Re: [ccp4bb] Ghostview in CCP4 configure interface
Thank you! this works perfectly fine! (I was not smart enough to put the path into both boxes) Yes, had to change forward to backward slash (or how one calls them) and it is saved now. Thank you very much!!! Cheers, Tanya On Fri, Jun 17, 2011 at 4:30 PM, Zhijie Li wrote: > ** > Hi Tatyana, > > It is funny that I just had that same problem a few days ago. > > Here is the solution: > > First of all, install Ghostgum and Ghostscript to your computer- which you > have done. I installed them to my C:\Program Files\ directory. > > Then in CCP4i->system configuration->Config CCP4interface->Hardware > resources, remove those default "xv"(the linux equivalent as I remember) > lines, then make a new line, fill the path to the gsview32.exe into both > brackets: > > Enter names and commands for Postscript Viewers > C:/Program Files/Ghostgum/gsview/gsview32.exe > C:/Program Files/Ghostgum/gsview/gsview32.exe > > Please also refer to the attached screenshot. > > When everything is set correctly, the behavior of the program is that when > you ask the ccp4i to display a .plt file, it fires up the gsview, and the > map slices are displayed in a multipage ps file. > > Zhijie > > > > *From:* Tatyana Sysoeva > *Sent:* Friday, June 17, 2011 12:53 PM > *To:* CCP4BB@JISCMAIL.AC.UK > *Subject:* [ccp4bb] Ghostview in CCP4 configure interface > > Hi! > > > I am having a problem of visualizing the PLT files in CCP4 6.1.13 CCP1 > interface 2.0.7 running on Windows 7/64. > I installed the GSscript and GSview but I am not sure how to change > parameters in the System administration. > > Any help and advice will be highly appreciated! > > > >
Re: [ccp4bb] Ghostview in CCP4 configure interface
Forgot to mention: the trick is, CCP4i uses the Linux/UNIX '/' to specify the subdirectories, not the Windows '\'. That is why if you copy the path from windows explorer and paste it it won't work. From: Tatyana Sysoeva Sent: Friday, June 17, 2011 12:53 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Ghostview in CCP4 configure interface Hi! I am having a problem of visualizing the PLT files in CCP4 6.1.13 CCP1 interface 2.0.7 running on Windows 7/64. I installed the GSscript and GSview but I am not sure how to change parameters in the System administration. Any help and advice will be highly appreciated!
Re: [ccp4bb] Ghostview in CCP4 configure interface
Hi Tatyana, It is funny that I just had that same problem a few days ago. Here is the solution: First of all, install Ghostgum and Ghostscript to your computer- which you have done. I installed them to my C:\Program Files\ directory. Then in CCP4i->system configuration->Config CCP4interface->Hardware resources, remove those default "xv"(the linux equivalent as I remember) lines, then make a new line, fill the path to the gsview32.exe into both brackets: Enter names and commands for Postscript Viewers C:/Program Files/Ghostgum/gsview/gsview32.exe C:/Program Files/Ghostgum/gsview/gsview32.exe Please also refer to the attached screenshot. When everything is set correctly, the behavior of the program is that when you ask the ccp4i to display a .plt file, it fires up the gsview, and the map slices are displayed in a multipage ps file. Zhijie From: Tatyana Sysoeva Sent: Friday, June 17, 2011 12:53 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Ghostview in CCP4 configure interface Hi! I am having a problem of visualizing the PLT files in CCP4 6.1.13 CCP1 interface 2.0.7 running on Windows 7/64. I installed the GSscript and GSview but I am not sure how to change parameters in the System administration. Any help and advice will be highly appreciated! <>
Re: [ccp4bb] Ghostview in CCP4 configure interface
