Re: [ccp4bb] Graphics for notebook
If using Linux, definitely a dedicated NVidia - their drivers are the best supported by far. There are also some issues right now with the drivers for some of the integrated Intel graphics cards, a bug with handling OpenGL applications which prevents O, Coot, and PyMOL from working properly, among others. If using Windows or Mac, anything will do but I would go with a dedicated card to keep the load off the CPU so it runs much smoother when moving. I've used discrete NVidia cards in all of my systems, always worked without any problems. Stuart ___ Stuart Endo-Streeter, Ph.D Dept. Computer Science 3245 French Family Science Center Duke University Medical Center 919-660-4068 stuart.endostree...@duke.edu -Original Message- From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of Eric Karg Sent: Sunday, September 19, 2010 11:46 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Graphics for notebook Dear all, I wanted to know which type of graphics card is more suitable for a notebook which is going to be used for structural biology. Integrated or dedicated? ATI or NVIDIA? At the moment I have to choose between an integrated Intel HD Graphics or a dedicated NVIDIA NVS 3100M Graphics. Any suggestions are highly appreciated. Thanks! Eric
[ccp4bb] anomalous phase extension to native data
Fellow crystallographers, I am helping a college with a structure and we've run into a bit of a jam. She has a 2.5 ang sel-met dataset, solved, and a 1.8 ang native dataset. We would like to extend the phase solution from the anomalous data to the native data. Unfortunately I have not been able to figure out how to do this using CCP4. The phase solution was calculated using PHENIX, which I have no real experience with yet, having worked with SHELX, CNS, and CCP4 in the past. Can anyone point out the programs, if any, in CCP4 (v6.1.3) to extend the phases from the 2.5 anomalous to the 1.8 native data? Thanks, Stuart Endo-Streeter
Re: [ccp4bb] configuration or install issue with tk
I was running from a root shell. Ubuntu does not let me login as root. That is normally a good thing, but if I remember correctly to finish the ccp4i setup last time I on a CentOS system I had to login as root. I will try to reinstall tomorrow using sudo, but frankly I hate using it. Stuart -Original Message- From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of Tim Gruene Sent: Monday, December 14, 2009 21:07 To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] configuration or install issue with tk With 'sudo' you should not have this issue. I agree, though, that having a separate user account to install crystallographic programs is quite an advantage from an administrative point of view. Tim -- Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A On Mon, 14 Dec 2009, Mark A. White wrote: Stuart, Are you logged-in as root or are you working in a root shell ( using su or sudo)? Depending on your security settings X-windows may not permit a program that is run from a root shell to access the display, which belongs to the user logged-in through X-windows. I get around the administrator access issue by installing CCP4, and all other non-OS software, with non-root ownership, a non-root administrator account, which shares the environment with all other users. For one thing, I do not want to source the multitude of /etc/csh.cshrc and .bashrc files as root. I am sure that others have different, and probably more elegant, solutions to this problem. PS. It also seems that the TCL/TK environment is not set in the root shell you are using. Good luck, Mark On Mon, 2009-12-14 at 16:51 -0600, Stuart Endostreeter wrote: Fellow users, I just installed v6.1.2 on Ubuntu 9.0.4 today and have run into the following problem when I try to run ccp4i for the first time as root to configure the program: r...@:/home//Documents# ccp4i No protocol specified Application initialization failed: couldn't connect to display :0.0 Error in startup script: can't read tk_version: no such variable while executing catch set system(TK_VERSION) $tk_version (file /usr/local/ccp4/ccp4-6.1.2/ccp4i/bin/ccp4i.tcl line 1) (file /usr/local/ccp4/ccp4-6.1.2//bin/ccp4i line 1) The odd thing is that I can launch ccp4i just fine as a regular user, but then of course I get the message about the first time ccp4i has been run and the need to configure it, which requires administrator level access. Anyone have any ideas? Thanks, Stuart Endo-Streeter Yours sincerely, Mark A. White, Ph.D. Assistant Professor, Dept. Biochemistry and Molecular Biology, Manager, Sealy Center for Structural Biology and Molecular Biophysics X-ray Crystallography Laboratory, Basic Science Building, Room 6.660 C University of Texas Medical Branch Galveston, TX 77555-0647 Tel. (409) 747-4747 Cell. (409) 539-9138 Fax. (409) 747-4745 mailto://wh...@xray.utmb.edu http://xray.utmb.edu http://xray.utmb.edu/~white
