Re: [ccp4bb] Problem with peakmax

peakmax MAPIN "myfile.ccp4" XYZOUT "myfiles_omit_atom.pdb" < wrote: > Paul was a little too terse, perhaps. > In script form > > peakmax MAPIN myfile.ccp4 XYZOUT myfiles_omit_atom.pdb << EOF-pmx > keywords in here > EOF-pmx > > at least that's what works for me in Csh. Bash proselytizers will

Re: [ccp4bb] Problem with peakmax

Thanks Paul, Is it possible to add Ctrl-D to my bash script? Best regards, On Tue, Jun 8, 2021 at 8:03 PM Mohamed Ibrahim wrote: > Thanks Paul, > Is it possible to add Ctrl-D to my bash script? > > Best regards, > > On Tue, Jun 8, 2021 at 7:51 PM Paul Emsley > wrote: > >> On Tue, 2021-06-08

[ccp4bb] Associate Researcher Position in the KU Protein Structure Laboratory

The Protein Structure Laboratory (PSL) at the University of Kansas (KU) is seeking a full-time Associate Researcher to assist with various structural biology projects. As a core laboratory, the PSL collaborates with a diverse range of investigators to obtain structures of their proteins of

Re: [ccp4bb] Problem with peakmax

echo “keyword1 arguments\nkeyword2 arguments\n etc. \nEND” | peakmax MAPIN myfile.ccp4 XYZOUT myfiles_omit_atom.pdb should work as well Thierry From: CCP4 bulletin board On Behalf Of Philip D. Jeffrey Sent: Tuesday, June 8, 2021 2:16 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Problem

Re: [ccp4bb] Problem with peakmax

The text following the "<<" in Eleanor's and Phil's example is known as a "heredoc" in Unix or Linux-speak (I had been using them for decades before I found out what they're called...). You can replace both "EOF-pmx"s in Phil's example and both "eof"s in Eleanor's with any text you like. See

[ccp4bb] Problem with peakmax

Dear All, I am trying to get the peak values from omit maps. The peakmax from the GUI works fine. However, I tried to run peakmax from the terminal, and it stuck when returning P1. Same map file works fine, when I use the GUI. Any ideas, how to solve this problem? command used peakmax MAPIN

Re: [ccp4bb] Problem with peakmax

On Tue, 2021-06-08 at 19:34 +0200, Mohamed Ibrahim wrote: > > I am trying to get the peak values from omit maps. The peakmax from the GUI > works fine. However, I tried to run > peakmax from the terminal, and it stuck when returning P1. Same map file > works fine, when I use the GUI. Any ideas,

Re: [ccp4bb] Problem with peakmax

Paul was a little too terse, perhaps. In script form peakmax MAPIN myfile.ccp4 XYZOUT myfiles_omit_atom.pdb << EOF-pmx keywords in here EOF-pmx at least that's what works for me in Csh. Bash proselytizers will correct me as necessary... Phil Jeffrey Princeton

Re: [ccp4bb] Problem with peakmax

Thank all, it works perfectly, using the "<< EOF" Best regards, Mohamed On Tue, Jun 8, 2021 at 8:32 PM CCP4BB < 193323b1e616-dmarc-requ...@jiscmail.ac.uk> wrote: > The text following the "<<" in Eleanor's and Phil's example is known as a > "heredoc" in Unix or Linux-speak (I had been using

Re: [ccp4bb] TWIN?

Maybe you have a bimolecular dimer when you expected a unimolecular hairpin? It’s happened before :) https://pubmed.ncbi.nlm.nih.gov/31584014/ Eric On Tue, Jun 8, 2021 at 10:15 AM Almudena Ponce Salvatierra < maps.fa...@gmail.com> wrote: > Hello everyone, > > I am working with an RNA-only

Re: [ccp4bb] self-inhibitory fragments from a protein - clarification

Dear All just to clarify, I'd be most interested in examples resulting from proteolysis, rather than say, packing effects Best Andy To unsubscribe from the CCP4BB list, click the following link:

Re: [ccp4bb] looking for proteins with no homologues in pdb

One short cut would be to focus on Pfam families that do not yet have a 3D representative. They can be browsed eg https://pfam.xfam.org/family/browse?browse=a or you can also install Pfam locally as MySQL for programmatic access. Choosing Families rather than Domains would make it easier to

Re: [ccp4bb] TWIN?

It’s difficult to tell exactly what is happening from your description and the attached image. Both your description and the image are OK. It’s just that there are a lot of ways for things to go off the rails. Are the molecules stacked end-to-end? In that case, you may have an incommensurate

Re: [ccp4bb] looking for proteins with no homologues in pdb

You can download such proteins/sequences from the CASP website: https://predictioncenter.org/ At the JCSG, we participated for many years in the annual CASP competition, where we would use/hold our novel experimental crystal structures (before PDB deposition, almost all our ~1500 targets/PDB

Re: [ccp4bb] TWIN?

First spacegrouop - trigonal spacegroups can also be indexed as C2 so it isnt so surprising that a P6/mmm should masquerade as C2. I would look very carefull at the POINTLESS symmetry scores and see if some are more convincing than others. But how I hate RNA & DNA - molecular replacement