On Fri, Jun 17, 2011 at 06:25:14PM +0100, Ian Tickle wrote: > Hi, the '.plt' files are in an internal CCP4 format & cannot be visualised > directly. You have to convert them first to PostScript (.ps) format using > the 'pltdev' program; then you can visualise them with ghostscript (or any > other PS viewer). Or you can view them directly with the 'xplot84driver' program which comes as part of CCP4? 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] Ghostview in CCP4 configure interface
Thanks! How do I get the pltdev? I checked the program list in CCP4 and it is not there, so I need to download it, I presume, and install. cheers, Tanya On Fri, Jun 17, 2011 at 1:25 PM, Ian Tickle wrote: > > Hi, the '.plt' files are in an internal CCP4 format & cannot be visualised > directly. You have to convert them first to PostScript (.ps) format using > the 'pltdev' program; then you can visualise them with ghostscript (or any > other PS viewer). > > Cheers > > -- Ian > > > On Fri, Jun 17, 2011 at 5:53 PM, Tatyana Sysoeva > wrote: > >> Hi! >> >> >> I am having a problem of visualizing the PLT files in CCP4 6.1.13 CCP1 >> interface 2.0.7 running on Windows 7/64. >> I installed the GSscript and GSview but I am not sure how to change >> parameters in the System administration. >> >> Any help and advice will be highly appreciated! >> >> >> >> >
Re: [ccp4bb] Ghostview in CCP4 configure interface
Hi, the '.plt' files are in an internal CCP4 format & cannot be visualised directly. You have to convert them first to PostScript (.ps) format using the 'pltdev' program; then you can visualise them with ghostscript (or any other PS viewer). Cheers -- Ian On Fri, Jun 17, 2011 at 5:53 PM, Tatyana Sysoeva wrote: > Hi! > > > I am having a problem of visualizing the PLT files in CCP4 6.1.13 CCP1 > interface 2.0.7 running on Windows 7/64. > I installed the GSscript and GSview but I am not sure how to change > parameters in the System administration. > > Any help and advice will be highly appreciated! > > > >
[ccp4bb] Ghostview in CCP4 configure interface
Hi! I am having a problem of visualizing the PLT files in CCP4 6.1.13 CCP1 interface 2.0.7 running on Windows 7/64. I installed the GSscript and GSview but I am not sure how to change parameters in the System administration. Any help and advice will be highly appreciated!
Re: [ccp4bb] Nanodrop versus Nanophotomter Pearl versus good old Bradford.
To add to this discussion:
Many of the comments to my question that started this thread do not
sufficiently differentiate between accuracy and precision.
While we all want an assay that is internally consistent (i.e., high
precision), we do care a lot about accuracy ("the degree of closeness of
measurements of a quantity to that quantity's actual (true) value" [from
http://en.wikipedia.org/wiki/Accuracy_and_precision])
One person actually stated that accuracy is not that important, but
rather that precision is important. I disagree. When it comes to
calculating kinetic parameters or binding spectrometry, an accurate
reading (i.e. true) of the protein concentration is paramount.
So what I have been hearing (corrections welcome) is the following;
1. The Nanodrop may have an issue with precision due to various factors,
such as evaporation while on the pedestal, dirt on the pedestal, and
drifting from calibration. But if you squint, one can be happy with the
machine
2. Bradford also as issues (low correlation with dye binding between
standard protein used for calibration and one's sample). However, this
assay can be highly precise.
There were only few comments on the NanoPhotometer™ Pearl, so more
real-life experiences on that instrument would be helpful.
Cheers.
Arnon
--
***
Arnon Lavie, Professor
Dept. of Biochemistry and Molecular Genetics
University of Illinois at Chicago
900 S. Ashland Ave.
Molecular Biology Research Building, Room 1108 (M/C 669)
Chicago, IL 60607
U.S.A.
