourcable) for ordinary users! Strangely, ccp4-others.setup has the usual permissions rwx r-x r-x (although rw- r-- r-- should be sufficient for sourcing). After rectifying the permissions of ccp4.setup, additional errors appear, concerning permissions of several scripts in the xia2 and phaser trees: ccp4-6.2.0/share/xia2/setup.csh ccp4-6.2.0/share/xia2/xia2core/setup.csh ccp4-6.2.0/share/xia2/xia2/setup.csh ccp4-6.2.0/src/phaser/bin/machine_type ccp4-6.2.0/src/phaser/conf/version.csh All these files have the same problematic permissions as ccp4.setup. After fixing them, ccp4.setup can be sourced without errors. The bad thing is that there may be many more issues of this kind, which will only surface when trying to run a specific ccp4 program... Maybe the developers or packagers could comment on this issue. It looks like this ccp4 version is supposed to be installed in a user's home directory, so that he/she can take ownership of all the files. While in general there is nothing wrong with this type of installation, it should _NOT_ be considered the default on unix-type (i.e. multi-user) operating systems. Best regards, Oliver PD Dr. Oliver H. Weiergräber Institute of Complex Systems ICS-6: Structural Biochemistry Tel.: +49 2461 61-2028 Fax: +49 2461 61-1448 Forschungszentrum Juelich GmbH 52425 Juelich Sitz der Gesellschaft: Juelich Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498 Vorsitzender des Aufsichtsrats: MinDirig Dr. Karl Eugen Huthmacher Geschaeftsfuehrung: Prof. Dr. Achim Bachem (Vorsitzender), Dr. Ulrich Krafft (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt, Prof. Dr. Sebastian M. Schmidt
Re: [ccp4bb] CCP4BB Digest - 17 Jul 2011 to 18 Jul 2011 (#2011-199)
Could you please unsuscribe me from this mailing list? My e-mail address is : a...@novalix-pharma.com Thanks, Regards, Aurélie Martinez. - Message d'origine - De: CCP4BB automatic digest system lists...@jiscmail.ac.uk Date: Tue, 19 Jul 2011 00:04:10 +0100 Sujet: CCP4BB Digest - 17 Jul 2011 to 18 Jul 2011 (#2011-199) À: CCP4BB@JISCMAIL.AC.UK There are 9 messages totaling 627 lines in this issue. Topics of the day: 1. Bypassing phase separation for nice crystals. (3) 2. unusual sighting of a crystal structure (2) 3. Off Topic: PDB validation server 4. un-subscribe 5. Data from old tapes (2) -- Date: Mon, 18 Jul 2011 09:52:31 -0400 From: F. Timur Senguen Subject: Bypassing phase separation for nice crystals. Hi everyone, I have been issues with a particular protein. I have been close for a while, but yet so far. Rather than going from a clear drop to crystal, my protein first undergoes phase separation (large oily drops) in which one phase contains most, if not all, of the protein. This phase separation occurs within a day of preparing the drop. A day after phase separation the oily phase is now a large disordered crystalline mass which does not diffract very well. I have tried changing buffer concentrations, precipitant amounts, ionic strengths and pH and in all cases this phenomenon is observed. I even screened protein concentrations to see if reducing protein concentration would prevent the phase separation. Is there any way to bypass this phase separation, which I think prevents me from obtaining nice crystals. Should I try detergents, chaotropes, or other additives? Thanks in advance. Timur -- F. Timur Senguen, Ph.D. Postdoctoral Research Fellow Boston Biomedical Research Institute 64 Grove Street, Watertown, MA 02472 USA -- Date: Mon, 18 Jul 2011 22:30:04 +0800 From: Albert Guskov Subject: Re: Bypassing phase separation for nice crystals. Hi Timur, have you tried seeding from your microstalline stuff? Might be worth to try! Cheers, Albert Albert GUSKOV (Dr) | Research Fellow | Division of Structural Computational Biology | Nanyang Technological University Proteos 7-01, Biopolis Drive 61, Singapore 138673 Tel: (65) 6586-9690 GMT+8h | Cell: (65) 8366-2779 | Email: a.gus...