[PyMOL] selecting atoms ..
Hi, I am trying to select a large number of atoms, using a pymol script. The first script file looks like this: --- select paska, id 36+37+38+39+40+41+42+43+44+45+46+47+48+49+50+51+52+53+54+55+56+57+58 The second one like this: select isopaska, id 36+37+38+39+40+41+42+43+44+45+46+47+48+49+50+51+52+53+54+55+56+57+58+59+60+61+62+63+64+65+66+67+68+69+70+71+72+73+74+75+76+77+78+79+80+81+82+83+84+85+86+87+88+89+90+91+92+93+94+95+96+97+98+99+100+101+102+103+104+105+106+107+108+109+110+111+112+113+114+115+116+117+118+119+120+121+122+123+124+125+126+127+128+129+130+131+132+133+134+135+136+137+138+139+140+141+142+143+144+145+146+147+148+149+150+151+152+153+154+155+156+157+158+159+160+161+162+163+164+165+166+167+168+169+170+171+172+173+174+175+176+177+178+179+180+181+182+183+184+185+186+187+188+189+190+191+192+193+194+195+196+197+198+199+200+201+202+203+204+205+206+207+208+209+210+211+212+213+214+215+216+217+218+219+220+221+222+223+224+225+226+227+228+229+230+231+232+233+234+235+236+237+238+239+240+241+242+243+244+245+246+247+248+249+250+251+252+253+254+255+256+257+258+259+260+261+262+263+264+265+266+267+268+269+270+271+272+273+274+275+276+277+278+279+280+281+282+283+284+285+286+287+288+289+290+291+292+293+294+295+296+297+298+299+300+30 1+302+303+304+305+306+307+308+309+310+311+312+313+314+315+316+317+318+319+320+321+322+323+324+325+326+327+328+329+330+331+332+333+334+335+336+337+338+339+340+341+342+343+344+345+346+347+348+349+350 - When running the first script, it works ok, however, if I run the second one, pymol crashes: --- *** buffer overflow detected ***: python2.7 terminated === Backtrace: = /lib/x86_64-linux-gnu/libc.so.6(__fortify_fail+0x5c)[0x7f171c6ce08c] /lib/x86_64-linux-gnu/libc.so.6(+0x111020)[0x7f171c6cd020] ... --- How can I select a laarge number of atoms based on their numbers? Regards, Sampsa -- Managing the Performance of Cloud-Based Applications Take advantage of what the Cloud has to offer - Avoid Common Pitfalls. Read the Whitepaper. http://pubads.g.doubleclick.net/gampad/clk?id=121054471iu=/4140/ostg.clktrk ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] selecting atoms ..
Hi Sampsa - The long list of ids crashes for me as well. Instead of listing each id separately, you can use ranges to define your selections. select paska, id 36-58 select isopaska, id 36-350 If you need to use non-continuous ids, you can use Boolean logic to join the ranges: select isopaska_without_id_59, id 36-58 or id 60-350 Cheers, Jared -- Jared Sampson Xiangpeng Kong Lab NYU Langone Medical Center 550 First Avenue New York, NY 10016 212-263-7898 http://kong.med.nyu.edu/ On Feb 18, 2014, at 1:50 PM, Sampsa Riikonen sampsa.riiko...@iki.fi wrote: Hi, I am trying to select a large number of atoms, using a pymol script. The first script file looks like this: --- select paska, id 36+37+38+39+40+41+42+43+44+45+46+47+48+49+50+51+52+53+54+55+56+57+58 The second one like this: select isopaska, id 36+37+38+39+40+41+42+43+44+45+46+47+48+49+50+51+52+53+54+55+56+57+58+59+60+61+62+63+64+65+66+67+68+69+70+71+72+73+74+75+76+77+78+79+80+81+82+83+84+85+86+87+88+89+90+91+92+93+94+95+96+97+98+99+100+101+102+103+104+105+106+107+108+109+110+111+112+113+114+115+116+117+118+119+120+121+122+123+124+125+126+127+128+129+130+131+132+133+134+135+136+137+138+139+140+141+142+143+144+145+146+147+148+149+150+151+152+153+154+155+156+157+158+159+160+161+162+163+164+165+166+167+168+169+170+171+172+173+174+175+176+177+178+179+180+181+182+183+184+185+186+187+188+189+190+191+192+193+194+195+196+197+198+199+200+201+202+203+204+205+206+207+208+209+210+211+212+213+214+215+216+217+218+219+220+221+222+223+224+225+226+227+228+229+230+231+232+233+234+235+236+237+238+239+240+241+242+243+244+245+246+247+248+249+250+251+252+253+254+255+256+257+258+259+260+261+262+263+264+265+266+267+268+269+270+271+272+273+274+275+276+277+278+279+280+281+282+283+284+285+286+287+288+289+290+291+292+293+294+295+296+297+298+299+300+ 