Tel:(312) 355-5029
Fax:(312) 355-4535
E-mail: la...@uic.edu
http://www.uic.edu/labs/lavie/
***
Re: [ccp4bb] Help! low resolution protein-DNA complex
Another thing you should bookmark and check out is the Molprobity page (google for it), upload your pdb file and let it evaluate what you have done. The chart it generates will guide you through your structure and you will be able to do a good job. Jürgen .. Jürgen Bosch Johns Hopkins Bloomberg School of Public Health Department of Biochemistry & Molecular Biology Johns Hopkins Malaria Research Institute 615 North Wolfe Street, W8708 Baltimore, MD 21205 Phone: +1-410-614-4742 Lab: +1-410-614-4894 Fax: +1-410-955-3655 http://web.mac.com/bosch_lab/ On Jun 17, 2011, at 8:30, Robbie Joosten wrote: > Dear Xun, > > > > I have a 3.2A dataset for a protein-DNA complex. The protein is > > > a homodimer, and the DNA is almost palindromic (except one base pair > > > in the middle and two or three base pairs at both two ends). It is my > > > first time solving structures, and unfortunately the resolution is > > > low. No body in our lab has used ccp4 or phenix, so I am really > > > frustrated as a second year student. > > Your frustration is understandable. It is somewhat of an expectation in > > academia that your advisor will either help you directly or if she/he is > > not familiar with the methodology you are forced to use, will find > > someone to help you. The questions you ask surely may be answered by > > someone in your department. IMHO, a second year student should not be > > left alone to battle his first structure which happens to be 3.2A > > protein/DNA complex. > Indeed, this is just asking for problems. It's a good call that you asked for > help. Perhaps your supervisor can arrage for you to be embedded in a > crystallography lab for a while. That should give you easy access to people > with experience. > > > > I mainly used ccp4. So far, the best R/Rfree I got is 0.27/0.34. > > and that is not bad given the resolution > You are heading the right way. You should be able to close the R/R-free gap a > bit more. > > > > I went to the crystallography meeting, and people suggested me to > > > rely more on geometry. I remember I got a DNA restraints file and a > > > refmac script from someone on this mailing list, and that really > > > helped (otherwise the DNA base pairing will be weird). Can someone > > > tell me how to restraint the protein (helix)? > > one way of doing it would be to restrain the hydrogen bonds that > > stabilize the helix. It is not advisable at higher resolution, but > > sounds alright at 3.2A. I once used a restraint file to keep DNA sane > > by forcing Watson-Crick pairing, the helical restraints would work > > pretty mnuch in the same way. Look at the structure of the restraint > > file that you have and modify it to include the helix-stabilizing > > hydrogen bonds. > I like real-space refining everything in Coot with tight helical restraints. > You may need to chainge the default restraint weight matrix (lower numbers > give tighter restraints). The options are under the "R/RC" button. > > > > People also suggested me to include NCS and TLS in the > > > refinement, but I don't know how to. For NCS, I should define a region > > > that are the same in both monomers? Should I use tight or loose > > > restraints? For TLS, I don't have a clue. > > Yes and tight (at least at first). For TLS you may want to take a look > > at the TLSMD server. (Also, consider tighter restraints on B-factors). > > Otherwise, just define TLS for the whole thing, then protein and DNA > > separately, then individual monomers and whatever pieces of DNA common > > sense suggests would move together. Keep whatever combination gives you > > the lowest Rfree. > In Refmac you can use "local NCS" which takes away the need to mess with NCS > selections (which can be really difficult). Although it is not needed for > Refmac, you should make sure that the same residues in different monomers > have the same residue number. Be conservative with TLS (in the beginning). > One group per chain sounds right. In the case of your DNA you can consider > putting both chains in one group. Tight B-factor weights may be needed, you > could also trying one overall B factor. I personally only do that when TLS > works well. Oh, and always use riding hydrogens in refinement. It helps a lot > at low resolution, because of the VDW restraints. For that same reason you > should not be too conservative with the sidechains (at least not for the ones > in the core of the protein). > > Since you have only started building you should probably go through the > entire structure a few times. After that, use structure validation tools > frequently. WHAT_CHECK and Molprobity are must-use tools for that. Coot also > has many usefull features for validation. Good luck. > > Cheers, > Robbie Joosten