@ntu.edu.sg | Web: www.ntu.edu.sg 2011/7/18 F. Timur Senguen Hi everyone, I have been issues with a particular protein. I have been close for a while, but yet so far. Rather than going from a clear drop to crystal, my protein first undergoes phase separation (large oily drops) in which one phase contains most, if not all, of the protein. This phase separation occurs within a day of preparing the drop. A day after phase separation the oily phase is now a large disordered crystalline mass which does not diffract very well. I have tried changing buffer concentrations, precipitant amounts, ionic strengths and pH and in all cases this phenomenon is observed. I even screened protein concentrations to see if reducing protein concentration would prevent the phase separation. Is there any way to bypass this phase separation, which I think prevents me from obtaining nice crystals. Should I try detergents, chaotropes, or other additives? Thanks in advance. Timur -- F. Timur Senguen, Ph.D. Postdoctoral Research Fellow Boston Biomedical Research Institute 64 Grove Street, Watertown, MA 02472 USA -- Date: Mon, 18 Jul 2011 17:05:07 +0200 From: Florian Sauer Subject: Re: Bypassing phase separation for nice crystals. Original-Nachricht Betreff: Re: [ccp4bb] Bypassing phase separation for nice crystals. Datum: Mon, 18 Jul 2011 17:01:27 +0200 Von: Florian Sauer An: F. Timur Senguen CC: CCP4BB@JISCMAIL.AC.UK Dear Timur, one possibility to handle this problem can be the change from vapor (I assume this is what you do) to the free interface diffusion method. Phase separation often occurs if the protein is immediately exposed to the full precipitant concentration while it might not escape into its own phase if it gets slowly equilibrated. There are commercial setups available for this method but you can also do it in a normal vapor diffusion plate. To do so, just put the protein and precipitant drops next to each other and then link them through a thin liquid bridge. Requires some practice and works best with large drops but helped me in several similar cases. Good luck! Florian Am 18.07.11 15:52, schrieb F. Timur Senguen: Hi everyone, I have been issues with a particular protein. I have been close for a while, but yet so far. Rather than going from a clear drop to crystal, my protein first undergoes phase separation (large oily drops) in which one phase contains most, if not all, of the protein.
[ccp4bb] arp/warp error
I've recently installed arp/warp(7.1) in ccp4 6.2 in linux i686,the problem is whenever I'm trying to run arp/warp navigator or any other programs under arp/warp it gives the error cannot get environment variable for warpbin Please help. Thanks in advance. Seema Nath
Re: [ccp4bb] Permissions and ownerships in ccp4 6.2.0
While we're on the subject of issues with the ccp4 6.20 distribution, I've had a problem with the Mac OS X package installer. It seems to be missing the ccp4i executable. Launching the application gives the following error: 19/07/2011 13:04:02 [0x0-0x269269].com.yourcompany.ccp4[17160] /Applications/ccp4-6.2.0/ccp4.app/Contents/Resources/ccp4.sh: line 202: /Applications/ccp4-6.2.0/bin/ccp4i: No such file or directory I've searched what gets installed in /Applications/ccp4-6.20 and there is no ccp4i. The package installer also has the aforementioned issues with script permissions. Regards, Chris -- Dr Chris Richardson :: Sysadmin, structural biology, icr.ac.uk The Institute of Cancer Research: Royal Cancer Hospital, a charitable Company Limited by Guarantee, Registered in England under Company No. 534147 with its Registered Office at 123 Old Brompton Road, London SW7 3RP. This e-mail message is confidential and for use by the addressee only. If the message is received by anyone other than the addressee, please return the message to the sender by replying to it and then delete the message from your computer and network.