Re: [ccp4bb] install issue on win vista - where is the ccp4i executable? RESOLVED
It looks like there is a problem with the single-user installer file. My previous install attemps had been using the single-user installer, launched from my vista user account. When I ran the all-user installer from my user account (in both cases I of course had to enter the adminstrator password to continue installation), after the mandatory reboot CCP4 so far looks okay. I do not know yet if everything is working, but at least now CCP4i launches. There is still no entry in the start menu, so that still needs to be fixed. Hardly a major issue, but it might have a similar cause to why the single-user installer does not seem to work. Thanks to Dima Klenchin for suggestions and analysis of the error messages I got from the single-user install, Stuart Endo-Streeter On Monday 27 July 2009 20:00, you wrote: I get the following error when trying to run ccp4i.tcl with bltwish.exe: Can't read env(CCP4I_TOP): no such variable while executing file join $env(CCP4I_TOP) bin $system(OPSYS) startup.tcl invoked from within source [file join $env(CCP4I_TOP) bin $system(OPSYS) startup.tcl] (file C:\CCP4-Packages\ccp4-6.1.1\ccp4i\bin\ccp4i.tcl line 20) OK, seems to me that your installation is totally hosed. You are missing a whole bunch of environment variables. Either they were never set (did you reboot?) or they are pointing to the wrong directories. I had no issues at all installing on XP. On Win2K, however, all the pointers to Tcl had wrong directory and outdated executable name. Had to fix it all manually. Maybe on Vista the installer does not do what it's meant to do on tested XP... Dima -- __ Stuart T. Endo-Streeter Structural Biology and Biophysics Dept. Biochemistry LSRC C266 Duke University 919-681-1668 stuart.endostree...@duke.edu
[ccp4bb] install issue on win vista - where is the ccp4i executable?
Hopefully someone knows what is going on here, I ran the installation for CCP4 6.1.1 from the automated installer on my new vista system. It ran with no error messages, but after completion there is no start menu entry (unlike what the wiki says should show up). I can not find an executable or any way at all to launch ccp4i in any directory. I have gone to /ccp4-6.1.1/ccp4i/bin and tried the files there, including the one named ccp4i, but it has no accociation and does not launch. Does anyone have a clue what is going on here? I did the single-user install, was prompted for the administrator password, entered it, the istallation ran and seemed fine. I re-ran the installer to see if something was missing, everything was listed as installed. The ccp4mg viewer seems to work fine. According to the installation page Tcl/Tk and BLT should have been installed with ccp4i, so I do not know why the ccp4i interface is not launching. The environment variables are set to match the instructions on the installation page. Is something missing/broken in the installation files for use on vista? This is extremely frustrating and upsetting that after following the instructions ccp4 is not working. Thanks for any help, Stuart Endo-Streeter __ Stuart T. Endo-Streeter Structural Biology and Biophysics Dept. Biochemistry LSRC C266 Duke University 919-681-1668 stuart.endostree...@duke.edu
Re: [ccp4bb] install issue on win vista - where is the ccp4i executable?
I get the following error when trying to run ccp4i.tcl with bltwish.exe: Can't read env(CCP4I_TOP): no such variable while executing file join $env(CCP4I_TOP) bin $system(OPSYS) startup.tcl invoked from within source [file join $env(CCP4I_TOP) bin $system(OPSYS) startup.tcl] (file C:\CCP4-Packages\ccp4-6.1.1\ccp4i\bin\ccp4i.tcl line 20) I do not know how the set the association within the shortcut. I added the %1 %* to the end of the target line, but saw no where to enter the \Tcl-Tk++\bin\bltwish.exe %1 %* in its entirety. Adding the entire line to the end of the shortcut gives the same error message. -Original Message- From: Dima Klenchin [mailto:klenc...@facstaff.wisc.edu] Sent: Monday, July 27, 2009 17:49 To: Stuart Endo-Streeter Subject: Re: [ccp4bb] install issue on win vista - where is the ccp4i executable? I can not find an executable or any way at all to launch ccp4i in any directory. The executable is a script ccp4i.tcl found in \cp4-6.1.1\ccp4i\bin\. If you make a shortcut with that file as a target, the GUI should launch. If *.tcl files have no associations, you may not have Tcl/Tk installed properly. If it's just the association not set, set it manually: \Tcl-Tk++\bin\bltwish.exe %1 %* Dima
