Re: [ccp4bb] Which version of ccp4 introduced i2run and/or where does it live?
Hi Kay, I did find /Applications/ccp4-8.0/Frameworks/Python.framework/Versions/3.7/lib/site-packages/ccp4i2/bin/i2run on my Mac, and was able to use that to successfully bring up the import_merged help documentation, so I think that's working - thanks! For general reference, thanks to an individual reply I got: Evidently i2run is located in 7.0/7.1 installations at ccp4-7.1/share/ccp4i2/bin/i2run (and I was able to produce the same import_merged help documentation via that approach as well). Thanks! Maggie On Mon, Feb 19, 2024 at 3:37 AM Kay Diederichs < kay.diederi...@uni-konstanz.de> wrote: > Hi Maggie, > > I have CCP4 version 8.0 on my Mac and it does have the file > > /Applications/ccp4-8.0/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/ccp4i2/bin/i2run > > If I run it without arguments, it says > CCP4 /Applications/ccp4-8.0 > ccp4i2 version 1.1.0 > ccp4i2 source revision 6539 > Failed with exception list index out of range > Traceback (most recent call last): > File > "/Applications/ccp4-8.0/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/ccp4i2/core/CCP4I2Runner.py", > line 721, in > theRunner = CI2Runner(sys.argv) > File > "/Applications/ccp4-8.0/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/ccp4i2/core/CCP4I2Runner.py", > line 34, in __init__ > self.add_arguments(theParser, cmdLineArgs) > File > "/Applications/ccp4-8.0/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/ccp4i2/core/CCP4I2Runner.py", > line 381, in add_arguments > taskName = cmdLineArgs[1] > IndexError: list index out of range > > so it seems to work in principle. However, the directory where i2run lives > is not in the $PATH so one might want to > sudo ln -s > /Applications/ccp4-8.0/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/ccp4i2/bin/i2run > /Applications/ccp4-8.0/bin > > in order to run it with just "i2run". > There is documentation in > > /Applications/ccp4-8.0/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/ccp4i2/docs/sphinx/build/html/_sources/i2run/i2run.rst.txt > > Hope this helps, > Kay > > > On Sat, 17 Feb 2024 19:21:21 -0500, Klureza, Maggie < > mklur...@g.harvard.edu> wrote: > > >Hi all, > > > >I would very much like to make use of i2run's capacity for scripting, > >rather than pressing the same sequence of GUI buttons a few dozen times, > >but I'm having trouble actually calling it. > > > >The documentation <https://ccp4i2.gitlab.io/rstdocs/i2run/i2run.html> I > >found gives example code snippets structured as "i2run [function] > >[options]", but even immediately after sourcing ccp4, entering e.g. "i2run > >import_merged --help" returns an error saying "bash: i2run: command not > >found". > > > >I found only one reference to i2run on the ccp4bb archive > ><https://www.mail-archive.com/ccp4bb@jiscmail.ac.uk/msg56079.html> > >(actually from just 2 days ago!), which included a script that called > i2run > >using the full path of > >"/ccp4-8.0/lib/python3.7/site-packages/ccp4i2/bin/i2run crank2". However, > I > >was not able to find any equivalent path in either of the 2 ccp4 > >installations I have access to. > > > >Ideally I'd like to use our lab's installation of ccp4 on our university > >computational cluster, which is currently ccp4-7.1. Attempting to follow > >the analogous path took me to "ccp4-7.1/lib/python2.7/site-packages", > which > >did not contain a ccp4i2 directory. I'm wondering if perhaps i2run wasn't > >introduced until ccp4-8.0, and we would need an updated installation? > >Except, I also have ccp4 downloaded on my laptop (a Mac, if that's > >relevant), and going to "ccp4-8.0/lib/python3.7/site-packages" there still > >did not produce a ccp4i2 directory. > > > >Therefore, I'm wondering: Does ccp4-7.1 contain i2run, or would I need to > >update to 8.0 no matter what? And, almost regardless of the answer to that > >first question: What is the proper way to call i2run/where does it live > >within a ccp4 installation? I've been searching through the online > >documentation, but all the information I could find seemed to assume that > >i2run was readily accessible given the existence of a ccp4 installation, > so > >I'm a bit stumped. > > > >Many thanks, > >Maggie > > > > > > > >To unsubscribe from the CCP4BB list, click the following link: > >https://www.jiscmail
[ccp4bb] Which version of ccp4 introduced i2run and/or where does it live?