Re: [ccp4bb] Permissions and ownerships in ccp4 6.2.0
Dear all,
ideally, permissions should be either
rw-r--r-- (0644)
or (for files that need to be executed as well as directories)
rwxr-xr-x (0755)
One quick fix:
find . -type d -exec chmod -v 0755 {} ;
find . -type f -exec chmod -v 0755 {} ;
but that last command makes every single file executable, which is
rather ugly (but doing a selective chmod 0755/0644 is a bit tricky
with all those script files - some need to be executed but others
arent). I don't see a need to have read-only files like all the CIF
dictionaries with permission 0755.
The correct permissions can only be set during packaging
unfortunately.
Cheers
Clemens
--
***
* Clemens Vonrhein, Ph.D. vonrhein AT GlobalPhasing DOT com
*
* Global Phasing Ltd.
* Sheraton House, Castle Park
* Cambridge CB3 0AX, UK
*--
* BUSTER Development Group (http://www.globalphasing.com)
***
Re: [ccp4bb] arp/warp error
Hello Seema, I believe this error occurs because ARP/wARP has not been setup within the startup file for the shell that you are using. For instance, if you use bash (the default under most Linux distributions) you need to add the following line to the .bashrc file in your home directory: source /path/to/arpwarp/arpwarp_setup.bash If this doesn't fix the problem, or my instructions are unclear, please don't hesitate to contact me directly. Saul Hazledine On Jul 19, 2011, at 1:51 PM, Seema Nath wrote: I've recently installed arp/warp(7.1) in ccp4 6.2 in linux i686,the problem is whenever I'm trying to run arp/warp navigator or any other programs under arp/warp it gives the error cannot get environment variable for warpbin Please help. Thanks in advance. Seema Nath
Re: [ccp4bb] Permissions and ownerships in ccp4 6.2.0
Dear all,
or use a modified version of Clemens's commands for that:
find . -perm 700 -exec chmod 755 {} \;
find . -perm 750 -exec chmod 755 {} \;
find . -perm 600 -exec chmod 644 {} \;
find . -perm 640 -exec chmod 644 {} \;
Best regards,
Dirk.
Am 19.07.11 14:34, schrieb Clemens Vonrhein:
Dear all,
ideally, permissions should be either
rw-r--r-- (0644)
or (for files that need to be executed as well as directories)
rwxr-xr-x (0755)
One quick fix:
find . -type d -exec chmod -v 0755 {} ;
find . -type f -exec chmod -v 0755 {} ;
but that last command makes every single file executable, which is
rather ugly (but doing a selective chmod 0755/0644 is a bit tricky
with all those script files - some need to be executed but others
arent). I don't see a need to have read-only files like all the CIF
dictionaries with permission 0755.
The correct permissions can only be set during packaging
unfortunately.
Cheers
Clemens
--
***
Dirk Kostrewa
Gene Center Munich, A5.07
Department of Biochemistry
Ludwig-Maximilians-Universität München
Feodor-Lynen-Str. 25
D-81377 Munich
Germany
Phone: +49-89-2180-76845
Fax:+49-89-2180-76999
E-mail: kostr...@genzentrum.lmu.de
WWW:www.genzentrum.lmu.de
***
[ccp4bb] CCP4 releases
Just a general curiosity - did I miss the release announcement for the 6.2.0 version on the bb or is it the CCP4 policy not to make such announcements? Perhaps the idea is to prevent people rushing to download the latest release and crushing the server :) -- I'd jump in myself, if I weren't so good at whistling. Julian, King of Lemurs
Re: [ccp4bb] Bypassing phase separation for nice crystals.