Re: [ccp4bb] Follow-up: non-waters among structured solvent atoms
For the record:-UNK is for unknown residues only. That means that you know that you are looking at an amino acid you just don't know which. You should assign element types. It used to be defined to CB (just like ALA), it now goes to CG. I don't see the point of this update.-UNL is for unknown hetero compounds.-UNX is for unknown solo atoms.-DN id for unknown deoxy nucleotide. Cheers,Robbie Date: Fri, 17 Jun 2011 12:22:50 +0100 From: twom...@globalphasing.com Subject: Re: [ccp4bb] Follow-up: non-waters among structured solvent atoms To: CCP4BB@JISCMAIL.AC.UK On 16 Jun 2011, at 17:19, Pavel Afonine wrote:Hi, On Thu, Jun 16, 2011 at 7:49 AM, Jan Dohnalek wrote: Modeling more UNKNOWN atoms might be the future for these cases? one needs to specify chemical element type in 77-78 position, otherwise these records are useless. But if you know the chemical element type then there's no point in calling it UNK. BUSTER uses the scattering factors for oxygen for modelling X, on the grounds that you'll have put in an X because it doesn't look enough unlike water to be obviously something else. Tom
Re: [ccp4bb] Help! low resolution protein-DNA complex
Dear Xun, > > I have a 3.2A dataset for a protein-DNA complex. The protein is > > a homodimer, and the DNA is almost palindromic (except one base pair > > in the middle and two or three base pairs at both two ends). It is my > > first time solving structures, and unfortunately the resolution is > > low. No body in our lab has used ccp4 or phenix, so I am really > > frustrated as a second year student. > Your frustration is understandable. It is somewhat of an expectation in > academia that your advisor will either help you directly or if she/he is > not familiar with the methodology you are forced to use, will find > someone to help you. The questions you ask surely may be answered by > someone in your department. IMHO, a second year student should not be > left alone to battle his first structure which happens to be 3.2A > protein/DNA complex.Indeed, this is just asking for problems. It's a good > call that you asked for help. Perhaps your supervisor can arrage for you to > be embedded in a crystallography lab for a while. That should give you easy > access to people with experience. > > I mainly used ccp4. So far, the > best R/Rfree I got is 0.27/0.34. > and that is not bad given the resolutionYou are heading the right way. You > should be able to close the R/R-free gap a bit more. > > I went to the crystallography meeting, and people suggested me to > > rely more on geometry. I remember I got a DNA restraints file and a > > refmac script from someone on this mailing list, and that really > > helped (otherwise the DNA base pairing will be weird). Can someone > > tell me how to restraint the protein (helix)? > one way of doing it would be to restrain the hydrogen bonds that > stabilize the helix. It is not advisable at higher resolution, but > sounds alright at 3.2A. I once used a restraint file to keep DNA sane > by forcing Watson-Crick pairing, the helical restraints would work > pretty mnuch in the same way. Look at the structure of the restraint > file that you have and modify it to include the helix-stabilizing > hydrogen bonds.I like real-space refining everything in Coot with tight > helical restraints. You may need to chainge the default restraint weight > matrix (lower numbers give tighter restraints). The options are under the > "R/RC" button. > > People also suggested me to include NCS and TLS in > the > > refinement, but I don't know how to. For NCS, I should define a region > > that are the same in both monomers? Should I use tight or loose > > restraints? For TLS, I don't have a clue. > Yes and tight (at least at first). For TLS you may want to take a look > at the TLSMD server. (Also, consider tighter restraints on B-factors). > Otherwise, just define TLS for the whole thing, then protein