Re: [ccp4bb] 27.5% R/29% Rfree for 1.75A structure (details updated)
How are you deciding your resolution limit? I/sigma, Rmrgd-F, Rmeas, etc. etc.? We recently had a person in a fellow lab that couldn't figure why their R/Rfree was mid- to high-twenties for their 1.8 angstrom structure. Turned out the data stopped at 2.1. Stuart On Tuesday 29 July 2008 17:34, JINJIN ZHANG wrote: Dear All, Here are updated details for the high R problem of my 1.75A structure. 1. Protein 100 aa, peptide 6 aa, co-crystalized 2. Space group: P43212. Overall R-fac: 0.03. Redundancy: 5 for 98% of reflections. B-factor:55 3. CNS refinement 4. Phenix xtriage checked, no twinning is suspected. 5. Water molecules added Thanks a lot for all your comments and suggestions. Best, Jinjin Zhang -- __ Stuart T. Endo-Streeter Structural Biology and Biophysics Dept. Biochemistry LSRC C266 Duke University 919-681-1668 [EMAIL PROTECTED]
Re: [ccp4bb] How to generate two molecules of proteins and two chains of RNA in CNS 1.2
Does the log from generate show it reading in both RNA chains and do you have enough loading statements? Stuart Endo-Streeter On Thursday 08 May 2008 22:38, Sun Tang wrote: Dear All, When I used CNS 1.2 to generate the pdb file for two molecules of proteins and two chains of RNA (with different chain ids in format of CCP4), only one RNA chain is generated. Can anyone tell me how to correctly generate the files used for refinement with CNS 1.2? I downloaded the input files from the CNS website and I tried true and false for the renaming segid but all did not work. Thank you very much! Best, Sun Tang - Be a better friend, newshound, and know-it-all with Yahoo! Mobile. Try it now. -- __ Stuart T. Endo-Streeter Structural Biology and Biophysics Dept. Biochemistry LSRC C266 Duke University 919-681-1668 [EMAIL PROTECTED]
Re: [ccp4bb] How to generate two molecules of proteins and two chains of RNA in CNS 1.2
Is this a copy-paste error in the e-mail text, or what is in actually the
input file?
{* separate chains by segid - a new segid starts a new chain *}
{+ choice: true false +}
{===} n{= water files
=}
I do not see a value entered for the separate chains by segid line, which you
have for the protein entry.
Secondly, have you looked at the output for error messages and whether or not
the first RNA chain is being loaded at all? The input only lines are not
very useful without seeing the output messages. Also, it is much easier to
examine the script/output if they are attached as files, rather than pasted
into the e-mail text as that tends to disrupt formating, which is vital in
scripts running properly. I suggest repeating the generate run and making
sure to pass the output to a log file, ie;
cns generate.inp generate.log
and attaching both.
Stuart Endo-Streeter
On Friday 09 May 2008 10:49, you wrote:
Hi Stuart,
Thank you very much for your reply. Here are parts of the input files and
input pdb files for protein and RNA.
{ protein files
}
{* Multiple coordinate files of the same type can be defined by duplicating
all of the entries below and incrementing the file number *}
{* protein coordinate file *}
{===} prot_coordinate_infile_1=pro1.pdb;
{* protein coordinate file *}
{===} prot_coordinate_infile_1=;
{* rename segid *}
{+ choice: true false +}
{===} prot_rename_1=false;
{* new segid *}
{===} prot_segid_1=;
{* convert chainid to segid if chainid is non-blank *}
{+ choice: true false +}
{===} prot_convert_1=false;
{* separate chains by segid - a new segid starts a new chain *}
{+ choice: true false +}
{===} prot_separate_1=true;
{= nucleic acid files
==}
{* Multiple coordinate files of the same type can be defined by duplicating
all of the entries below and incrementing the file number *}
{* nucleic acid coordinate file *}
{===} nucl_coordinate_infile_1=rna1_fix1.pdb;
{* rename segid *}
{+ choice: true false +}
{===} nucl_rename_1=false;
{* new segid *}
{===} nucl_segid_1=;
{* convert chainid to segid if chainid is non-blank *}
{+ choice: true false +}
{===} nucl_convert_1=false;
{* separate chains by segid - a new segid starts a new chain *}
{+ choice: true false +}
{===} n{= water files
=}
{* Multiple coordinate files of the same type can be defined by duplicating
all of the entries below and incrementing the file number *}
{* water coordinate file *}
{===} water_coordinate_infile_1=wat1.pdb;
{* rename segid *}
{+ choice: true false +}
{===} water_rename_1=false;