Thanks for all the suggestions. I forgot to mention that I had tried microseeding and it was partially successful. I am trying this while also pursuing other venues. At Florian's suggestion I have set up a free interface diffusion method and it looks very promising. I have a few free floating crystals that seem somewhat flawed, but otherwise very nice. I will try combining microseeding techniques and free interface diffusion to make THE crystal. Timur On Mon, Jul 18, 2011 at 11:01 AM, Florian Sauer sa...@embl-hamburg.dewrote: Dear Timur, one possibility to handle this problem can be the change from vapor (I assume this is what you do) to the free interface diffusion method. Phase separation often occurs if the protein is immediately exposed to the full precipitant concentration while it might not escape into its own phase if it gets slowly equilibrated. There are commercial setups available for this method but you can also do it in a normal vapor diffusion plate. To do so, just put the protein and precipitant drops next to each other and then link them through a thin liquid bridge. Requires some practice and works best with large drops but helped me in several similar cases. Good luck! Florian Am 18.07.11 15:52, schrieb F. Timur Senguen: Hi everyone, I have been issues with a particular protein. I have been close for a while, but yet so far. Rather than going from a clear drop to crystal, my protein first undergoes phase separation (large oily drops) in which one phase contains most, if not all, of the protein. This phase separation occurs within a day of preparing the drop. A day after phase separation the oily phase is now a large disordered crystalline mass which does not diffract very well. I have tried changing buffer concentrations, precipitant amounts, ionic strengths and pH and in all cases this phenomenon is observed. I even screened protein concentrations to see if reducing protein concentration would prevent the phase separation. Is there any way to bypass this phase separation, which I think prevents me from obtaining nice crystals. Should I try detergents, chaotropes, or other additives? Thanks in advance. Timur -- F. Timur Senguen, Ph.D. Postdoctoral Research Fellow Boston Biomedical Research Institute 64 Grove Street, Watertown, MA 02472 USA -- F. Timur Senguen, Ph.D. Postdoctoral Research Fellow Boston Biomedical Research Institute 64 Grove Street, Watertown, MA 02472 USA
Re: [ccp4bb] off-topic: LCD monitors
You don't mention many other details about your stereo setup, so I will asssume you have/plan to get a nVidia 3D Vision setup. If those are the only 3 choices, I would cross off the Samsung. It is a year older technology, with lower resolution and significant crosstalk. The ASUS and the Alienware are largely equivalent in resolution, screen size, and other specs. The clearest difference is that the ASUS has a glossy screen, rather than the more common anti-glare coating. So if you plan to use it in a room with other equipment and can't dim the lights, it may be more prone to annoying reflections. This is one of those features that some people like and some people hate. I tend toward the hate side. If you want to expand your list of choices, here is the nVidia page for qualified display devices: http://www.nvidia.com/object/3d-vision-requirements.html There are some new options coming out now like the Acer GN245HQ, which has A) LED backlighting and B) the stereo IR emitter built into the monitor. I have not yet seen a clear statement from either nVidia or Acer about Linux compatibility though. On 07/18/11 19:12, Padmaja Mehta-D'souza wrote: Pardon the off-topic query, but I would like to get some feedback about any personal preference for 3D LCD monitors. I am trying to decide between the following 3 monitors: *Samsung 2233RZ* 1680 x 1050 2D and 3d Widescreen LCD Monitor Asus VG236H 23 2ms 1920x1080 Full HD 120Hz 3D multimedia Height Swivel Adjustable WideScreen LCD Alienware OptX AW2310 23 3D Full HD Widescreen Monitor The monitor will display off of a Mac Pro Two Quad-Core Intel Xeon computer running both Apple and Linux OS. Any input will be much appreciated. Padmaja -- === All Things Serve the Beam === David J. Schuller modern man in a post-modern world MacCHESS, Cornell University schul...@cornell.edu
Re: [ccp4bb] Permissions and ownerships in ccp4 6.2.0
Another option is to use the recursive feature of chmod to
change the permissions on the files. E.g.
chmod -R a+rX .
which will recursively add read for all users to files (and directories) and
will
also add execute if the file is a directory or if it already has at least one
execute
bit set.
