Re: [ccp4bb] renaming chains
Hi All, I have a very similar question; why can't we retain the same water numbering as the deposited files. For articles that discuss waters, it is a considerable challenge. For example, for serial crystallography structures, it becomes confusing and harder for the readers to follow the water numbering. Since the authors use the same numbering system for the similar waters in the different structures of the same protein at different time points during the enzyme activity, however, after depositing, the waters are renumbered in each model differently. Cheers, Mohamed On Mon, Nov 1, 2021 at 4:01 PM Oganesyan, Vaheh < vaheh.oganes...@astrazeneca.com> wrote: > Hi All, > > > > This question is mostly for RCSB and PDBe: why are you renaming chains in > the deposited PDB files? Why does it matter what letter is assigned to the > chain? For 1,2 or 3 chain structures it is manageable, but for more chains > and/or many complexes per asu this becomes quite a challenge. And if chains > are similar in shape it is a real pain. Reading associated manuscripts and > looking at those structures is an additive that feels unnecessary. > > > > Thank you in advance for explaining the logic behind. > > > > *Vaheh Oganesyan, Ph.D.* > > *R* *| Biologics Engineering* > > One Medimmune Way, Gaithersburg, MD 20878 > > T: 301-398-5851 > > *vaheh.oganes...@astrazeneca.com * > > > > -- > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 > -- *--* *Dr. Mohamed Ibrahim* *Postdoctoral Researcher * *Humboldt University * *Berlin, Germany * *Tel: +49 30 209347931 * 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/
Re: [ccp4bb] Problem with peakmax
Many thanks, James, for the tips. This one worked also, peakmax MAPIN "mymap.ccp4" XYZOUT "mypeaks_output.pdb" <<- EOF EOF Best regards, On Thu, Jun 10, 2021 at 5:19 PM James Holton wrote: > > I'm afraid the only bash command I know is: "tcsh" > > However, in addition to suggestions so far, I expect this will work: > > echo "" | peakmax MAPIN "myfile.ccp4" XYZOUT "myfiles_omit_atom.pdb" > > Your peakmax is waiting for options to come in on "standard input". The > vertical bar "|" is a "pipe" that takes the "standard output" of the first > command (echo ""), and re-directs it to the standard input of the next > command. Pipes are a very powerful tool. Save a lot of > cutting-and-pasting. Fortunately, both bash and tcsh recognize "|" in the > same way. Unfortunately, they differ on how to re-direct output to a file. > > Oh, and that magic little "#!" that you put at the start of the first line > of the script is called a "shebang". > > -James Holton > MAD Scientist > > On 6/8/2021 11:06 AM, Mohamed Ibrahim wrote: > > 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 < > mohamed.ibra...@hu-berlin.de> 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 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, >>> > how to solve this problem? >>> > >>> > command used >>> > peakmax MAPIN "myfile.ccp4" XYZOUT "myfiles_omit_atom.pdb" >>> > >>> >>> Ctrl-D >>> >>> ############ >>> >>> 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/ >>> >> >> >> -- >> >> * --* >> *Dr. Mohamed Ibrahim* >> *Postdoctoral Researcher * >> >> *Humboldt University * >> *Berlin, Germany* >> *Tel: +49 30 209347931 * >> > > > -- > > * --* > *Dr. Mohamed Ibrahim* > *Postdoctoral Researcher * > > *Humboldt University * > *Berlin, Germany* > > *Tel: +49 30 209347931 * > > -- > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 > > > -- *--* *Dr. Mohamed Ibrahim* *Postdoctoral Researcher * *Humboldt University * *Berlin, Germany * *Tel: +49 30 209347931 * 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/
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 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 https://linuxize.com/post/bash-heredoc/. > > Harry > -- > Dr Harry Powell > > On 8 Jun 2021, at 19:22, Fischmann, Thierry < > 22f7fda0a875-dmarc-requ...@jiscmail.ac.uk> wrote: > > 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 with peakmax > > > > *EXTERNAL EMAIL* – Use caution with any links or file attachments. > > 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 > > > -- > > *From:* CCP4 bulletin board on behalf of Mohamed > Ibrahim > *Sent:* Tuesday, June 8, 2021 2:06 PM > *To:* CCP4BB@JISCMAIL.AC.UK > *Subject:* 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 < > mohamed.ibra...@hu-berlin.de> 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 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, > > how to solve this problem? > > > > command used > > peakmax MAPIN "myfile.ccp4" XYZOUT "myfiles_omit_atom.pdb" > > > > Ctrl-D > > ############ > > 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/ > > > > > -- > > > > ** > > *--* > > *Dr. Mohamed Ibrahim* > > *Postdoctoral Researcher* > > > > > > > > > > *Humboldt University * > > > > > > *Berlin, Germany* > > > > > > *Tel: +**49 30 209347931 * > > > > > -- > > > > ** > > *--* > > *Dr. Mohamed Ibrahim* > > *Postdoctoral Researcher* > > > > > > > > > > *Humboldt University * > > > > > > *Berlin, Germany* > > > > > > *Tel: +**49 30 209347931 * > > > -- > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 > > > -- > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 > > Notice: This e-mail message, together with any attachments, contains > information of Merck & Co., Inc. (2000 Galloping Hill Road, Kenilworth, > New Jersey, USA 07033), and/or its affiliates Direct contact information > for affiliates is available at > http://www.merck.com/contact/contacts.html) that may be confidential, > proprietary copyrighted and/or legally privileged. It is intended solely > for the use of the individual or entity named on this message. If you are > not the intended recipient, and have received this message in error
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 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, >> > how to solve this problem? >> > >> > command used >> > peakmax MAPIN "myfile.ccp4" XYZOUT "myfiles_omit_atom.pdb" >> > >> >> Ctrl-D >> >> >> >> 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/ >> > > > -- > > *--* > *Dr. Mohamed Ibrahim* > *Postdoctoral Researcher * > > *Humboldt University * > *Berlin, Germany * > *Tel: +49 30 209347931 * > -- *--* *Dr. Mohamed Ibrahim* *Postdoctoral Researcher * *Humboldt University * *Berlin, Germany * *Tel: +49 30 209347931 * 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] 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 "myfile.ccp4" XYZOUT "myfiles_omit_atom.pdb" Thank you! -- *------* *Dr. Mohamed Ibrahim* *Postdoctoral Researcher * *Humboldt University * *Berlin, Germany * *Tel: +49 30 209347931 * 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/