{* new segid *}
{===} water_segid_1=;
{* convert chainid to segid if chainid is non-blank *}
{+ choice: true false +}
{===} water_convert_1=false;
ucl_separate_1=true;
Protein file (in ccp4 format, chain id A and B, I tried TER in between two
chains but I only got one chain without chain id in the output file):
ATOM 3648 N MET A 441 -23.689 56.526 -2.956 1.00 44.50
N ATOM 3649 CA MET A 441 -24.310 57.384 -1.938 1.00 44.45
C ATOM 3650 CB MET A 441 -25.149 58.499 -2.579 1.00 44.50
C ATOM 3651 CG MET A 441 -24.501 59.879 -2.532 1.00
44.46 C ATOM 3652 SD MET A 441 -22.874 59.965 -3.311
1.00 44.56 S ATOM 3653 CE MET A 441 -22.269 61.536
-2.683 1.00 44.75 C ATOM 3654 C MET A 441 -25.123
56.631 -0.897 1.00 44.48 C ATOM 3655 O MET A 441
-24.696 56.498 0.246 1.00 44.45 O ATOM 3656 N MET B 1
-45.555 -9.417 -57.617 1.00113.93 N ATOM 3657 CA MET B
1 -45.130 -10.808 -57.279 1.00113.94 C ATOM 3658 CB MET
B 1 -43.612 -10.967 -57.423 1.00113.96 C ATOM 3659 CG
MET B 1 -43.090 -10.777 -58.844 1.00114.01 C ATOM 3660
SD MET B 1 -41.347 -11.208 -59.036 1.00114.04 S ATOM
3661 CE MET B 1 -41.442 -12.983 -59.254 1.00113.94 C
ATOM 3662 C MET B 1 -45.569 -11.200 -55.870 1.00113.87
C ATOM 3663 O MET B 1 -45.526 -10.384 -54.946 1.00113.85
O ATOM 8004 O3' CYT C 34 -52.544 55.320 4.307 1.00 19.69
O TER
ATOM 8005 P GUA D 1 -6.118 -6.004 -20.448 0.00 70.19
P
RNA file:
ATOM 8003 C3' CYT C 24 -53.327 54.167 4.053 1.00 19.76
C ATOM 8004 O3' CYT C 24 -52.544 55.320 4.307 1.00 19.69
O TER
ATOM 8005 P GUA D 1 -6.118 -6.004 -20.448 0.00 70.19
P ATOM 8006 O1P GUA D 1 -4.884 -5.391 -20.997 0.00 70.16
O
The output file only has the second chain
Re: [ccp4bb] Seeking Linux experts' adivice
Sounds like an OpenGL graphics driver misconfiguration to me. What is the graphics card and driver, and like Kay asked, how was the driver configured? A friend's computer at one of the lab's here had similar issues, turns out the NVidia driver was severly misconfigured. Fixed following the readme and everything was fine. I'm also running CentOS 4 i386, no issues. Stuart On Wednesday 19 September 2007 05:46, Yanming Zhang wrote: Hi, All, After lunching pymol, if I drag the Xterm window produced by PYMOL using mouse, my computer will suddenly freeze, the keyboard seems no longer functioning. The only thing I can do is to re-boot my Linux system. This problem makes it almost impossible for me to use PYMOL on my LINUX box(CENTOS 4 i386). I have had the same problem when using COOT, ccp4i. Relacing the keyboard and mouse with new ones can not solving this problem. Thanks for your help Yanming -- __ Stuart T. Endo-Streeter Structural Biology and Biophysics Dept. Biochemistry LSRC C266 Duke University 919-681-1668 [EMAIL PROTECTED]
Re: [ccp4bb] Archiving onto DVD with RH linux
Acording to the product specs from NEC that drive model is only designed to write up to 8X speed, it was never intended to write any faster. Nothing wrong with the drive, it just is not designed to burn any faster. For burning 16X discs at 8X speed, maybe a firmware update, or maybe it is a settings issue, but using 16X discs will just cost you more so I would suggest not worrying about it and either sticking with 8X discs or getting a new, higher-speed burner. Stuart On Wednesday 19 September 2007 10:41, david lawson (JIC) wrote: Dear ccp4BB, Sorry for the non-ccp4 post. I have been using a NEC DVD_RW ND-2500A drive to archive onto DVD-Rs (using 'mkisofs' and 'dvdrecord' commands) from our RH linux system. This has worked very well with 8x compatible DVD-R disks, but doesn't recognise the newer 16x disks that only seem to be available now. I suspect I will need to buy a new drive. I would be grateful of any recommendations - particularly drives that are likely to be more 'future-proof' if we go to 32x, 64x ... Thanks in advance, Dave --- Dr. David M. Lawson Biological Chemistry Dept., John Innes Centre, Norwich, NR4 7UH, UK. Tel: +44-(0)1603-450725 Fax: +44-(0)1603-450018 Email: [EMAIL PROTECTED] Web: http://www.jic.bbsrc.ac.uk/staff/david-lawson/index.htm -- __ Stuart T. Endo-Streeter Structural Biology and Biophysics Dept. Biochemistry LSRC C266 Duke University 919-681-1668 [EMAIL PROTECTED]
Re: [ccp4bb] Problem converting CNS cv file to mtz using f2mtz
What are you entering for the fortran format section and how many lines are
you skipping? Helps to know what you have tried and how. May also help to
attach your CNS cv header and first two-three reflections instead of
cut-pasting into the e-mail body since the formating, spacing tends to get
changed. Looks like you would use the following fortran format, does this
match what you have used?