Regards,
Mitch
From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] On Behalf Of Dirk Kostrewa
[kostr...@genzentrum.lmu.de]
Sent: Tuesday, July 19, 2011 6:14 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Permissions and ownerships in ccp4 6.2.0
Dear all,
or use a modified version of Clemens's commands for that:
find . -perm 700 -exec chmod 755 {} \;
find . -perm 750 -exec chmod 755 {} \;
find . -perm 600 -exec chmod 644 {} \;
find . -perm 640 -exec chmod 644 {} \;
Best regards,
Dirk.
Am 19.07.11 14:34, schrieb Clemens Vonrhein:
Dear all,
ideally, permissions should be either
rw-r--r-- (0644)
or (for files that need to be executed as well as directories)
rwxr-xr-x (0755)
One quick fix:
find . -type d -exec chmod -v 0755 {} ;
find . -type f -exec chmod -v 0755 {} ;
but that last command makes every single file executable, which is
rather ugly (but doing a selective chmod 0755/0644 is a bit tricky
with all those script files - some need to be executed but others
arent). I don't see a need to have read-only files like all the CIF
dictionaries with permission 0755.
The correct permissions can only be set during packaging
unfortunately.
Cheers
Clemens
--
***
Dirk Kostrewa
Gene Center Munich, A5.07
Department of Biochemistry
Ludwig-Maximilians-Universität München
Feodor-Lynen-Str. 25
D-81377 Munich
Germany
Phone: +49-89-2180-76845
Fax:+49-89-2180-76999
E-mail: kostr...@genzentrum.lmu.de
WWW:www.genzentrum.lmu.de
***
Re: [ccp4bb] off-topic: LCD monitors
My $0.02. My old lab had the Samsung and an Acer. The Samsung was small and worked well in a dedicated graphics room. The Acer died just after the warrantee period. I now have a 23in Zalman attached to my macbook pro. Outside of stereo viewing the text is alright, but not as clear as my Asus 27in monitor that does 1900x1200. The stereo viewing in PyMOL is fantastic and I think on par with the 3d Vision shutter system without the need for emitter compatibility and batteries in the glasses. Plus, if I need extra glasses, I just bring a set home after going to see a 3D movie at the theater. The real draw back to the Zalman is menu/text viewing in stereo. Then the resolution is poor and reading is impossible so memorize where the functions you use most are. The biggest drawback to all these monitors is the display size, which makes the new 27in consumer monitor by Acer, HN274H bmiiid, a monitor worth looking into, IMHO. Keep up the discussion. Chris -- Christopher L. Colbert, Ph.D. Assistant Professor Department of Chemistry and Biochemistry North Dakota State University P.O. Box 6050 Dept. 2710 Fargo, ND 58108-6050 PH: (701) 231-7946 FAX: (701) 231-8324 From: David Schuller dj...@cornell.edumailto:dj...@cornell.edu Reply-To: schul...@cornell.edumailto:schul...@cornell.edu schul...@cornell.edumailto:schul...@cornell.edu Date: Tue, 19 Jul 2011 06:57:21 -0700 To: CCP4BB@JISCMAIL.AC.UKmailto:CCP4BB@JISCMAIL.AC.UK CCP4BB@JISCMAIL.AC.UKmailto:CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] off-topic: LCD monitors
[ccp4bb] Poor proline electron density
Dear all, Recently I crystallized and solved the structure of a protein using molecular replacement. The crystal diffracts to 1.8A and has the R free of 0.21. During refmac and phenix refinement, I found that the N-terminal (~25 amino acids) electron density wasn't quite good, especially a proline residue. It not only has little side chain electron density, but also doesn't have continuous electron density between backbone C-N until the sigma level going down until 1.2. A normal backbone sigma contour level is above 2.5 in this structure. I calculated composite omit map as well as the difference map. In addition, NCS maps of those were calculated. But its density is still unclear. As proline normally has rigid structure and good electron density, will this mean some potential mistake in the structure? There seems no other way to trace the backbone. And the upstream and downstream residues are not that bad. If no way to find the solution, could there be an explanation about the poor electron density of protein. By the way, this proline is connecting a beta-sheet and an alpha-helix, which is on the surface of the protein. Also, the protein is soluble and has about 300 amino acids. You kind suggestions will be greatly appreciated! Dolphin
Re: [ccp4bb] Permissions and ownerships in ccp4 6.2.0
but that last command makes every single file executable, which is
rather ugly (but doing a selective chmod 0755/0644 is a bit tricky
I was wondering about having every file executable in the source
distributions a while back, and came up with an quick way to make it
less ugly (inline due to attachment filtering on my end):
##
#!/usr/bin/env bash
noexe()