and DNA > separately, then individual monomers and whatever pieces of DNA common > sense suggests would move together. Keep whatever combination gives you > the lowest Rfree.In Refmac you can use "local NCS" which takes away the need > to mess with NCS selections (which can be really difficult). Although it is > not needed for Refmac, you should make sure that the same residues in > different monomers have the same residue number. Be conservative with TLS (in > the beginning). One group per chain sounds right. In the case of your DNA you > can consider putting both chains in one group. Tight B-factor weights may be > needed, you could also trying one overall B factor. I personally only do that > when TLS works well. Oh, and always use riding hydrogens in refinement. It > helps a lot at low resolution, because of the VDW restraints. For that same > reason you should not be too conservative with the sidechains (at least not > for the ones in the core of the protein). Since you have only started building you should probably go through the entire structure a few times. After that, use structure validation tools frequently. WHAT_CHECK and Molprobity are must-use tools for that. Coot also has many usefull features for validation. Good luck. Cheers,Robbie Joosten
Re: [ccp4bb] Help! low resolution protein-DNA complex
Thank you!! It's really encouraging & refreshing to begin a day with so many advices! ccp4bb is always helpful~ Thanks to one of my committee member who suggested me to get out a paper from the structure, and thanks to all the people at the mid-Atlantic crystallography meeting who told me my structure was solvable and encouraged me to do it. Xun
Re: [ccp4bb] Follow-up: non-waters among structured solvent atoms
On 16 Jun 2011, at 17:19, Pavel Afonine wrote: > Hi, > > On Thu, Jun 16, 2011 at 7:49 AM, Jan Dohnalek wrote: > > Modeling more UNKNOWN atoms might be the future for these cases? > > one needs to specify chemical element type in 77-78 position, otherwise these > records are useless. But if you know the chemical element type then there's no point in calling it UNK. BUSTER uses the scattering factors for oxygen for modelling X, on the grounds that you'll have put in an X because it doesn't look enough unlike water to be obviously something else. Tom
[ccp4bb] Fortran runtime error, Refmac
Hello everyone, I got this error, attached below, while running a restrained refinement in Refmac-5.5.0109. I tried to run the refinement by removing the SCALE entries in pdb file but got the same error. * Information from CCP4Interface script *** The program run with command: /home/indico/abhik/softwares/xtal/CCP4-Lin-generic /ccp4-6.1.13/bin/refmac5 XYZIN "/home/indico/abhik/structures/alfama/HB/Hem_x2_5 54_Maio11/2QSS_bov_hb_6.3_refmac15-coot-0_mo7_model.pdb" XYZOUT "/home/indico/ab hik/structures/alfama/HB/Hem_x2_554_Maio11/2QSS_bov_hb_6.3_refmac16.pdb" HKLIN " /home/indico/abhik/structures/alfama/HB/Hem_x2_554_Maio11/x2_554_5_0001_pointles s_dm1.mtz" HKLOUT "/home/indico/abhik/structures/alfama/HB/Hem_x2_554_Maio11/x2_ 554_5_0001_pointless_refmac2_model.mtz" LIBIN "/home/indico/abhik/structures/alf ama/HB/Hem_x2_554_Maio11/heme_554_may11_9_lib.cif" LIBOUT "/home/indico/abhik/st ructures/alfama/HB/Hem_x2_554_Maio11/heme_554_may11_31_lib.cif" has failed with error message At line 1117 of file /usr/local/xtal/ccp4-6.1.13/src/refmac5_/make_PDB.f Fortran runtime error: Bad value during floating point read *** #CCP4I TERMINATION STATUS 0 At line 1117 of file /usr/local/xtal/ccp4-6.1.13/src /refmac5_/make_PDB.f Fortran runtime error: Bad value during floating point read #CCP4I TERMINATION TIME 16 Jun 2011 18:12:48 #CCP4I MESSAGE Task failed What could be the possible reason for this error message. Thanks in advance. Abhik
Re: [ccp4bb] Off topic question. NACCESS
On 06/17/2011 05:25 PM, Armando Albert wrote: Does anyone has got some information about how to get a mac version (intel), of the old unix program naccess?. It was meant to calculate the solvent accessibility per residue from a pdb file. Armando Maybe this server can do the job: http://cgal.inria.fr/abs/Vorlume/ And many other servers will be proposed maybe. Regards, F.
[ccp4bb] Off topic question. NACCESS
Does anyone has got some information about how to get a mac version (intel), of the old unix program naccess?. It was meant to calculate the solvent accessibility per residue from a pdb file. Armando