'(6X,3F5.0,6X,F10.3,17X,F10.3,6X,F10.0)'
Number of lines to skip = 5
I've been converting files like crazy the last couple of days, I ran into the
cannot read first reflection message when the format was not set correctly.
Stuart Endo-Streeter
On Friday 27 July 2007 20:29, Ryan Watkins wrote:
Hello Colleagues,
I'm trying to convert a cns cv file to a CCP4 mtz file. I have only
Fobs and SigFs. Unfortunately, I cannot get f2mtz to work and am
looking for some help. The program dies either with a cannot read
first reflection or with a child killed: bus error error. Here are
the 1st few lines of my file:
NREFlection=140763
ANOMalous=FALSe { equiv. to HERMitian=TRUE}
DECLare NAME=FOBS DOMAin=RECIprocal TYPE=COMP END
DECLare NAME=SIGMA DOMAin=RECIprocal TYPE=REAL END
DECLare NAME=TEST DOMAin=RECIprocal TYPE=INTE END
INDE -4601 FOBS=63.800 0.000 SIGMA=33.060
TEST= 0
INDE -4602 FOBS= 168.800 0.000 SIGMA=19.440
TEST= 0
INDE -4603 FOBS= 331.700 0.000 SIGMA=13.850
TEST= 0
INDE -4611 FOBS= 210.000 0.000 SIGMA=13.400
TEST= 0
INDE -4612 FOBS= 297.800 0.000 SIGMA=11.830
TEST= 0
INDE -4501 FOBS= 559.100 0.000 SIGMA=18.030
TEST= 1
INDE -4502 FOBS= 500.400 0.000 SIGMA=16.800
TEST= 0
Thank you,
Ryan
Ryan Watkins
Postdoctoral Fellow
Brennan Lab
MD Anderson Cancer Center
--
__
Stuart T. Endo-Streeter
Structural Biology and Biophysics
Dept. Biochemistry
LSRC C266
Duke University
919-681-1668
[EMAIL PROTECTED]
Re: [ccp4bb] need help for viewing hardware stereo
Are you using the NVidia drivers and if so, how have you configured your xorg.conf file? It may be a hardware or a configuration issue. A fellow lab here was having a problem with no OpenGL programs running properly and odd resolution issues after installing the NVidia drivers, turned out the xorg.conf file had not been properly edited. - Original Message - From: venkadesan krishnan To: CCP4BB@JISCMAIL.AC.UK Sent: Monday, July 16, 2007 19:56 Subject: Re: [ccp4bb] need help for viewing hardware stereo Dear all, I think our earlier posting is not clear. So we would like to draw to your attention regarding our stereo viewing problem. As Dr. Paul Emsley suggested it seems to be a harware problem, we are experiencing the same problem not only using coot but other programs too. We will be thankful to you if you could anyone help us to fix the problem for your kind information here is our system graphics card specification 256MB PClex16 nVidia Quadro Fx 3450, Dual DVI or Dual VGA or DVI + VGA. Thanking you vengadesan On 7/16/07, Paul Emsley [EMAIL PROTECTED] wrote: Hello venkadesan krishnan, On Mon, 2007-07-16 at 15:57 -0500, venkadesan krishnan wrote: Hello everyone, We have bought a new Dell Precision Workstation 690 (32-bit) and installed Fedora core 6. We are having problem while viewing molecules in harware stereo mode using programs coot, pymol, etc. The graphics card came with system is, 256MB PClex16 nVidia Quadro Fx 3450, Dual DVI or Dual VGA or DVI + VGA. In coot it shows the following message in the terminal, WARNING:: Can't enable stereo visual - falling back INFO:: Hardware stereo widget opened successfully INFO:: switch to hardware_stereo_mode succeeded That is a confusing message. I can't imagine how you got it if you simply installed a binary package :-/ However, that code path does mean that Coot failed to get a hardware stereo graphics context, which leads me to think that it's a hardware issue, not software. (Oh, we are talking about 0.3.3, aren't we?) Paul.