{
local fn=$1
local pfx=`echo $fn | cut -c -3`
#don't mess with mercurial store; adjust as needed for different
# vcs
if [ $pfx = .hg ]; then
return
fi
local ft=`file $fn | grep exe`
if [ $ft = ]; then
#not supposed to be executable, fix it
chmod -x $fn
fi
}
#using while loop rather than find -exec because -exec doesn't
# recognize bash functions.
find . -type f |while read i; do noexe $i ; done
with all those script files - some need to be executed but others
arent). I don't see a need to have read-only files like all the CIF
dictionaries with permission 0755.
The correct permissions can only be set during packaging
unfortunately.
Cheers
Clemens
Re: [ccp4bb] Data from old tapes
did you try looking if there is a company offering data recovery services from these kind of tapes? if there is, there may not be a need to buy a tape drive yourself.Mark Quoting Min, Xiaoshan: Dear CCP4 community, We have a few datasets that reside in tapes (Sony QG-112M 8 mm tape and Maxell DDS-2 4 mm tape). I have been searching the internet for tape drives ( and cable) but haven't found anything. Does anyone know where we can purchase compatible tape drives for these lovely tapes? Or if you have a spare working set sitting in your graphic room and would like to sell them, that will be wonderful. Thanks. Xiaoshan Min. Ph.D. Molecular Structure Amgen San Francisco 1120 Veterans Blvd. South San Francisco, CA 94080 Mark J van Raaij Laboratorio M-4 Dpto de Estructura de Macromoléculas Centro Nacional de Biotecnología - CSIC c/Darwin 3, Campus Cantoblanco 28049 Madrid tel. 91 585 4616 email: mjvanra...@cnb.csic.es
Re: [ccp4bb] off-topic: LCD monitors
Dear Padmaja, I have use Samsung 2233RZ for stereo running on Linux and Windows systems. Perfomance is great. HTH Guenter Pardon the off-topic query, but I would like to get some feedback about any personal preference for 3D LCD monitors. I am trying to decide between the following 3 monitors: *Samsung 2233RZ* 1680 x 1050 2D and 3d Widescreen LCD Monitor Asus VG236H 23 2ms 1920x1080 Full HD 120Hz 3D multimedia Height Swivel Adjustable WideScreen LCD Alienware OptX AW2310 23 3D Full HD Widescreen Monitor The monitor will display off of a Mac Pro Two Quad-Core Intel Xeon computer running both Apple and Linux OS. Any input will be much appreciated. Padmaja
Re: [ccp4bb] Off Topic: How to delete loops from a protein/homology modeling
Hi Obayed, even though there is 20% sequence identity you may be able to get a very good homology model, especially if there is more than one protein structure in the PDB with 20% homology. Then you can overlap the pdbs and find out what structurally needs to be preserved as opposed to what is in total homology preserved. Typically it is the position of turns residues G, D, S, P, N etc. You won't know until you thread your protein through both pdbs and compare them all. Swiss Pro's Expasy has an easy program that will take an alignment with a pdb and generate a homology model with loops spliced in and energy minimized. There are many other more or less complicated programs, but it's a good one to start with. Paul Dr. Paul Kraft Structural Biologist cell 586-596-2770 email: haresea...@yahoo.com email: kraft_proteome_resea...@yahoo.com This communication and any attachments contain information which is confidential and may also be privileged. It is for the exclusive use of the intended recipient(s). If you are not the intended recipient(s) please note that any form of disclosure, distribution, copying or use of this communication or the information in it or in any attachments is strictly prohibited and may be unlawful. If you have received this communication in error, please notify the sender and delete the email and destroy any copies of it. E-mail communications cannot be guaranteed to be secure or error free, as information could be intercepted, corrupted, amended, lost, destroyed, arrive late or incomplete, or contain viruses. We do not accept liability for any such matters or their consequences. Anyone who communicates with us by e-mail is taken to accept the risks in doing so. --- On Tue, 7/19/11, James Stroud xtald...