Hi all, I would very much like to make use of i2run's capacity for scripting, rather than pressing the same sequence of GUI buttons a few dozen times, but I'm having trouble actually calling it. The documentation <https://ccp4i2.gitlab.io/rstdocs/i2run/i2run.html> I found gives example code snippets structured as "i2run [function] [options]", but even immediately after sourcing ccp4, entering e.g. "i2run import_merged --help" returns an error saying "bash: i2run: command not found". I found only one reference to i2run on the ccp4bb archive <https://www.mail-archive.com/ccp4bb@jiscmail.ac.uk/msg56079.html> (actually from just 2 days ago!), which included a script that called i2run using the full path of "/ccp4-8.0/lib/python3.7/site-packages/ccp4i2/bin/i2run crank2". However, I was not able to find any equivalent path in either of the 2 ccp4 installations I have access to. Ideally I'd like to use our lab's installation of ccp4 on our university computational cluster, which is currently ccp4-7.1. Attempting to follow the analogous path took me to "ccp4-7.1/lib/python2.7/site-packages", which did not contain a ccp4i2 directory. I'm wondering if perhaps i2run wasn't introduced until ccp4-8.0, and we would need an updated installation? Except, I also have ccp4 downloaded on my laptop (a Mac, if that's relevant), and going to "ccp4-8.0/lib/python3.7/site-packages" there still did not produce a ccp4i2 directory. Therefore, I'm wondering: Does ccp4-7.1 contain i2run, or would I need to update to 8.0 no matter what? And, almost regardless of the answer to that first question: What is the proper way to call i2run/where does it live within a ccp4 installation? I've been searching through the online documentation, but all the information I could find seemed to assume that i2run was readily accessible given the existence of a ccp4 installation, so I'm a bit stumped. Many thanks, Maggie To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
[ccp4bb] switching space group
Hi, I have a structure which should have space group P212121, but it has been processed to P21212. It can not be solved and refined. Right now I do not have HKL2000, but I need change the space group to P212121. Is there a way for me to do this using CCP4? Thank you, Maggie
Re: [ccp4bb] AW: [ccp4bb] insertion code problem
Thank you, guys. My problem has been solved. AutoMR in CCP4 removed the insertion code. But I used it before, and it did not mess up with the insertion code at those times. Rain On Thu, Jun 27, 2013 at 12:56 PM, Ian Tickle ianj...@gmail.com wrote: Last time I checked pdbset doesn't renumber the LINK, CISPEP, SSBOND records at the same time (but maybe it was fixed). -- Ian On 26 June 2013 07:41, Francois Berenger beren...@riken.jp wrote: I think pdbset from CCP4 can renumber a PDB and hence get rid of the uggly insertion codes. On 06/26/2013 03:33 PM, herman.schreu...@sanofi.com wrote: Dear Rain, Insertion codes are still a sore point for many CCP4 programs and one of the reasons I prefer Buster over Refmac. Refmac5 does not remove insertion codes so I suspect the problem was with autoMR. The easiest is to superimpose your search model with insertion codes onto the pdb file which came out of the autoMR procedure. You could use lsqkab, but I think you can also do it in Coot. Then you continue refinement with this superimposed model. However, when I refined some structure with insertion codes in Refmac last week, Refmac created LINKR gap records for the inserted residues, cutting all peptide links. With an editor I had to change the gap to TRANS and then it worked. Good luck! Herman --**--** *Von:* CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] *Im Auftrag von *MAGGIE *Gesendet:* Mittwoch, 26. Juni 2013 04:07 *An:* CCP4BB@JISCMAIL.AC.UK *Betreff:* [ccp4bb] insertion code problem Dear group, I have a insertion code question. I used molecular replacement (CCP4, autoMR) to solve two structures: one is monomer, and another one is tetramer. The model I used is one chain of a dimer and the model has insertion code. After molecular replacement and refinement using refmac5 in CCP4, the new structures lost the insertion code, and the residues were numbered consecutively. Can anyone tell me how to keep the insertion code in the new structures? Thank you, Rain
[ccp4bb] insertion code problem
Dear group, I have a insertion code question. I used molecular replacement (CCP4, autoMR) to solve two structures: one is monomer, and another one is tetramer. The model I used is one chain of a dimer and the model has insertion code. After molecular replacement and refinement using refmac5 in CCP4, the new structures lost the insertion code, and the residues were numbered consecutively. Can anyone tell me how to keep the insertion code in the new structures? Thank you, Rain
[ccp4bb] GPCR DOCK 2013 announcement
Since there may some on this bb who have modelers as colleagues... On behalf of the PSI GPCR Network group: -- Dear GPCR modeling and docking researcher, We are writing to announce the 3rd round of the GPCR Docking and Modeling Assessment, GPCR Dock 2013, and to invite you to submit your predictions of GPCR-ligand structures for comparison prior to publication of the results. The first two GPCR Dock assessments were conducted in 2008 and 2010 and were based on the structures of A2A adenosine receptor (GPCR Dock 2008; NRDD 2009), dopamine D3 receptor and chemokine receptor CXCR4 (GPCR Dock 2010; Structure 2011). As before, the results from GPCR Dock 2013 will be published once an analysis is complete. The present round of the assessment will be focused on four target complexes. Participants can choose to predict any one, two, three, or all four targets. Predicting all four targets is strongly encouraged. Registered participants will receive receptor and ligand information at midnight (Pacific standard time) on Feb 1st, and will have until midnight (PST) March 3rd (30 days) to deposit models. Further information about the assessment and registration forms to participate can be found at http://gpcr.scripps.edu/GPCRDock2013 If you have any questions, please email (gpcrd...@scripps.edu) we will try to get back to you quickly and will also post any general comments to all registered participants. GPCR Network Ray Stevens Ruben Abagyan Irina Kufareva Angela Walker Seva Katritch Margaret J. Gabanyi, Ph.D. Asst. Research Professor, Department of Chemistry and Chemical Biology Sr. Outreach Coordinator, PSI Structural Biology Knowledgebase Rutgers, The State University of New Jersey 174 Frelinghuysen Rd Piscataway, NJ 08854-8076 phone: 848-445-4932 gaba...@rcsb.rutgers.edu Discover more at http://sbkb.org --