301+302+303+304+305+306+307+308+309+310+311+312+313+314+315+316+317+318+319+320+321+322+323+324+325+326+327+328+329+330+331+332+333+334+335+336+337+338+339+340+341+342+343+344+345+346+347+348+349+350 - When running the first script, it works ok, however, if I run the second one, pymol crashes: --- *** buffer overflow detected ***: python2.7 terminated === Backtrace: = /lib/x86_64-linux-gnu/libc.so.6(__fortify_fail+0x5c)[0x7f171c6ce08c] /lib/x86_64-linux-gnu/libc.so.6(+0x111020)[0x7f171c6cd020] ... --- How can I select a laarge number of atoms based on their numbers? Regards, Sampsa -- Managing the Performance of Cloud-Based Applications Take advantage of what the Cloud has to offer - Avoid Common Pitfalls. Read the Whitepaper. http://pubads.g.doubleclick.net/gampad/clk?id=121054471iu=/4140/ostg.clktrk ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net This email message, including any attachments, is for the sole use of the intended recipient(s) and may contain information that is proprietary, confidential, and exempt from disclosure under applicable law. Any unauthorized review, use, disclosure, or distribution is prohibited. If you have received this email in error please notify the sender by return email and delete the original message. Please note, the recipient should check this email and any attachments for the presence of viruses. The organization accepts no liability for any damage caused by any virus transmitted by this email. = -- Managing the Performance of Cloud-Based Applications Take advantage of what the Cloud has to offer - Avoid Common Pitfalls. Read the Whitepaper. http://pubads.g.doubleclick.net/gampad/clk?id=121054471iu=/4140/ostg.clktrk ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
[PyMOL] selecting atoms around a ligand in a protein structure
Hi Pymol-users, I need to select only the atoms [and NOT complete amino acid residues] which are lying in a radius of 4.5 Angstroms from the ligand from a ligand-bound protein structure. I am aware that the command: select site, br. resn FAD and chain A and resi 45 around 4.5 and not HETselects complete amino acid residues which are lying in the vicinity of the ligand within a radius of 4.5 Angstroms. However, I am only interested in selecting all the atoms which are present in this region and not the complete amino acid residues. How can this be done? Please let me know. - Anasuya -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. -- Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] selecting atoms around a ligand in a protein structure
Hi Anasuya, br. is short for byres (by residue). So just drop that from your selection expression. select site, (resn FAD and chain A and resi 45) around 4.5 and not HET Cheers, Thomas Anasuya Dighe wrote, On 07/23/12 09:00: Hi Pymol-users, I need to select only the atoms [and NOT complete amino acid residues] which are lying in a radius of 4.5 Angstroms from the ligand from a ligand-bound protein structure. I am aware that the command: select site, br. resn FAD and chain A and resi 45 around 4.5 and not HETselects complete amino acid residues which are lying in the vicinity of the ligand within a radius of 4.5 Angstroms. However, I am only interested in selecting all the atoms which are present in this region and not the complete amino acid residues. How can this be done? Please let me know. - Anasuya -- Thomas Holder MPI for Developmental Biology Spemannstr. 35 D-72076 Tübingen -- Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
[PyMOL] selecting atoms with PROview
I'm using PROView (I believe it's a PyMOL-enhanced tool) on a Windows 2000 machine, and was trying to pick some atoms in the structure window, but there is no visual indication of the selection. I tried it on a WinXP, and there were some visible pink dots showing up following my clicks. Have others encountered the same problem? Is it a Win2000-specific problem? -IJR _ The new MSN 8: smart spam protection and 2 months FREE* http://join.msn.com/?page=features/junkmail