@gmail.com wrote: From: James Stroud xtald...@gmail.com Subject: Re: [ccp4bb] Off Topic: How to delete loops from a protein To: CCP4BB@JISCMAIL.AC.UK Date: Tuesday, July 19, 2011, 2:37 AM I've found that predator is one of the best services of this sort: Ref: PROTEINS: Structure, Function, and Genetics 27:329–335 (1997) Server: http://mobyle.pasteur.fr/cgi-bin/portal.py?#forms::predator The server is slow but the service is good. James On Jul 18, 2011, at 10:47 PM, Francois Berenger wrote: Hi Obayed, If I understood your question well, you are looking for something called secondary structure prediction. I googled these keywords and found this server: http://bioinf.cs.ucl.ac.uk/psipred/ You may find other interesting servers on the web and some literature comparing them. I think such methods need only the sequence of your protein to predict its secondary structures. Hope this helps, Francois. On 07/19/2011 02:14 PM, Eric Larson wrote: Hi Obayed, you could give in situ protolysis a try. This is where you add a bit of protease along with you target protein to the crystallization drop. It has been quite successful for the folks at the SGC. Here are the relevant references: Dong A, et al. In situ proteolysis for protein crystallization and structure determination. Nat Methods. 2007 Dec;4(12):1019-21.PMID: 17982461. (http://www.ncbi.nlm.nih.gov/pubmed/17982461) Wernimont A, Edwards A. In situ proteolysis to generate crystals for structure determination: an update. PLoS One. 2009;4(4):e5094. PMID: 19352432. (http://www.ncbi.nlm.nih.gov/pubmed/19352432) good luck, Eric Eric T. Larson, PhD Biomolecular Structure Center Department of Biochemistry Box 357742 University of Washington Seattle, WA 98195 email: larso...@u.washington.edu On Mon, 18 Jul 2011, Obayed Ullah wrote: Hi all I wrote last time but got only one feedback. I know some of you guys must have this experience that how to delete loops from the protein. Please help me with suggestions. I am working with a human protein which have around 20% sequence identity with the other proteins of the same family. Structure of some of the proteins from this family have been solved. All the solved structures have around 20% identity with my protein. I am trying to crystallize the protein but it looks like very hard to get crystal. I have tried different N and C terminally truncated constructs for crystallization but no crystal. My feeling is that probably there is some flexible loops with in the protein which limiting the crystallization. So I want to delete the loops with in the protein (not to truncate in the terminal, I already have done this). I am not asking suggestion about how to delete the loop rather how to decide where the loop is. I am not sure how much it will be helpful to get a homology model of such a protein having low sequence identity. Is there any strategy to decide where the loop could be? Does anybody know any established/ rational method to do that. Waiting for your suggestions Obayed Ullah
Re: [ccp4bb] Off Topic: How to delete loops from a protein/homology modeling
Homer is one of the best services for homology modeling: http://protein.cribi.unipd.it/Homer/ James On Jul 19, 2011, at 2:06 PM, Paul Kraft wrote: Hi Obayed, even though there is 20% sequence identity you may be able to get a very good homology model, especially if there is more than one protein structure in the PDB with 20% homology. Then you can overlap the pdbs and find out what structurally needs to be preserved as opposed to what is in total homology preserved. Typically it is the position of turns residues G, D, S, P, N etc. You won't know until you thread your protein through both pdbs and compare them all. Swiss Pro's Expasy has an easy program that will take an alignment with a pdb and generate a homology model with loops spliced in and energy minimized. There are many other more or less complicated programs, but it's a good one to start with. Paul Dr. Paul Kraft Structural Biologist cell 586-596-2770 email: haresea...