Well - not recognising the fragment is probably due to some defect in the coordinate format. How did you prepare the input cooudinates? Obviously that file must include the CRYST1 record, or its mmCIF equivalent, but there may be other requirements as well. Could you email a copy of a fragment which fails in the latest version?
Eleanor On Mon, 20 Jan 2020 at 08:56, Adrian Schlarb < [email protected]> wrote: > Dear Members, > > I am doing an internship at my university with the current task to find > out the number of salt bridges and hydrogen bonds as well as the buried > surface area of different fragments within protein kinase A. > My supervisor is not familiar with the program PISA but told me that it > will offer me this information. > Now first of all I am confused about the different versions of PISA. > It appears that on the official website of PISA ( > https://www.ebi.ac.uk/pdbe/pisa/) there is version 1.48, at the website > of ccp4 (http://www.ccp4.ac.uk/pisa/) there is the browser version 2.0.4 > and in the downloaded PISA version via ccp4 it is version 2.1.1. > Now I assumed like anyone probably that the newest version is the best but > if I try any of my pdb.files (for example 5n1d) the terminal/desktop > version does not recognize the fragment at all. > The browser version from ccp4 neither but the version from the official > website with the oldest version. However I was not sure, if the amount of > hydrogen bonds and salt bridges is right because one phd student of my > group (of Prof. Klebe, Marburg) was investing some of the structures and > got different results. > My supervisor also gave me some data from a program called contacsym which > determines the number of hydrogen bonds as well for the pdb.file of 4y3e. > Of course I tried PISA with this file too and the results differ again. > Now the question is, why does the newest(?) version of PISA not recognize > the fragment at all and why does the online version differ from results > from other programs or evaluation? > Is there any way to see the criteria with which PISA states hydrogen bonds > or salt bridges? > I would be very happy if someone could help me with it! > > Best regards, > > Adrian > > ######################################################################## > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 > ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
