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Re: [PyMOL] solvent accessibility with pymol
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From: Tsjerk W. <ts...@gm...> - 2009-04-23 20:23:07
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Hi Warren, e.a., I agree that posts in which people react on the 'tone' of the communication of one another should in principle be kept private and settled thus. For me, there were three reasons to bounce this mail to the mailing list. First and for all, I had hoped for the response you gave regarding the mailing list archive as this was a very good illustration of the need for such. Second, the answer to the original question should be archived anyway, which hadn't happened the first time, as I simply pressed 'reply'. Third, the reference to 'how to ask questions the smart way' is always a good one to be posted now and again (and to be archived). That being said, it doesn't hurt if a discussion like this comes by once in a while. It makes both posters and repliers aware that there's people involved with feelings that can be touched. This is especially true when the list concerns people from all over the world and have all different kinds of backgrounds. Then, you can't rely on your own background to make inferences about what's written between the lines or expect that what you write between the lines is picked up in the way you intend. Actually that is one of the most exciting parts of intercultural communication: try to choose your words such that they are unlikely to be misinterpreted, and try to find the proper viewing angle to interpret the words from others. Both of these are tough. Here we usually put things quite explicitly, without hard feelings, and suppose that the direct manner of speech leaves little room for misinterpretation. However, I admit that this explicit way of putting things is very likely to be overinterpreted from a background in which signals are usually put implicitly. Although there's some more on my mind, I think I'll leave it like this. Just as a final comment, I think this is just a sign that both Pymol and the user list really grow to be mature now. I'll be happy to elaborate on this and possible consequences thereof privately with anyone :) Warren, if you feel I crossed boundaries here, I apologize. You know I'm not troll enough to want to jeopardize the mailing list ;) Mehmet, let's have a drink on intercultural and mailing list communication. Cheers, Tsjerk On Thu, Apr 23, 2009 at 5:44 PM, Warren DeLano <wa...@de...> wrote: > Folks, > > Please endeavor to be respectful, kind, and patient with one another. > Toxic interactions on the mailing list hurt all of us, so please avoid > such posts altogether or keep them private. > > Unfortunately, is appears that we can no longer rely on either > SourceForge or Google to provide a PyMOL mailing list search capacity, > so we will be looking at what else we can do instead to provide > convenient access to the accumulated knowledge contained inside the > pymol-users archives. Restoring this capability should help cut down on > the number of repeat questions. > > Cheers, > Warren > >> -----Original Message----- >> From: Tsjerk Wassenaar [mailto:ts...@gm...] >> Sent: Thursday, April 23, 2009 5:00 AM >> To: Mehmet Cetin; pymol-users >> Subject: Re: [PyMOL] solvent accessibility with pymol >> >> Hi Mehmet, >> >> > 1. I have just become a member today so I don't know who >> posted what 2 >> > days ago. and as far as I can see there is no search >> function on the archives. >> >> True, that's why I didn't answer 'search the archives', like >> I would on other lists. >> >> > 2. I do search the web before asking. I couldn't find something >> > satisfying, that's why I asked. >> >> The wiki did have the answer, maybe you searched but you >> couldn't find it, or did not know of its existence. In that >> case, indicate what you tried in order to find the answer >> yourself (like noticing the archives have no search >> function). That will make people like me feel to be taken >> seriously and not used like some helpdesk. Maybe it is not a >> bad idea to read http://www.catb.org/~esr/faqs/smart-questions.html >> >> > 3. I am not looking for a "substitute for my brain's >> function" either. >> > I just asked a simple question. just delete it if you don't >> want to answer. >> > and I suggest you think more carefully before you lecture >> people you >> > don't know. >> >> I gave you an answer, despite not being paid for it. You can >> appreciate that and take the other comments for granted, >> doing with it what you think is right. You can think badly of >> me and hope for somebody more polite to answer, disregarding >> what I said, or you can lecture me like you do here and make >> me think twice before opening a post of yours and answering >> your question. >> The fact that you feel insulted by me, suggesting that you >> would regard us as a 'substitute ...', is a good sign. It >> gives the feeling that you're willing to learn and find >> things out for yourself, although in this case you didn't >> manage. Reflect that in your posts. >> I've seen to many which boiled down to 'please do my homework for me' >> or 'make me avoid straining my neurons', and after the years >> involved in mailing lists like these mails invoking such >> feelings trigger a response like the one I gave or even >> worse. Not a personal thing though; I don't even know you. >> >> I hope this settles things a bit. >> >> Cheers, >> >> Tsjerk >> >> > >> > Mehmet >> > >> > >> > --- On Thu, 4/23/09, Tsjerk Wassenaar <ts...@gm...> wrote: >> > >> > From: Tsjerk Wassenaar <ts...@gm...> >> > Subject: Re: [PyMOL] solvent accessibility with pymol >> > To: "Mehmet Cetin" <mm...@ya...> >> > Date: Thursday, April 23, 2009, 2:43 AM >> > >> > Mehmet, >> > >> > Really, two days ago we got this post: >> > >> > --- >> > Dear all, >> > >> > Is there any PyMOL command to calculate surface areas? >> > Many thanks, >> > >> > Luisa Rodrigues >> > --- >> > >> > And now you come with this: >> > >> > On Thu, Apr 23, 2009 at 4:30 AM, Mehmet Cetin >> <mm...@ya...> wrote: >> >> >> >> Hi all, I am looking for a way to figure out the solvent >> >> accessibility of a particular region on a protein. could >> anyone tell >> >> me if there is a command (or script) in Pymol that I can >> use to do it? thanks in advance. >> >> >> > >> > The answer given should be good enough for you. >> > >> > --- >> > Did you try to search for information yourself first? >> > >> > Anyways, the pymolwiki.org >> > >> > is always a good place to go and then you would have found >> something >> > like this: >> > http://pymolwiki.org/index.php/Get_Area >> > >> > I hope this is what you are looking for? >> > >> > Best regards, >> > Folmer Fredslund >> > --- >> > >> > Please do bear in mind that we're not an easy substitute >> for your own >> > brains function! Before posting, search the internet, and >> especially >> > search on the wiki pages. Also, be sure to read the questions and >> > answers that come by on this list as these may provide you answers >> > before you know you were looking for them. >> > >> > Cheers, >> > >> > Tsjerk >> > >> > >> > -- >> > Tsjerk A. Wassenaar, Ph.D. >> > Junior UD (post-doc) >> > Biomolecular NMR, Bijvoet Center >> > Utrecht University >> > Padualaan 8 >> > 3584 CH Utrecht >> > The Netherlands >> > P: +31-30-2539931 >> > F: +31-30-2537623 >> > >> > >> >> >> >> -- >> Tsjerk A. Wassenaar, Ph.D. >> Junior UD (post-doc) >> Biomolecular NMR, Bijvoet Center >> Utrecht University >> Padualaan 8 >> 3584 CH Utrecht >> The Netherlands >> P: +31-30-2539931 >> F: +31-30-2537623 >> > > > ------------------------------------------------------------------------------ > Stay on top of everything new and different, both inside and > around Java (TM) technology - register by April 22, and save > $200 on the JavaOne (SM) conference, June 2-5, 2009, San Francisco. > 300 plus technical and hands-on sessions. Register today. > Use priority code J9JMT32. http://p.sf.net/sfu/p > _______________________________________________ > PyMOL-users mailing list > PyM...@li... > https://lists.sourceforge.net/lists/listinfo/pymol-users > -- Tsjerk A. Wassenaar, Ph.D. Junior UD (post-doc) Biomolecular NMR, Bijvoet Center Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands P: +31-30-2539931 F: +31-30-2537623 |