@yahoo.com email: kraft_proteome_resea...@yahoo.com This communication and any attachments contain information which is confidential and may also be privileged. It is for the exclusive use of the intended recipient(s). If you are not the intended recipient(s) please note that any form of disclosure, distribution, copying or use of this communication or the information in it or in any attachments is strictly prohibited and may be unlawful. If you have received this communication in error, please notify the sender and delete the email and destroy any copies of it. E-mail communications cannot be guaranteed to be secure or error free, as information could be intercepted, corrupted, amended, lost, destroyed, arrive late or incomplete, or contain viruses. We do not accept liability for any such matters or their consequences. Anyone who communicates with us by e-mail is taken to accept the risks in doing so. --- On Tue, 7/19/11, James Stroud xtald...@gmail.com wrote: From: James Stroud xtald...@gmail.com Subject: Re: [ccp4bb] Off Topic: How to delete loops from a protein To: CCP4BB@JISCMAIL.AC.UK Date: Tuesday, July 19, 2011, 2:37 AM I've found that predator is one of the best services of this sort: Ref: PROTEINS: Structure, Function, and Genetics 27:329–335 (1997) Server: http://mobyle.pasteur.fr/cgi-bin/portal.py?#forms::predator The server is slow but the service is good. James On Jul 18, 2011, at 10:47 PM, Francois Berenger wrote: Hi Obayed, If I understood your question well, you are looking for something called secondary structure prediction. I googled these keywords and found this server: http://bioinf.cs.ucl.ac.uk/psipred/ You may find other interesting servers on the web and some literature comparing them. I think such methods need only the sequence of your protein to predict its secondary structures. Hope this helps, Francois. On 07/19/2011 02:14 PM, Eric Larson wrote: Hi Obayed, you could give in situ protolysis a try. This is where you add a bit of protease along with you target protein to the crystallization drop. It has been quite successful for the folks at the SGC. Here are the relevant references: Dong A, et al. In situ proteolysis for protein crystallization and structure determination. Nat Methods. 2007 Dec;4(12):1019-21.PMID: 17982461. (http://www.ncbi.nlm.nih.gov/pubmed/17982461) Wernimont A, Edwards A. In situ proteolysis to generate crystals for structure determination: an update. PLoS One. 2009;4(4):e5094. PMID: 19352432. (http://www.ncbi.nlm.nih.gov/pubmed/19352432) good luck, Eric Eric T. Larson, PhD Biomolecular Structure Center Department of Biochemistry Box 357742 University of Washington Seattle, WA 98195 email: larso...@u.washington.edu On Mon, 18 Jul 2011, Obayed Ullah wrote: Hi all I wrote last time but got only one feedback. I know some of you guys must have this experience that how to delete loops from the protein. Please help me with suggestions. I am working with a human protein which have around 20% sequence identity with the other proteins of the same family. Structure of some of the proteins from this family have been solved. All the solved structures have around 20% identity with my protein. I am trying to crystallize the protein but it looks like very hard to get crystal. I have tried different N and C terminally truncated constructs for crystallization but no crystal. My feeling is that probably there is some flexible loops with in the protein which limiting the crystallization. So I want to delete the loops with in the protein (not to truncate in the terminal, I already have done this). I am not asking suggestion about how to delete the loop rather how to decide where the loop is. I am not sure how much it will be
